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Zhu S, Chen X, He D, Zhang M, Man X, Tang Y, Diao Y. Role of long non-coding RNA DLY6E in regulating TMUV infection. Virus Res 2024; 343:199350. [PMID: 38438020 PMCID: PMC10982077 DOI: 10.1016/j.virusres.2024.199350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Long non-coding RNA (lncRNA) is a type of RNA with a length greater than 200 nt and lacking coding ability. In recent years, a considerable number of lncRNAs have been found to have important functions. The lncRNA plays an important role in growth and development, body metabolism, immune function, and regulation of viral replication. A lncRNA, MSTRG8505.2, was screened and named lncRNA DLY6E, which was a new duck-derived lncRNA. The lncRNADLY6E in this study has a complex secondary structure, specifically distributed in the heart, liver and other organs. The expression of lncRNA DLY6E was significantly up-regulated after TMUV infection, which was time-dependent and non-dose-dependent. Overexpression of three structural proteins and seven non-structural proteins of TMUV in DEF cells showed no significant difference in the expression of lncRNADLY6E. Meanwhile, using lipopolysaccharides (LPS) and poly (I:C) to stimulate DEF cells, the results showed that the induced expression of lncRNA DLY6E was associated with the dsRNA-related TLR3/RIG-I/MDA5 pathway rather than the LPS activated signaling pathway. To further explore the function of lncRNA DLY6E, an eukaryotic expression vector was constructed. Overexpression of lncRNA DLY6E in DEF cells can increase the replication of TMUV. After overexpression of lncRNADLY6E, the transcriptional level of its target gene LY6E was detected, and the results showed that lncRNADLY6E did not act through its target gene. Overexpression of lncRNA DLY6E significantly inhibited the mRNA levels of OAS, Mx and PKR, suggesting that lncRNA DLY6E may promote the virus by inhibiting the transcription of antiviral proteins in innate immunity. This phenomenon provides new ideas for the prevention and control of TMUV, which is worth further thinking and exploration.
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Affiliation(s)
- Siming Zhu
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China
| | - Xin Chen
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China
| | - Dalin He
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China
| | - Meijuan Zhang
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China
| | - Xinhong Man
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China.
| | - Youxiang Diao
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong 271018, China.
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Effect of Inonotus obliquus Extract Supplementation on Endurance Exercise and Energy-Consuming Processes through Lipid Transport in Mice. Nutrients 2022; 14:nu14235007. [PMID: 36501037 PMCID: PMC9737630 DOI: 10.3390/nu14235007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 11/26/2022] Open
Abstract
Inonotus obliquus (IO) is used as functional food to treat diabetes. This study investigated the effect of IO supplementation on body composition in relation to changes in energy expenditure and exercise performance. Male Institute of Cancer Research mice were divided into four groups (n = 8 per group) and orally administered IO once daily for 6 wk at 0 (vehicle), 824 (IO-1×), 1648 (IO-2×), and 2472 mg/kg (IO-3×). IO supplementation increased muscle volume, exhaustive treadmill time, and glycogen storage in mice. Serum free fatty acid levels after acute exercise improved in the IO supplementation group, which exhibited changes in energy expenditure through the peroxisome proliferator-activated receptor (PPAR) pathway. RNA sequencing revealed significantly increased PPAR signaling; phenylalanine, ascorbate, aldarate, and cholesterol metabolism; chemical carcinogenesis; and ergosterol biosynthesis in the IO group compared with the vehicle group. Thus, IO supplements as nutraceuticals have a positive effect on lipid transport and exercise performance. In addition, this study was only IO supplementation without training-related procedures.
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Liu S, Huang Z, Fan R, Jia J, Deng X, Zou X, Li H, Cao B. Cycling and activated CD8 + T lymphocytes and their association with disease severity in influenza patients. BMC Immunol 2022; 23:40. [PMID: 36064355 PMCID: PMC9441835 DOI: 10.1186/s12865-022-00516-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND T cell lymphopenia was a significant characteristic of severe influenza infection and it was associated with the functional changes of T cells. It is necessary to clarify the T cells characteristics of kinetic changes and their correlation with disease severity. METHODS In a cohort of hospitalized influenza patients with varying degrees of severity, we characterized lymphocyte populations using flow cytometry. RESULTS The numbers of cycling (Ki67+) T cells at the acute phase of severe influenza were higher, especially in the memory (CD45RO+) T cell subsets. T cells from hospitalized influenza patients also had significantly higher levels of the exhausted marker PD-1. Cycling status of T cells was associated with T cell activation during the acute phase of influenza infection. The recruitment of cycling and activated (CD38+HLA-DR+) CD8+ T cells subset is delayed in severe influenza patients. CONCLUSIONS The increased numbers of cycling memory (Ki67+CD45RO+) T cells subsets and delayed kinetics of activated (CD38+HLA-DR+) CD8+ T cells, could serve as possible biological markers for disease severity.
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Affiliation(s)
- Shuai Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.,Shandong Key Laboratory of Infectious Respiratory Disease, Jinan, Shandong, China
| | - Zhisheng Huang
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Ruyue Fan
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Ju Jia
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaoyan Deng
- Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohui Zou
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Hui Li
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Bin Cao
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China. .,Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China. .,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China.
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4
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Hejazian SS, Hejazian SM, Farnood F, Abedi Azar S. Dysregulation of immunity in COVID-19 and SLE. Inflammopharmacology 2022; 30:1517-1531. [PMID: 36028612 PMCID: PMC9417079 DOI: 10.1007/s10787-022-01047-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/30/2022] [Indexed: 12/15/2022]
Abstract
The immune response plays a crucial role in preventing diseases, such as infections. There are two types of immune responses, specific and innate immunity, each of which consists of two components: cellular immunity and humoral immunity. Dysfunction in any immune system component increases the risk of developing certain diseases. Systemic lupus erythematosus (SLE), an autoimmune disease in the human body, develops an immune response against its own components. In these patients, due to underlying immune system disorders and receipt of immunosuppressive drugs, the susceptibility to infections is higher than in the general population and is the single largest cause of mortality in this group. COVID-19 infection, which first appeared in late 2019, has caused several concerns in patients with SLE. However, there is no strong proof of additional risk of developing COVID-19 in patients with SLE, and in some cases, studies have shown less severity of the disease in these individuals. This review paper discusses the immune disorders in SLE and COVID-19.
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Affiliation(s)
- Seyyed Sina Hejazian
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Farahnoosh Farnood
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Sima Abedi Azar
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Differential expression profile and in-silico functional analysis of long noncoding RNA and mRNA in duck embryo fibroblasts infected with duck plague virus. BMC Genomics 2022; 23:509. [PMID: 35836133 PMCID: PMC9281093 DOI: 10.1186/s12864-022-08739-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 07/06/2022] [Indexed: 12/04/2022] Open
Abstract
Background Duck plague virus (DPV), belonging to herpesviruses, is a linear double-stranded DNA virus. There are many reports about the outbreak of the duck plague in a variety of countries, which caused huge economic losses. Recently, increasing reports revealed that multiple long non-coding RNAs (lncRNAs) can possess great potential in the regulation of host antiviral immune response. Furthermore, it remains to be determined which specific molecular mechanisms are responsible for the DPV-host interaction in host immunity. Here, lncRNAs and mRNAs in DPV infected duck embryonic fibroblast (DEF) cells were identified by high-throughput RNA-sequencing (RNA-seq). And we predicted target genes of differentially expressed genes (DEGs) and formed a complex regulatory network depending on in-silico analysis and prediction. Result RNA-seq analysis results showed that 2921 lncRNAs were found at 30 h post-infection (hpi). In our study, 218 DE lncRNAs and 2840 DE mRNAs were obtained in DEF after DPV infection. Among these DEGs and target genes, some have been authenticated as immune-related molecules, such as a Macrophage mannose receptor (MR), Anas platyrhynchos toll-like receptor 2 (TLR2), leukocyte differentiation antigen, interleukin family, and their related regulatory factors. Furthermore, according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis, we found that the target genes may have important effects on biological development, biosynthesis, signal transduction, cell biological regulation, and cell process. Also, we obtained, the potential targeting relationship existing in DEF cells between host lncRNAs and DPV-encoded miRNAs by software. Conclusions This study revealed not only expression changes, but also the possible biological regulatory relationship of lncRNAs and mRNAs in DPV infected DEF cells. Together, these data and analyses provide additional insight into the role of lncRNAs and mRNAs in the host's immune response to DPV infection. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08739-7.
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He D, Liu G, Yang J, Jiang X, Wang H, Fan Y, Gong S, Wei F, Diao Y, Tang Y. Specific High-Sensitivity Enzymatic Molecular Detection System Termed RPA-Based CRISPR-Cas13a for Duck Tembusu Virus Diagnostics. Bioconjug Chem 2022; 33:1232-1240. [PMID: 35586918 DOI: 10.1021/acs.bioconjchem.2c00200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In China, drastic losses in the economy have been caused by the Tembusu virus (TMUV), the causative agent of the egg-drop syndrome, to the duck-raising industry. To succeed in preventing and controlling infections, extant techniques must be upgraded to achieve fast detection of viruses. This work is the first attempt to present the development of a recombinase polymerase amplification (RPA)-based clustered regularly interspaced short palindromic repeats (CRISPRs)-Cas13a approach for the TMUV infection diagnosis, where the CRISPR-Cas13a system is exploited, i.e., the programmability of CRISPR RNA (crRNA) and the promiscuous RNase collateral cleavage of Cas13a upon recognition of target RNAs. A prokaryotic expression system was utilized for the expression of LwCas13a soluble protein, while its purification was accomplished by nickel-nitrilotriacetic acid (Ni-NTA) agarose. In the design of a particular crRNA, the target used was the TMUV NS3 RNA transcribed in vitro. The signals used for the Cas13a activity validation were an RNA-bound fluorescent group (single-stranded) and a quenching fluorophore. In the present work, a specific high-sensitivity enzymatic molecular detection system termed RPA-based CRISPR-Cas13a was established by combining Cas13a with T7 transcription and RPA for sensitive detection of TMUV at room temperature. This system can detect 102 copies of the target TMUV DNA standard/μL within 50 min. A comparison revealed that the specificity was superior to that for other avian viruses. Furthermore, the RPA-based CRISPR-Cas13a detection system was successfully applied for clinical samples, and its performance is comparable to the reverse-transcriptase real-time quantitative polymerase chain reaction (RT-qPCR). Being satisfyingly reliable, simple, specific, and sensitive, our RPA-based CRISPR-Cas13a detection system could be expanded and universalized for identifying other viruses, enabling quick detection in the field with a portable lateral flow dipstick.
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Affiliation(s)
- Dalin He
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Gang Liu
- Shandong Provincial Animal Husbandry General Station, Jinan 250102, China
| | - Jing Yang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Xiaoning Jiang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Hongzhi Wang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Yaru Fan
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Shangyu Gong
- Jinzhou Agricultural and Rural Comprehensive Service Center, Jinzhou 121000, China
| | - Feng Wei
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Youxiang Diao
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
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7
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Sui N, Zhang R, Jiang Y, Yu H, Xu G, Wang J, Zhu Y, Xie Z, Hu J, Jiang S. Long Noncoding RNA Expression Rofiles Elucidate the Potential Roles of lncRNA- XR_003496198 in Duck Hepatitis A Virus Type 1 Infection. Front Cell Infect Microbiol 2022; 12:858537. [PMID: 35531338 PMCID: PMC9074814 DOI: 10.3389/fcimb.2022.858537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/24/2022] [Indexed: 12/11/2022] Open
Abstract
Duck hepatitis A virus type 1 (DHAV-1) is a highly lethal virus that severely affects the duck industry worldwide. Long noncoding RNAs (lncRNAs) exert crucial roles in pathogen attacks. Here, we conducted deep transcriptome analysis to investigate the dynamic changes of host lncRNAs profiles in DHAV-1-infected duck embryo fibroblasts. We identified 16,589 lncRNAs in total and characterized their genomic features. Moreover, 772 and 616 differentially expressed lncRNAs (DELs) were screened at 12 and 24 h post-infection. Additionally, we predicted the DELs’ cis- and trans-target genes and constructed lncRNA-target genes regulatory networks. Functional annotation analyses indicated that the putative target genes of DELs participated in diverse vital biological processed, including immune responses, cellular metabolism, and autophagy. For example, we confirmed the dysregulation of pattern recognition receptors (TLR3, RIG-I, MDA5, LGP2, cGAS), signal transducers (STAT1), transcription factors (IRF7), immune response mediators (IL6, IL10, TRIM25, TRIM35, TRIM60, IFITM1, IFITM3, IFITM5), and autophagy-related genes (ULK1, ULK2, EIF4EBP2) using RT-qPCR. Finally, we confirmed that one DHAV-1 induced lncRNA-XR_003496198 is likely to inhibit DHAV-1 replication in DEFs. Our study comprehensively analyzed the lncRNA profiles upon DHAV-1 infection and screened the target genes involved in the innate immune response and autophagy signaling pathway, thereby revealing the essential roles of duck lncRNAs and broadening our understanding of host-virus interactions.
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Affiliation(s)
- Nana Sui
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Ruihua Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Yue Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Honglei Yu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Guige Xu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Jingyu Wang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Yanli Zhu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Zhijing Xie
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Jiaqing Hu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
- Shandong GreenBlue Biotechnology Co. Ltd., Taian, China
- *Correspondence: Jiaqing Hu, ; Shijin Jiang,
| | - Shijin Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
- *Correspondence: Jiaqing Hu, ; Shijin Jiang,
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8
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Lagarrigue S, Lorthiois M, Degalez F, Gilot D, Derrien T. LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 2021; 33:248-270. [PMID: 34773482 PMCID: PMC9114084 DOI: 10.1007/s00335-021-09928-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.
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Affiliation(s)
| | - Matthias Lorthiois
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, 35590, Saint-Gilles, France
| | - David Gilot
- CLCC Eugène Marquis, INSERM, Université Rennes, UMR_S 1242, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France.
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Gupta A, Gupta GS. Status of mannose-binding lectin (MBL) and complement system in COVID-19 patients and therapeutic applications of antiviral plant MBLs. Mol Cell Biochem 2021; 476:2917-2942. [PMID: 33745077 PMCID: PMC7981598 DOI: 10.1007/s11010-021-04107-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by a virus called "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)." In the majority of patients, infection with COVID-19 may be asymptomatic or may cause only mild symptoms. However, in some patients, there can also be immunological problems, such as macrophage activation syndrome (CSS) that results in cytokine storm syndrome (CSS) and acute respiratory distress syndrome (ARDS). Comprehension of host-microbe communications is the critical aspect in the advancement of new therapeutics against infectious illnesses. Endogenous animal lectins, a class of proteins, may perceive non-self glycans found on microorganisms. Serum mannose-binding lectin (sMBL), as a part of the innate immune framework, recognizes a wide range of microbial microorganisms and activates complement cascade via an antibody-independent pathway. Although the molecular basis for the intensity of SARS-CoV-2 infection is not generally understood, scientific literature indicates that COVID-19 is correlated with unregulated activation of the complement in terms of disease severity. Disseminated intravascular coagulation (DIC), inflammation, and immune paralysis contribute to unregulated complement activation. Pre-existing genetic defects in MBL and their association with complement play a major role in immune response dysregulation caused by SARS-CoV-2. In order to generate anti-complement-based therapies in Covid-19, an understanding of sMBL in immune response to SARS-CoV-2 and complement is therefore essential. This review highlights the role of endogenous sMBL and complement activation during SARS-CoV-2 infection and their therapeutic management by various agents, mainly plant lectins, since antiviral mannose-binding plant lectins (pMBLs) offer potential applications in the prevention and control of viral infections.
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Affiliation(s)
- Anita Gupta
- Chitkara School of Health Sciences, Chitkara University, Rajpura, Punjab, India
| | - G S Gupta
- Department of Biophysics, Sector 25, Panjab University, Chandigarh, 160014, India.
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10
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Low ZY, Yip AJW, Sharma A, Lal SK. SARS coronavirus outbreaks past and present-a comparative analysis of SARS-CoV-2 and its predecessors. Virus Genes 2021; 57:307-317. [PMID: 34061288 PMCID: PMC8167830 DOI: 10.1007/s11262-021-01846-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/10/2021] [Indexed: 02/08/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19), a pneumonic disease caused by the SARS Coronavirus 2 (SARS-CoV-2), is the 7th Coronavirus to have successfully infected and caused an outbreak in humans. Genome comparisons have shown that previous isolates, the SARS-related coronavirus (SARSr-CoV), including the SARS-CoV are closely related, yet different in disease manifestation. Several explanations were suggested for the undetermined origin of SARS-CoV-2, in particular, bats, avian and Malayan pangolins as reservoir hosts, owing to the high genetic similarity. The general morphology and structure of all these viral isolates overlap with analogous disease symptoms such as fever, dry cough, fatigue, dyspnoea and headache, very similar to the current SARS-CoV-2. Chest CT scans for SARS-CoV-2, SARS-CoV and MERS-CoV reveal pulmonary lesions, bilateral ground-glass opacities, and segmental consolidation in the lungs, a common pathological trait. With greatly overlapping similarities among the previous coronavirus, the SARS-CoV, it becomes interesting to observe marked differences in disease severity of the SARS-CoV-2 thereby imparting it the ability to rapidly transmit, exhibit greater stability, bypass innate host defences, and increasingly adapt to their new host thereby resulting in the current pandemic. The most recent B.1.1.7, B.1.351 and P.1 variants of SARS-CoV-2, highlight the fact that changes in amino acids in the Spike protein can contribute to enhanced infection and transmission efficiency. This review covers a comparative analysis of previous coronavirus outbreaks and highlights the differences and similarities among different coronaviruses, including the most recent isolates that have evolved to become easily transmissible with higher replication efficiency in humans.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Anshika Sharma
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Sunil K Lal
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia.
- Tropical Medicine and Biology Platform, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia.
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Low ZY, Yip AJW, Sharma A, Lal SK. SARS coronavirus outbreaks past and present-a comparative analysis of SARS-CoV-2 and its predecessors. Virus Genes 2021. [PMID: 34061288 DOI: 10.1007/s11262‐021‐01846‐9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19), a pneumonic disease caused by the SARS Coronavirus 2 (SARS-CoV-2), is the 7th Coronavirus to have successfully infected and caused an outbreak in humans. Genome comparisons have shown that previous isolates, the SARS-related coronavirus (SARSr-CoV), including the SARS-CoV are closely related, yet different in disease manifestation. Several explanations were suggested for the undetermined origin of SARS-CoV-2, in particular, bats, avian and Malayan pangolins as reservoir hosts, owing to the high genetic similarity. The general morphology and structure of all these viral isolates overlap with analogous disease symptoms such as fever, dry cough, fatigue, dyspnoea and headache, very similar to the current SARS-CoV-2. Chest CT scans for SARS-CoV-2, SARS-CoV and MERS-CoV reveal pulmonary lesions, bilateral ground-glass opacities, and segmental consolidation in the lungs, a common pathological trait. With greatly overlapping similarities among the previous coronavirus, the SARS-CoV, it becomes interesting to observe marked differences in disease severity of the SARS-CoV-2 thereby imparting it the ability to rapidly transmit, exhibit greater stability, bypass innate host defences, and increasingly adapt to their new host thereby resulting in the current pandemic. The most recent B.1.1.7, B.1.351 and P.1 variants of SARS-CoV-2, highlight the fact that changes in amino acids in the Spike protein can contribute to enhanced infection and transmission efficiency. This review covers a comparative analysis of previous coronavirus outbreaks and highlights the differences and similarities among different coronaviruses, including the most recent isolates that have evolved to become easily transmissible with higher replication efficiency in humans.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Anshika Sharma
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia
| | - Sunil K Lal
- School of Science, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia. .,Tropical Medicine and Biology Platform, Monash University, Sunway Campus, 47500, Bandar Sunway, Selangor DE, Malaysia.
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