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Zhao D, Li C, Zeng N, Wang D, Yu G, Zhang N, Li B. Transcriptomic and metabolomic analyses reveal the positive effect of moderate concentration of sodium chloride treatment on the production of β-carotene, torulene, and torularhodin in oleaginous red yeast Rhodosporidiobolus odoratus XQR. FOOD CHEMISTRY. MOLECULAR SCIENCES 2024; 9:100221. [PMID: 39399738 PMCID: PMC11470240 DOI: 10.1016/j.fochms.2024.100221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 08/13/2024] [Accepted: 08/25/2024] [Indexed: 10/15/2024]
Abstract
Carotenoids, a family of lipid-soluble pigments, have garnered growing interest for their health-promoting benefits and are widely utilized in the food, feed, pharmaceutical, and cosmetic industries. Rhodosporidiobolus odoratus, a representative oleaginous red yeast, is considered a promising alternative for producing high-value carotenoids including β-carotene, torulene, and torularhodin. Here, the impact of varying concentrations of NaCl treatments on carotenoid contents in R. odoratus XQR after 120 h of incubation was examined. The results indicated that, as compared to the control (59.37 μg/gdw), the synthesis of total carotenoids was significantly increased and entirely suppressed under low-to-moderate (0.25 mol/L: 68.06 μg/gdw, 0.5 mol/L: 67.62 μg/gdw, and 0.75 mol/L: 146.47 μg/gdw) and high (1.0, 1.25, and 1.5 mol/L: 0 μg/gdw) concentrations of NaCl treatments, respectively. Moreover, the maximum production of β-carotene (117.62 μg/gdw), torulene (21.81 μg/gdw), and torularhodin (7.04 μg/gdw) was achieved with a moderate concentration (0.75 mol/L) of NaCl treatment. Transcriptomic and metabolomic analyses suggested that the increase in β-carotene, torulene, and torularhodin production might be primarily attributed to the up-regulation of some key protein-coding genes involved in the terpenoid backbone biosynthesis (atoB, HMGCS, and mvaD), carotenoid biosynthesis (crtYB and crtI), and TCA cycle (pckA, DLAT, pyc, MDH1, gltA, acnA, IDH1/2, IDH3, sucA, sucB, sucD, LSC1, SDHA, and fumA/fumB). The present study not only demonstrates a viable method to concurrently increase the production of β-carotene, torulene, torularhodin, and total carotenoids in R. odoratus XQR, but it also establishes a molecular foundation for further enhancing their production through genetic engineering.
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Affiliation(s)
- Die Zhao
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, China
| | - Chunji Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510225, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
| | - Nan Zeng
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, China
| | - Dandan Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Guohui Yu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510225, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
| | - Ning Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Bingxue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, China
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Ebrahim N, Kondratyev N, Artyuhov A, Timofeev A, Gurskaya N, Andrianov A, Izrailov R, Volchkov E, Dyuzheva T, Kopantseva E, Kiseleva E, Golimbet V, Dashinimaev E. Human pancreatic islet-derived stromal cells reveal combined features of mesenchymal stromal cells and pancreatic stellate cells. Stem Cell Res Ther 2024; 15:351. [PMID: 39380125 PMCID: PMC11463112 DOI: 10.1186/s13287-024-03963-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 09/26/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND Mesenchymal stromal cells (MSCs) are recognized for their potential in regenerative medicine, attributed to their multipotent differentiation capabilities and immunomodulatory properties. Despite this potential, the classification and detailed characterization of MSCs, especially those derived from specific tissues like the pancreas, remains challenging leading to a proliferation of terminology in the literature. This study aims to address these challenges by providing a thorough characterization of human pancreatic islets-derived mesenchymal stromal cells (hPD-MSCs). METHODS hPD-MSCs were isolated from donor islets using enzymatic digestion, immortalized through lentiviral transduction of human telomerase reverse transcriptase (hTERT). Cells were characterized by immunostaining, flow cytometry and multilineage differentiation potential into adipogenic and osteogenic lineages. Further a transcriptomic analysis was done to compare the gene expression profiles of hPD-MSCs with other mesenchymal cells. RESULTS We show that hPD-MSCs express the classical MSC features, including morphological characteristics, surface markers expression (CD90, CD73, CD105, CD44, and CD106) and the ability to differentiate into both adipogenic and osteogenic lineages. Furthermore, transcriptomic analysis revealed distinct gene expression profiles, showing notable similarities between hPD-MSCs and pancreatic stellate cells (PSCs). The study also identified specific genes that distinguish hPD-MSCs from MSCs of other origins, including genes associated with pancreatic function (e.g., ISL1) and neural development (e.g., NPTX1, ZNF804A). A novel gene with an unknown function (ENSG00000286190) was also discovered. CONCLUSIONS This study enhances the understanding of hPD-MSCs, demonstrating their unique characteristics and potential applications in therapeutic strategies. The identification of specific gene expression profiles differentiates hPD-MSCs from other mesenchymal cells and opens new avenues for research into their role in pancreatic function and neural development.
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Affiliation(s)
- Nour Ebrahim
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia, 117997
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia, 141701
| | | | - Alexander Artyuhov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia, 117997
- Research Institute of Molecular and Cellular Medicine, RUDN University, Moscow, Russia, 117198
| | - Alexei Timofeev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia, 117997
| | - Nadya Gurskaya
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia, 117997
| | - Alexey Andrianov
- Loginov Moscow Clinical Scientific Center, Moscow, Russia, 111123
| | - Roman Izrailov
- Loginov Moscow Clinical Scientific Center, Moscow, Russia, 111123
| | - Egor Volchkov
- Research Institute of Molecular and Cellular Medicine, RUDN University, Moscow, Russia, 117198
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev, NMRCPHOI) of Ministry of Healthcare of the Russian Federation, 1, Samory Mashela St, Moscow, Russia, 117997
| | - Tatyana Dyuzheva
- Department of Hospital Surgery, Sklifosovsky Institute for Clinical Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia, 119435
| | - Elena Kopantseva
- Research Institute of Molecular and Cellular Medicine, RUDN University, Moscow, Russia, 117198
| | - Ekaterina Kiseleva
- Research Institute for Systems Biology and Medicine, Moscow, Russia, 117246
| | - Vera Golimbet
- Mental Health Research Center, Moscow, Russia, 115522
| | - Erdem Dashinimaev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia, 117997.
- Research Institute of Molecular and Cellular Medicine, RUDN University, Moscow, Russia, 117198.
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia, 141701.
- Institute of Medicine, Banzarov Buryat State University, Ulan-Ude, Russia, 670000.
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3
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Garg R, Dang S, Gauba P. Genomic characterization of Enterobacter sp. PGRG2 and Achromobacter insolitus PGRG5: bacterial strains isolated from soil present near electronics manufacture industry for heavy metal remediation. Microbiol Resour Announc 2024; 13:e0061724. [PMID: 39162463 PMCID: PMC11385718 DOI: 10.1128/mra.00617-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/22/2024] [Indexed: 08/21/2024] Open
Abstract
This article reports the whole-genome sequence of PGRG5 and the draft genome sequence of PGRG2. These strains were isolated from electronic waste contaminated soil. According to microbial identification, strain PGRG2 was identified as Enterobacter sp. (unclassified) with a size of ~4.4 Mbp and PGRG5 as Achromobacter insolitus with a size of ~6.2 Mbp.
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Affiliation(s)
- Ritika Garg
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Shweta Dang
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Pammi Gauba
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
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Sun Y, Zhao X, Fan X, Wang M, Li C, Liu Y, Wu P, Yan Q, Sun L. Assessing the impact of sequencing platforms and analytical pipelines on whole-exome sequencing. Front Genet 2024; 15:1334075. [PMID: 38818042 PMCID: PMC11137314 DOI: 10.3389/fgene.2024.1334075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/30/2024] [Indexed: 06/01/2024] Open
Affiliation(s)
- Yanping Sun
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xiaochao Zhao
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xue Fan
- Clinical Research Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Miao Wang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Chaoyang Li
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yongfeng Liu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Ping Wu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Sun
- GeneMind Biosciences Company Limited, Shenzhen, China
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Jiang P, Jing Y, Zhao S, Lan C, Yang L, Dai X, Luo L, Cai S, Zhu Y, Miller H, Lai J, Zhang X, Zhao X, Wu Y, Yang J, Zhang W, Guan F, Zhong B, Umehara H, Lei J, Dong L, Liu C. Expression of USP25 associates with fibrosis, inflammation and metabolism changes in IgG4-related disease. Nat Commun 2024; 15:2627. [PMID: 38521787 PMCID: PMC10960850 DOI: 10.1038/s41467-024-45977-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 02/08/2024] [Indexed: 03/25/2024] Open
Abstract
IgG4-related disease (IgG4-RD) has complex clinical manifestations ranging from fibrosis and inflammation to deregulated metabolism. The molecular mechanisms underpinning these phenotypes are unclear. In this study, by using IgG4-RD patient peripheral blood mononuclear cells (PBMCs), IgG4-RD cell lines and Usp25 knockout mice, we show that ubiquitin-specific protease 25 (USP25) engages in multiple pathways to regulate fibrotic and inflammatory pathways that are characteristic to IgG4-RD. Reduced USP25 expression in IgG4-RD leads to increased SMAD3 activation, which contributes to fibrosis and induces inflammation through the IL-1β inflammatory axis. Mechanistically, USP25 prevents ubiquitination of RAC1, thus, downregulation of USP25 leads to ubiquitination and degradation of RAC1. Decreased RAC1 levels result in reduced aldolase A release from the actin cytoskeleton, which then lowers glycolysis. The expression of LYN, a component of the B cell receptor signalosome is also reduced in USP25-deficient B cells, which might result in B cell activation deficiency. Altogether, our results indicate a potential anti-inflammatory and anti-fibrotic role for USP25 and make USP25 a promising diagnostic marker and potential therapeutic target in IgG4-RD.
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Affiliation(s)
- Panpan Jiang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yukai Jing
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Siyu Zhao
- Department Immunology, School of Medicine, Yangtze University, Jingzhou, 434000, China
| | - Caini Lan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Lu Yang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xin Dai
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Li Luo
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Shaozhe Cai
- Department of Rheumatology and Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Yingzi Zhu
- Department of Rheumatology and Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Heather Miller
- Cytek Biosciences, R&D Clinical Reagents, Fremont, CA, USA
| | - Juan Lai
- GeneMind Biosciences Company Limited, Shenzhen, 518001, China
| | - Xin Zhang
- GeneMind Biosciences Company Limited, Shenzhen, 518001, China
| | - Xiaochao Zhao
- GeneMind Biosciences Company Limited, Shenzhen, 518001, China
| | - Yonggui Wu
- Department of Nephropathy, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, PR China; Center for Scientific Research of Anhui Medical University, Hefei, Anhui, 230032, PR China
| | - Jingzhi Yang
- Department of Orthopedics, Qilu Hospital of Shandong University, Jinan, Shandong, 250063, PR China
| | - Wen Zhang
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, 100730, China
| | - Fei Guan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Bo Zhong
- Department of Gastrointestinal Surgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Hisanori Umehara
- Department of Medicine, Nagahama City Hospital, Nagahama, 949-1701, Japan
| | - Jiahui Lei
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Lingli Dong
- Department of Rheumatology and Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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Al-Rashed F, Arefanian H, Madhoun AA, Bahman F, Sindhu S, AlSaeed H, Jacob T, Thomas R, Al-Roub A, Alzaid F, Malik MDZ, Nizam R, Thanaraj TA, Al-Mulla F, Hannun YA, Ahmad R. Neutral Sphingomyelinase 2 Inhibition Limits Hepatic Steatosis and Inflammation. Cells 2024; 13:463. [PMID: 38474427 PMCID: PMC10931069 DOI: 10.3390/cells13050463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is manifested by hepatic steatosis, insulin resistance, hepatocyte death, and systemic inflammation. Obesity induces steatosis and chronic inflammation in the liver. However, the precise mechanism underlying hepatic steatosis in the setting of obesity remains unclear. Here, we report studies that address this question. After 14 weeks on a high-fat diet (HFD) with high sucrose, C57BL/6 mice revealed a phenotype of liver steatosis. Transcriptional profiling analysis of the liver tissues was performed using RNA sequencing (RNA-seq). Our RNA-seq data revealed 692 differentially expressed genes involved in processes of lipid metabolism, oxidative stress, immune responses, and cell proliferation. Notably, the gene encoding neutral sphingomyelinase, SMPD3, was predominantly upregulated in the liver tissues of the mice displaying a phenotype of steatosis. Moreover, nSMase2 activity was elevated in these tissues of the liver. Pharmacological and genetic inhibition of nSMase2 prevented intracellular lipid accumulation and TNFα-induced inflammation in in-vitro HepG2-steatosis cellular model. Furthermore, nSMase2 inhibition ameliorates oxidative damage by rescuing PPARα and preventing cell death associated with high glucose/oleic acid-induced fat accumulation in HepG2 cells. Collectively, our findings highlight the prominent role of nSMase2 in hepatic steatosis, which could serve as a potential therapeutic target for NAFLD and other hepatic steatosis-linked disorders.
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Affiliation(s)
- Fatema Al-Rashed
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (H.A.); (F.B.); (H.A.); (T.J.); (R.T.); (A.A.-R.)
| | - Hossein Arefanian
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (H.A.); (F.B.); (H.A.); (T.J.); (R.T.); (A.A.-R.)
| | - Ashraf Al Madhoun
- Animal and Imaging Core Facilities, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.A.M.); (S.S.)
| | - Fatemah Bahman
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (H.A.); (F.B.); (H.A.); (T.J.); (R.T.); (A.A.-R.)
| | - Sardar Sindhu
- Animal and Imaging Core Facilities, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.A.M.); (S.S.)
| | - Halemah AlSaeed
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (H.A.); (F.B.); (H.A.); (T.J.); (R.T.); (A.A.-R.)
| | - Texy Jacob
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (H.A.); (F.B.); (H.A.); (T.J.); (R.T.); (A.A.-R.)
| | - Reeby Thomas
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (H.A.); (F.B.); (H.A.); (T.J.); (R.T.); (A.A.-R.)
| | - Areej Al-Roub
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (H.A.); (F.B.); (H.A.); (T.J.); (R.T.); (A.A.-R.)
| | - Fawaz Alzaid
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France;
| | - MD Zubbair Malik
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (M.Z.M.); (R.N.); (T.A.T.); (F.A.-M.)
| | - Rasheeba Nizam
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (M.Z.M.); (R.N.); (T.A.T.); (F.A.-M.)
| | - Thangavel Alphonse Thanaraj
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (M.Z.M.); (R.N.); (T.A.T.); (F.A.-M.)
| | - Fahd Al-Mulla
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (M.Z.M.); (R.N.); (T.A.T.); (F.A.-M.)
| | - Yusuf A. Hannun
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA;
| | - Rasheed Ahmad
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman 15462, Kuwait; (H.A.); (F.B.); (H.A.); (T.J.); (R.T.); (A.A.-R.)
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Fang B, Lai J, Liu Y, Yu TT, Yu X, Li X, Dong L, Zhang X, Yang W, Yan Q, Sun L, Liu LL. Genetic characterization of human adenoviruses in patients using metagenomic next-generation sequencing in Hubei, China, from 2018 to 2019. Front Microbiol 2023; 14:1153728. [PMID: 37007506 PMCID: PMC10060807 DOI: 10.3389/fmicb.2023.1153728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/24/2023] [Indexed: 03/18/2023] Open
Abstract
ObjectivesThis study aimed to characterize the genomic epidemiology of human adenoviruses (HAdVs) in Hubei, China, using metagenomic next-generation sequencing (mNGS).MethodsIn total, 25 HAdV-positive samples collected from 21 pediatric patients were sequenced and subjected to mNGS using the NextSeq 550 and GenoLab M sequencing platforms. The metagenomic data were assembled de novo for molecular typing, phylogenetic and recombination analyzes.ResultsWe assembled 50 HAdV genomes, 88% (22/25) genomes from GenoLab M, and 84% (21/25) genomes from NextSeq 550 have perfect alignments to reference genomes with greater than 90%. The most fully assembled 25 genomes were categorized into 7 HAdV genotypes, the most abundant of which were HAdV-B3 (9/25) and HAdV-C2 (6/25). Phylogenetic analyzes revealed that the newly isolated HAdV-B3 strains diverged into separate clusters according to their genotypes. Vigilance is needed that HAdV-B3 isolates have begun to form new distinct clusters. High nucleotide identity was observed in the whole genome level within the same HAdV genotypes, while marked differences of three capsid genes across HAdV genotypes were noted. The high nucleotide diversity regions were concordant with the reported hypervariable regions. Further, three recombinant strains were identified: S64 and S71 originated from the parental strains HAdV-B14 and HAdV-B11, and S28 originated from HAdV-C1, HAdV-C5, and HAdV-CBJ113. GenoLab M and NextSeq 550 showed comparable performance with respect to data yield, duplication rate, human ratio, and assembly completeness.ConclusionThe sequencing quality and assembly accuracy showed that mNGS assembled genomes can be used for subsequently HAdV genotyping and genomic characterization. The high nucleotide diversity of capsid genes and high frequency of recombination events has highlighted the necessity for HAdV epidemiological surveillance in China.
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Affiliation(s)
- Bin Fang
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
| | - Juan Lai
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yongfeng Liu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Tian-tian Yu
- School of Public Health, Department of Nutritional Hygiene and Toxicology, Wuhan University of Science and Technology, Wuhan, China
| | - Xiao Yu
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
| | - Xiang Li
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
| | - Lijun Dong
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xin Zhang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Wei Yang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Sun
- GeneMind Biosciences Company Limited, Shenzhen, China
- *Correspondence: Lei Sun,
| | - Lin-lin Liu
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
- Lin-lin Liu,
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8
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Pavel I, Irina L, Tatiana G, Denis P, Philipp K, Sergei K, Evgeny D. Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics. BMC Genomics 2023; 24:102. [PMID: 36882687 PMCID: PMC9990361 DOI: 10.1186/s12864-023-09192-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/17/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND The Illumina sequencing systems demonstrate high efficiency and power and remain the most popular platforms. Platforms with similar throughput and quality profiles but lower costs are under intensive development. In this study, we compared two platforms Illumina NextSeq 2000 and GeneMind Genolab M for 10x Genomics Visium spatial transcriptomics. RESULTS The performed comparison demonstrates that GeneMind Genolab M sequencing platform produces highly consistent with Illumina NextSeq 2000 sequencing results. Both platforms have similar performance in terms of sequencing quality and detection of UMI, spatial barcode, and probe sequence. Raw read mapping and following read counting produced highly comparable results that is confirmed by quality control metrics and strong correlation between expression profiles in the same tissue spots. Downstream analysis including dimension reduction and clustering demonstrated similar results, and differential gene expression analysis predominantly detected the same genes for both platforms. CONCLUSIONS GeneMind Genolab M instrument is similar to Illumina sequencing efficacy and is suitable for 10x Genomics Visium spatial transcriptomics.
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Affiliation(s)
- Iamshchikov Pavel
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia.,Laboratory of Translational Cellular and Molecular Biomedicine, Tomsk State University, Tomsk, 634050, Russia
| | - Larionova Irina
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia. .,Laboratory of Translational Cellular and Molecular Biomedicine, Tomsk State University, Tomsk, 634050, Russia.
| | - Gerashchenko Tatiana
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia.,Laboratory of Single Cell Biology, Research Institute of Molecular and Cellular Medicine, Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russia
| | - Piankov Denis
- Laboratory of Molecular Pathology, Genomed Ltd, Moscow, 115093, Russia
| | - Koshkin Philipp
- Laboratory of Molecular Pathology, Genomed Ltd, Moscow, 115093, Russia
| | - Korostelev Sergei
- Laboratory of Molecular Pathology, Genomed Ltd, Moscow, 115093, Russia
| | - Denisov Evgeny
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia. .,Laboratory of Single Cell Biology, Research Institute of Molecular and Cellular Medicine, Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russia.
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9
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Wang Y, Zhao J, Chen Q, Zheng K, Deng X, Gao W, Pei W, Geng S, Deng Y, Li C, Chen Q, Qu Y. Quantitative trait locus mapping and identification of candidate genes for resistance to Verticillium wilt in four recombinant inbred line populations of Gossypium hirsutum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 327:111562. [PMID: 36509244 DOI: 10.1016/j.plantsci.2022.111562] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 05/16/2023]
Abstract
Improving resistance to Verticillium wilt is of great significance for achieving high and stable yields of Upland cotton (Gossypium hirsutum). To deeply understand the genetic basis of cotton resistance to Verticillium wilt, Verticillium wilt-resistant Upland Lumianyan 28 and four Verticillium wilt-susceptible Acala cotton cultivars were used to create four recombinant inbred line (RIL) populations of 469 families through nested hybridization. Phenotypic data collected in five stressful environments were used to select resistant and sensitive lines and create a mixed pool of extreme phenotypes for BSA-seq. A total of 8 QTLs associated with Verticillium wilt resistance were identified on 4 chromosomes, of which qVW-A12-5 was detected simultaneously in the RIL populations and in one of the RIL populations and was identified for the first time. According to the sequence comparison and transcriptome analysis of candidate genes in the QTL interval between parents and pools, 4 genes were identified in the qVW-A12-5 interval. qRT-PCR of parental and phenotypically extreme lines revealed that Gh_CPR30 was induced by and may be a candidate gene for resistance to Verticillium wilt in G. hirsutum. Furthermore, VIGS technology revealed that the disease severity index (DSI) of the Gh_CPR30-silenced plants was significantly higher than that of the control. These results indicate that the Gh_CPR30 gene plays an important role in the resistance of G. hirsutum to Verticillium wilt, and the study provides a molecular basis for analyzing the molecular mechanism underlying G. hirsutum resistance to Verticillium wilt.
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Affiliation(s)
- Yuxiang Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Jieyin Zhao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Qin Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Kai Zheng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Xiaojuan Deng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Wenju Gao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shiwei Geng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Yahui Deng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Chunping Li
- Institute of Cash Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830052, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Yanying Qu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China.
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10
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Liu Y, Han R, Zhou L, Luo M, Zeng L, Zhao X, Ma Y, Zhou Z, Sun L. Correction to: Comparative performance of the GenoLab M and NovaSeq 6000 sequencing platforms for transcriptome and LncRNA analysis. BMC Genomics 2022; 23:81. [PMID: 35081913 PMCID: PMC8790902 DOI: 10.1186/s12864-022-08307-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Yongfeng Liu
- GeneMind Biosciences Company Limited, ShenZhen, China
| | - Ran Han
- Beijing Guoke Biotechnology Co., LTD, Beijing, China
| | - Letian Zhou
- GeneMind Biosciences Company Limited, ShenZhen, China
| | - Mingjie Luo
- GeneMind Biosciences Company Limited, ShenZhen, China
| | - Lidong Zeng
- GeneMind Biosciences Company Limited, ShenZhen, China
| | - Xiaochao Zhao
- GeneMind Biosciences Company Limited, ShenZhen, China
| | - Yukun Ma
- Beijing Guoke Biotechnology Co., LTD, Beijing, China
| | - Zhiliang Zhou
- GeneMind Biosciences Company Limited, ShenZhen, China
| | - Lei Sun
- GeneMind Biosciences Company Limited, ShenZhen, China.
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