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Li H, Di X, Wang S, Li Q, Weng S, He J, Li C. Nucleic Acid Sensing by STING Induces an IFN-like Antiviral Response in a Marine Invertebrate. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1945-1957. [PMID: 38700419 DOI: 10.4049/jimmunol.2300669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/09/2024] [Indexed: 05/05/2024]
Abstract
The cytosolic detection of pathogen-derived nucleic acids has evolved as an essential strategy for host innate immune defense in mammals. One crucial component in this process is the stimulator of IFN genes (STING), which acts as a vital signaling adaptor, connecting the cytosolic detection of DNA by cyclic GMP-AMP (cGAMP) synthase (cGAS) to the downstream type I IFN signaling pathway. However, this process remains elusive in invertebrates. In this study, we present evidence demonstrating that STING, an ortholog found in a marine invertebrate (shrimp) called Litopenaeus vannamei, can directly detect DNA and initiate an IFN-like antiviral response. Unlike its homologs in other eukaryotic organisms, which exclusively function as sensors for cyclic dinucleotides, shrimp STING has the ability to bind to both double-stranded DNA and cyclic dinucleotides, including 2'3'-cGAMP. In vivo, shrimp STING can directly sense DNA nucleic acids from an infected virus, accelerate IFN regulatory factor dimerization and nuclear translocation, induce the expression of an IFN functional analog protein (Vago4), and finally establish an antiviral state. Taken together, our findings unveil a novel double-stranded DNA-STING-IKKε-IRF-Vago antiviral axis in an arthropod, providing valuable insights into the functional origins of DNA-sensing pathways in evolution.
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Affiliation(s)
- Haoyang Li
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Xuanzheng Di
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Sheng Wang
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Qinyao Li
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Chaozheng Li
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
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2
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Ramachandran L, Mangaiyarkarasi SP, Subramanian A, Senthilkumar S. Shrimp classification for white spot syndrome detection through enhanced gated recurrent unit-based wild geese migration optimization algorithm. Virus Genes 2024:10.1007/s11262-023-02049-0. [PMID: 38253919 DOI: 10.1007/s11262-023-02049-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024]
Abstract
The major dangerous viral infection for cultivated shrimps is WSSV. The virus is extremely dangerous, spreads swiftly, and may result in up to 100% mortality in 3-10 days. The vast wrapped double stranded DNA virus known as WSSV describes a member of the Nimaviridae viral family's species Whispovirus. It impacts a variety of crustacean hosts but predominantly marine shrimp species that are raised for commercial purposes. The entire age groups are affected by the virus, which leads to widespread mortality. Mesodermal and ectodermal tissues, like the lymph nodes, gills, and cuticular epithelium, represents the centres of infection. Complete genome sequencing related to the WSSV strains from Thailand, China, and Taiwan has identified minute genetic variations amongst them. There exist conflicting findings on the causes of WSSV pathogenicity, which involve variations in the size associated with the genome, the count of tandem repeats, and the availability or lack of certain proteins. Hence, this paper plans to perform the shrimp classification for the WSSV on the basis of novel deep learning methodology. Initially, the data is gathered from the farms as well as internet sources. Next, the pre-processing of the gathered shrimp images is accomplished using the LBP technique. These pre-processed images undergo the segmentation process utilizing the TGVFCMS approach. The extraction of the features from these segmented images is performed by the PLDA technique. In the final step, the classification of the shrimp into healthy shrimp and WSSV affected shrimp is done by the EGRU, in which the parameter tuning is accomplished by the wild GMO algorithm with the consideration of accuracy maximization as the major objective function. Performance indicators for accuracy have been compared with those of various conventional methods, and the results show that the methodology is capable of accurately identifying the shrimp WSSV illness.
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Affiliation(s)
- L Ramachandran
- Department of Electronics and Communication Engineering, E.G.S. Pillay Engineering College, Nagapattinam, Tamilnadu, 611002, India.
| | - S P Mangaiyarkarasi
- Department of Electrical and Electronics Engineering, University College of Engineering, Panruti Campus, Panruti, Tamilnadu, 607106, India
| | - A Subramanian
- Srinivasa Ramanujan Centre, SASTRA Deemed to Be University, Kumbakonam, Tamilnadu, 612001, India
| | - S Senthilkumar
- Department of Electronics and Communication Engineering, E.G.S. Pillay Engineering College, Nagapattinam, Tamilnadu, 611002, India
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Kumar P, Rani A, Singh S, Kumar A. Recent advances on
DNA
and omics‐based technology in Food testing and authentication: A review. J Food Saf 2022. [DOI: 10.1111/jfs.12986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Pramod Kumar
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Alka Rani
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Shalini Singh
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Anuj Kumar
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
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4
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Zhang S, Zhu L, Hou C, Yuan H, Yang S, Dehwah MAS, Shi L. GSK3β Plays a Negative Role During White Spot Syndrome Virus (WSSV) Infection by Regulating NF-κB Activity in Shrimp Litopenaeus vannamei. Front Immunol 2020; 11:607543. [PMID: 33324423 PMCID: PMC7725904 DOI: 10.3389/fimmu.2020.607543] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/30/2020] [Indexed: 11/28/2022] Open
Abstract
Glycogen synthase kinase-3 (GSK3), a cytoplasmic serine/threonine-protein kinase involved in a large number of key cellular processes, is a little-known signaling molecule in virus study. In this study, a GSK3 protein which was highly similar to GSK3β homologs from other species in Litopenaeus vannamei (designated as LvGSK3β) was obtained. LvGSK3β was expressed constitutively in the healthy L. vannamei, at the highest level in the intestine and the lowest level in the eyestalk. White spot syndrome virus (WSSV) reduced LvGSK3β expression was in immune tissues including the hemocyte, intestine, gill and hepatopancreas. The inhibition of LvGSK3β resulted in significantly higher survival rates of L. vannamei during WSSV infection than the control group, and significantly lower WSSV viral loads in LvGSK3β-inhibited L. vannamei were observed. Knockdown of LvGSK3β by RNAi resulted in increases in the expression of LvDorsal and several NF-κB driven antimicrobial peptide (AMP) genes (including ALF, PEN and crustin), but a decrease in LvCactus expression. Accordingly, overexpression of LvGSK3β could reduce the promoter activity of LvDorsal and several AMPs, while the promoter activity of LvCactus was increased. Electrophoretic mobility shift assays (EMSA) showed that LvDorsal could bind to the promoter of LvGSK3β. The interaction between LvGSK3β and LvDorsal or LvCactus was confirmed using co-immunoprecipitation (Co-IP) assays. In addition, the expression of LvGSK3β was dramatically reduced by knockdown of LvDorsal. In summary, the results presented in this study indicated that LvGSK3β had a negative effect on L. vannamei by mediating a feedback regulation of the NF-κB pathway when it is infected by WSSV.
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Affiliation(s)
- Shuang Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China.,Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, China
| | - Lulu Zhu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Cuihong Hou
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Hang Yuan
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Sheng Yang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Mustafa Abdo Saif Dehwah
- Department of Medical Laboratories, Faculty of Medical and Health Science, Taiz University/AL-Turba Branch, Taiz, Yemen
| | - Lili Shi
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
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5
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Xiao B, Fu Q, Niu S, Zhu P, He J, Li C. Penaeidins restrict white spot syndrome virus infection by antagonizing the envelope proteins to block viral entry. Emerg Microbes Infect 2020; 9:390-412. [PMID: 32397950 PMCID: PMC7048182 DOI: 10.1080/22221751.2020.1729068] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Emerging studies have indicated that some penaeidins restrict virus infection; however, the mechanism(s) involved are poorly understood. In the present study, we uncovered that penaeidins are a novel family of antiviral effectors against white spot syndrome virus (WSSV), which antagonize the envelope proteins to block viral entry. We found that the expression levels of four identified penaeidins from Litopenaeus vannamei, including BigPEN, PEN2, PEN3, and PEN4, were significantly induced in hemocytes during the early stage of WSSV infection. Knockdown of each penaeidin in vivo via RNA interference resulted in elevated viral loads and rendered shrimp more susceptible to WSSV, while the survival rate was rescued via the injection of recombinant penaeidins. All penaeidins, except PEN4, were shown to interact with several envelope proteins of WSSV, and all four penaeidins were observed to be located on the outer surface of the WSSV virion. Co-incubation of each recombinant penaeidin with WSSV inhibited virion internalization into hemocytes. More importantly, we found that PEN2 competitively bound to the envelope protein VP24 to release it from polymeric immunoglobulin receptor (pIgR), the cellular receptor required for WSSV infection. Moreover, we also demonstrated that BigPEN was able to bind to VP28 of WSSV, which disrupted the interaction between VP28 and Rab7 – the Rab GTPase that contributes to viral entry by binding with VP28. Taken together, our results demonstrated that penaeidins interact with the envelope proteins of WSSV to block multiple viral infection processes, thereby protecting the host against WSSV.
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Affiliation(s)
- Bang Xiao
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ School of Marine Sciences, Sun Yat-sen University, Guangzhou, P. R. People's Republic of China.,State Key Laboratory of Biocontrol/ School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. People's Republic of China
| | - Qihui Fu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ School of Marine Sciences, Sun Yat-sen University, Guangzhou, P. R. People's Republic of China.,State Key Laboratory of Biocontrol/ School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. People's Republic of China
| | - Shengwen Niu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ School of Marine Sciences, Sun Yat-sen University, Guangzhou, P. R. People's Republic of China.,State Key Laboratory of Biocontrol/ School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. People's Republic of China
| | - Peng Zhu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gluf University, Qinzhou, P. R. People's Republic of China
| | - Jianguo He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ School of Marine Sciences, Sun Yat-sen University, Guangzhou, P. R. People's Republic of China.,State Key Laboratory of Biocontrol/ School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. People's Republic of China
| | - Chaozheng Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ School of Marine Sciences, Sun Yat-sen University, Guangzhou, P. R. People's Republic of China.,State Key Laboratory of Biocontrol/ School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. People's Republic of China
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6
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Worasilchai N, Permpalung N, Chindamporn A. High-resolution melting analysis: A novel approach for clade differentiation in Pythium insidiosum and pythiosis. Med Mycol 2018; 56:868-876. [PMID: 29228389 DOI: 10.1093/mmy/myx123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/12/2017] [Indexed: 01/02/2023] Open
Abstract
Pythium insidiosum causes life-threatening human pythiosis. Based on phylogenetic analysis using internal transcribed spacer (ITS) region, mitochondrial cytochrome C oxidase II (COX2) gene, intergenic spacer (IGS) region and exo-1,3-β-glucanase gene (exo1), P. insidiosum is classified into clade ATH, BTH, and CTH related to geographic distribution. At present, polymerase chain reaction in any of these specific regions with DNA sequencing is the only technique to provide clade diagnosis. In this study, P. insidiosum-specific primers targeting COX2 gene were designed and used in real-time quantitative polymerase chain reaction (qPCR) with subsequent high-resolution melting (HRM) to provide rapid identification as well as clade classification for P. insidiosum. Based on the qPCR-HRM method, 15 P. insidiosum isolates could be differentiated from 28 related organisms with 100% specificity and 1 pg limit of detection. This technique was, in addition, directly tested on clinical samples from proved human pythiosis cases: nine corneal scrapes and six arterial clots. The qPCR-HRM results of all nine corneal samples were a 100% match with the results from the conventional PCR at clade level. However, the qPCR-HRM results of arterial clot samples were only matched with the nucleotide sequencing results from the conventional PCR at species level. In conclusion, the qPCR-HRM is a simple one closed tube, inexpensive and user-friendly method to identify P. insidiosum into clade level.
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Affiliation(s)
- Navaporn Worasilchai
- Interdisciplinary Program, Medical Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Nitipong Permpalung
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina, USA
| | - Ariya Chindamporn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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7
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Li H, Yin B, Wang S, Fu Q, Xiao B, Lǚ K, He J, Li C. RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides. PLoS Pathog 2018; 14:e1007109. [PMID: 30256850 PMCID: PMC6175524 DOI: 10.1371/journal.ppat.1007109] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 10/08/2018] [Accepted: 09/10/2018] [Indexed: 12/21/2022] Open
Abstract
The function of Toll pathway defense against bacterial infection has been well established in shrimp, however how this pathway responds to viral infection is still largely unknown. In this study, we report the Toll4-Dorsal-AMPs cascade restricts the white spot syndrome virus (WSSV) infection of shrimp. A total of nine Tolls from Litopenaeus vannamei namely Toll1-9 are identified, and RNAi screening in vivo reveals the Toll4 is important for shrimp to oppose WSSV infection. Knockdown of Toll4 results in elevated viral loads and renders shrimp more susceptible to WSSV. Furthermore, Toll4 could be a one of upstream pattern recognition receptor (PRR) to detect WSSV, and thereby leading to nuclear translocation and phosphorylation of Dorsal, the known NF-κB transcription factor of the canonical Toll pathway. More importantly, silencing of Toll4 and Dorsal contributes to impaired expression of a specific set of antimicrobial peptides (AMPs) such as anti-LPS-factor (ALF) and lysozyme (LYZ) family, which exert potent anti-WSSV activity. Two AMPs of ALF1 and LYZ1 as representatives are demonstrated to have the ability to interact with several WSSV structural proteins to inhibit viral infection. Taken together, we therefore identify that the Toll4-Dorsal pathway mediates strong resistance to WSSV infection by inducing some specific AMPs. The TLR pathway mediated antiviral immune response is well identified in mammals, yet, Toll pathway governing this protection in invertebrates remains unknown. In the present study, we uncover that a shrimp Toll4 from a total of nine Tolls in L. vannamei confers resistance to WSSV thought inducing the NF-κB transcription factor Dorsal to inspire the production of some antimicrobial peptides (AMPs) with antiviral activity. The anti-LPS-factor (ALF) and lysozyme (LYZ) family are identified as the Toll4-Dorsal pathway targeted genes with the ability to interact with viral structural proteins in response to WSSV infection. These results suggest that the Toll receptor induces the expression of AMPs with antiviral activity could be a general antiviral mechanism in invertebrates and Toll pathway established antiviral defense could be conserved during evolution.
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Affiliation(s)
- Haoyang Li
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, P. R. China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-sen University, Guangzhou, P. R. China
| | - Bin Yin
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, P. R. China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-sen University, Guangzhou, P. R. China
| | - Sheng Wang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, P. R. China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-sen University, Guangzhou, P. R. China
| | - Qihui Fu
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, P. R. China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-sen University, Guangzhou, P. R. China
| | - Bang Xiao
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, P. R. China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-sen University, Guangzhou, P. R. China
| | - Kai Lǚ
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, P. R. China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-sen University, Guangzhou, P. R. China
| | - Jianguo He
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, P. R. China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-sen University, Guangzhou, P. R. China
- * E-mail: (JH); (CL)
| | - Chaozheng Li
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, P. R. China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-sen University, Guangzhou, P. R. China
- * E-mail: (JH); (CL)
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8
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Wang HB, Mo QH, Wang Q, Wu BM, Feng ZL, Lin JC, Yang Z. Probe-free and sensitive detection of diarrhea-causing pathogens using RT-PCR combined high resolution melting analysis. Biologicals 2016; 44:360-6. [DOI: 10.1016/j.biologicals.2016.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 06/24/2016] [Accepted: 06/29/2016] [Indexed: 11/29/2022] Open
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9
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Salihah NT, Hossain MM, Lubis H, Ahmed MU. Trends and advances in food analysis by real-time polymerase chain reaction. Journal of Food Science and Technology 2016; 53:2196-209. [PMID: 27407185 PMCID: PMC4921084 DOI: 10.1007/s13197-016-2205-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 03/06/2016] [Accepted: 03/14/2016] [Indexed: 02/05/2023]
Abstract
Analyses to ensure food safety and quality are more relevant now because of rapid changes in the quantity, diversity and mobility of food. Food-contamination must be determined to maintain health and up-hold laws, as well as for ethical and cultural concerns. Real-time polymerase chain reaction (RT-PCR), a rapid and inexpensive quantitative method to detect the presence of targeted DNA-segments in samples, helps in determining both accidental and intentional adulterations of foods by biological contaminants. This review presents recent developments in theory, techniques, and applications of RT-PCR in food analyses, RT-PCR addresses the limitations of traditional food analyses in terms of sensitivity, range of analytes, multiplexing ability, cost, time, and point-of-care applications. A range of targets, including species of plants or animals which are used as food ingredients, food-borne bacteria or viruses, genetically modified organisms, and allergens, even in highly processed foods can be identified by RT-PCR, even at very low concentrations. Microfluidic RT-PCR eliminates the separate sample-processing step to create opportunities for point-of-care analyses. We also cover the challenges related to using RT-PCR for food analyses, such as the need to further improve sample handling.
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Affiliation(s)
- Nur Thaqifah Salihah
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410 Brunei Darussalam
| | | | - Hamadah Lubis
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410 Brunei Darussalam
| | - Minhaz Uddin Ahmed
- Biosensors and Biotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410 Brunei Darussalam
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10
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The use of real-time polymerase chain reaction with high resolution melting (real-time PCR-HRM) analysis for the detection and discrimination of nematodes Bursaphelenchus xylophilus and Bursaphelenchus mucronatus. Mol Cell Probes 2016; 30:113-7. [PMID: 26880540 DOI: 10.1016/j.mcp.2016.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 02/05/2016] [Accepted: 02/07/2016] [Indexed: 12/12/2022]
Abstract
The real-time PCR-HRM analysis was developed for the detection and discrimination of the quarantine nematode Bursaphelenchus xylophilus and Bursaphelenchus mucronatus. A set of primers was designed to target the ITS region of rDNA. The results have demonstrated that this analysis is a valuable tool for differentiation of these both species.
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Cowley J. Nidoviruses of Fish and Crustaceans. AQUACULTURE VIROLOGY 2016. [PMCID: PMC7150020 DOI: 10.1016/b978-0-12-801573-5.00032-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Viruses with diverse virion architectures demarcated into four families in the order Nidovirales have been discovered in vertebrate mammalian and fish species, as well as in invertebrate crustacean and mosquito species. The order is unified by nidoviruses sharing intermediate (12.7 kb) to very long (31.7 kb) (+) ssRNA genomes, each possessing a long 5′-terminal gene encoding overlapping ORF1a and ORF1b reading frames that contain a diversity of functionally related enzymes and that are translated in toto using a −1 ribosomal frameshift mechanism, as well as by semiconserved strategies for transcribing a nested set of 3′-coterminal subgenomic mRNAs that translate the viral proteins. The nidovirus that is most important to an aquaculture species is yellow head virus (YHV), which causes disease in shrimp farmed throughout the Eastern Hemisphere and is classified in the genus Okavirus, family Roniviridae. Fathead minnow nidovirus, genus Bafinivirus, subfamily Torovirinae, family Coronaviridae, also causes disease in minnows grown for the baitfish industry in the United States. Virions similar in morphology to okaviruses and bafiniviruses have also been detected in several crab species. Of these, however, only Eriocheir sinensis ronivirus, which causes disease in the Chinese mitten crab, an important freshwater aquaculture species in China, has been shown to possess a ~22 kb ssRNA genome that supports its being a nidovirus, but its taxonomic classification awaits genome sequence analysis. This chapter provides an overview of the structure, replication and biology of these viruses with a particular focus on YHV disease characteristics, diagnostic methods and disease prevention strategies.
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Lafferty KD, Harvell CD, Conrad JM, Friedman CS, Kent ML, Kuris AM, Powell EN, Rondeau D, Saksida SM. Infectious diseases affect marine fisheries and aquaculture economics. ANNUAL REVIEW OF MARINE SCIENCE 2015; 7:471-96. [PMID: 25251276 DOI: 10.1146/annurev-marine-010814-015646] [Citation(s) in RCA: 280] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Seafood is a growing part of the economy, but its economic value is diminished by marine diseases. Infectious diseases are common in the ocean, and here we tabulate 67 examples that can reduce commercial species' growth and survivorship or decrease seafood quality. These impacts seem most problematic in the stressful and crowded conditions of aquaculture, which increasingly dominates seafood production as wild fishery production plateaus. For instance, marine diseases of farmed oysters, shrimp, abalone, and various fishes, particularly Atlantic salmon, cost billions of dollars each year. In comparison, it is often difficult to accurately estimate disease impacts on wild populations, especially those of pelagic and subtidal species. Farmed species often receive infectious diseases from wild species and can, in turn, export infectious agents to wild species. However, the impact of disease export on wild fisheries is controversial because there are few quantitative data demonstrating that wild species near farms suffer more from infectious diseases than those in other areas. The movement of exotic infectious agents to new areas continues to be the greatest concern.
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Affiliation(s)
- Kevin D Lafferty
- Western Ecological Research Center, US Geological Survey, c/o Marine Science Institute, University of California, Santa Barbara, California 93106; *
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Komorowska B, Fiore N, Zamorano A, Li R. Simultaneous detection of Cherry necrotic rusty mottle virus and Cherry green ring mottle virus using real-time PCR and high resolution melting analysis. Mol Cell Probes 2014; 28:186-91. [DOI: 10.1016/j.mcp.2014.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/09/2014] [Accepted: 03/12/2014] [Indexed: 11/30/2022]
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Ning P, Li H, Liang W, Guo K, Tan X, Cao W, Cheng L, Zhang Y. Detection and differentiation of classical swine fever virus strains C and Shimen by high-resolution melt analysis. J Virol Methods 2013; 194:129-31. [DOI: 10.1016/j.jviromet.2013.07.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/25/2013] [Accepted: 07/26/2013] [Indexed: 10/26/2022]
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Hasiów-Jaroszewska B, Komorowska B. A new method for detection and discrimination of Pepino mosaic virus isolates using high resolution melting analysis of the triple gene block 3. J Virol Methods 2013; 193:1-5. [DOI: 10.1016/j.jviromet.2013.04.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 04/22/2013] [Accepted: 04/29/2013] [Indexed: 11/30/2022]
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Pradeep B, Rai P, Mohan SA, Shekhar MS, Karunasagar I. Biology, Host Range, Pathogenesis and Diagnosis of White spot syndrome virus. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2012; 23:161-74. [PMID: 23997440 PMCID: PMC3550756 DOI: 10.1007/s13337-012-0079-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 06/26/2012] [Indexed: 01/31/2023]
Abstract
White spot syndrome virus (WSSV) is the most serious viral pathogen of cultured shrimp. It is a highly virulent virus that can spread quickly and can cause up to 100 % mortality in 3-10 days. WSSV is a large enveloped double stranded DNA virus belonging to genus Whispovirus of the virus family Nimaviridae. It has a wide host range among crustaceans and mainly affects commercially cultivated marine shrimp species. The virus infects all age groups causing large scale mortalities and the foci of infection are tissues of ectodermal and mesodermal origin, such as gills, lymphoid organ and cuticular epithelium. The whole genome sequencing of WSSV from China, Thailand and Taiwan have revealed minor genetic differences among different strains. There are varying reports regarding the factors responsible for WSSV virulence which include the differences in variable number of tandem repeats, the genome size and presence or absence of different proteins. Aim of this review is to give current information on the status, host range, pathogenesis and diagnosis of WSSV infection.
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Affiliation(s)
- Balakrishnan Pradeep
- />Krishi Vigyan Kendra, Indian Institute of Spices Research, Peruvannamuzhi, Kozhikode, 673528 Kerala India
| | - Praveen Rai
- />Department of Fishery Microbiology, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002 India
| | - Seethappa A. Mohan
- />Department of Fishery Microbiology, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002 India
| | - Mudagandur S. Shekhar
- />Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, Chennai, India
| | - Indrani Karunasagar
- />Department of Fishery Microbiology, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002 India
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Safeena MP, Rai P, Karunasagar I. Molecular Biology and Epidemiology of Hepatopancreatic parvovirus of Penaeid Shrimp. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2012; 23:191-202. [PMID: 23997443 PMCID: PMC3550755 DOI: 10.1007/s13337-012-0080-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 06/26/2012] [Indexed: 12/29/2022]
Abstract
Hepatopancreatic parvovirus (HPV) is one of the major shrimp parvovirus which is known to cause slow growth in penaeid shrimps. HPV has been found in wild and cultured penaeid shrimps throughout the world and there is high genetic variation among the different geographic isolates/host species. Given its high prevalence, wide distribution and ability to cause considerable economic loss in shrimp aquaculture industry, HPV deserves more attention than it has received. Till date, a total of four complete genome sequences of HPV have been reported in addition to a large number of partial sequences. HPV infection is seldom observed alone in epizootics and has occurred in multiple infections with other more pathogenic viruses and in most cases, heavy infections result in no visible inflammatory response. A great deal of information has accumulated in recent years on the clinical signs, geographical distribution, transmission and genetic diversity of HPV infection in shrimp aquaculture. However, the mechanism by which HPV enters the shrimp tissues and pathogenesis of virus is still unknown. To date, no effective prophylactic measures are available to reduce the infection in shrimps. To control and prevent HPV infection, considerable research efforts are on. This review provides information on current knowledge on HPV infection in penaeid shrimp aquaculture.
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Affiliation(s)
- Muhammed P. Safeena
- Department of Fishery Microbiology, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002 India
| | - Praveen Rai
- Department of Fishery Microbiology, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002 India
| | - Indrani Karunasagar
- Department of Fishery Microbiology, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002 India
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