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Mishra A, Kim HS, Kumar R, Srivastava V. Advances in Vibrio-related infection management: an integrated technology approach for aquaculture and human health. Crit Rev Biotechnol 2024:1-28. [PMID: 38705837 DOI: 10.1080/07388551.2024.2336526] [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: 08/03/2023] [Accepted: 11/25/2023] [Indexed: 05/07/2024]
Abstract
Vibrio species pose significant threats worldwide, causing mortalities in aquaculture and infections in humans. Global warming and the emergence of worldwide strains of Vibrio diseases are increasing day by day. Control of Vibrio species requires effective monitoring, diagnosis, and treatment strategies at the global scale. Despite current efforts based on chemical, biological, and mechanical means, Vibrio control management faces limitations due to complicated implementation processes. This review explores the intricacies and challenges of Vibrio-related diseases, including accurate and cost-effective diagnosis and effective control. The global burden due to emerging Vibrio species further complicates management strategies. We propose an innovative integrated technology model that harnesses cutting-edge technologies to address these obstacles. The proposed model incorporates advanced tools, such as biosensing technologies, the Internet of Things (IoT), remote sensing devices, cloud computing, and machine learning. This model offers invaluable insights and supports better decision-making by integrating real-time ecological data and biological phenotype signatures. A major advantage of our approach lies in leveraging cloud-based analytics programs, efficiently extracting meaningful information from vast and complex datasets. Collaborating with data and clinical professionals ensures logical and customized solutions tailored to each unique situation. Aquaculture biotechnology that prioritizes sustainability may have a large impact on human health and the seafood industry. Our review underscores the importance of adopting this model, revolutionizing the prognosis and management of Vibrio-related infections, even under complex circumstances. Furthermore, this model has promising implications for aquaculture and public health, addressing the United Nations Sustainable Development Goals and their development agenda.
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Affiliation(s)
- Anshuman Mishra
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, South Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, South Korea
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
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2
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Li L, Shen Y, Xu X, Yang W, Li J. Tracing and exploring the evolutionary origin and systematic function of fish complement C9. Mol Genet Genomics 2021; 296:665-676. [PMID: 33718983 DOI: 10.1007/s00438-021-01773-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/08/2021] [Indexed: 01/03/2023]
Abstract
Complement C9, as a member of terminal complement component (TCC) protein, plays important roles in innate immunity. However, some complement components appear to show difference and evolutionary complexity between higher and lower vertebrates. Hence, it is essential to carry on a study of evolutionary origin and systematic function of C9 in fish and non-fish vertebrates. This study aims to explore the complement gene evolution and potential function in fish based on molecular and structural biology. Herein, we found complete divergence of C9 throughout the gene evolution. The optimal codons of C9 sequences tended to be closer to the genomes of lower vertebrates compared to higher vertebrates. Further, conserved amino acids in the C9 TMH1 region were identified, implying their potential functional association with MAC growth and pore formation. Transposons and simple repeats, as gene elements, exhibited a differential distribution in the genomic regions in different animal groups but were sparsely scattered around the sixth exon (TMH1 region). Notably, this demonstrated the regulatory complexity of the C9 gene in higher vertebrates. The negative selection pressures on fish and non-fish groups improved both the sequence conservation and similarity. Through gene/protein regulatory network and pathway analyses, the systematic function of C9 protein was showcased; thus, we could reveal the divergence of the systematic function of C9 across species from different evolutionary positions. In addition, more complicated functions of C9 in higher vertebrates could established by the altered spatial conformation of the protein. Collectively, the present study illustrates the C9 gene evolutionary process and the difference in its systematic function across multiple species. Such advances provide new insights for understanding the evolutionary and potential functions of complement C9.
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Affiliation(s)
- Lisen Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, College of Aquaculture and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, College of Aquaculture and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, College of Aquaculture and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Weining Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, College of Aquaculture and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, College of Aquaculture and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China.
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3
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Li H, Huang X, Li W, Lu Y, Dai X, Zhou Z, Li Q. MicroRNA comparison between poplar and larch provides insight into the different mechanism of wood formation. PLANT CELL REPORTS 2020; 39:1199-1217. [PMID: 32577818 DOI: 10.1007/s00299-020-02559-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 06/12/2020] [Indexed: 05/22/2023]
Abstract
MiRNA transcriptome analysis of different tissues in poplar and larch suggests variant roles of miRNAs in regulating wood formation between two kinds of phyla. Poplar and larch belong to two different phyla. Both are ecological woody species and major resources for wood-related industrial applications. However, wood properties are different between these two species and the molecular basis is largely unknown. In this study, we performed high-throughput sequencing of microRNAs (miRNAs) in the three tissues, xylem, phloem and leaf of Populus alba × Populus glandulosa and Larix kaempferi. Differentially expressed miRNA (DEmiRNA) analysis identified 85 xylem-specific miRNAs in P. alba × P. glandulosa and 158 xylem-specific miRNAs in L. kaempferi. Among 36 common miRNAs, 12 were conserved between the two species. GO and KEGG analyses of the miRNA target genes showed similar metabolism in two species. Through KEGG and BLASTN, we predicted target genes of xylem differentially expressed (DEmiRNA) in the wood formation-related pathways and located DEmiRNAs in these pathways. A network was built for wood formation-related DEmiRNAs, their target genes and orthologous genes in Arabidopsis thaliana. Comparison of DEmiRNA and target gene annotation between P. alba × P. glandulosa and L. kaempferi suggested the different functions of DEmiRNAs and divergent mechanism in wood formation between two species, providing knowledge to understand wood formation mechanism in gymnosperm and angiosperm woody plants.
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Affiliation(s)
- Hui Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wanfeng Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yan Lu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Zaizhi Zhou
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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Ninsuwon J, Waiyamitra P, Roongsitthichai A, Surachetpong W. Expressions of miR-155 and miR-181 and predictions of their structures and targets in pigs ( Sus scrofa). Vet World 2020; 13:1667-1673. [PMID: 33061243 PMCID: PMC7522940 DOI: 10.14202/vetworld.2020.1667-1673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/30/2020] [Indexed: 12/17/2022] Open
Abstract
Background and Aim: MicroRNAs (miRNAs) are responsible for gene expression control at the post-transcription level in many species. Several miRNAs are required in the regulation of immune responses, such as B-cell differentiation, T-cell receptor signaling pathway, CD4+ T cell selection, and so on. Studies on miRNAs have been extensively conducted in humans and mice; however, reports relevant to miRNAs, especially miR-155 and miR-181, in pigs are limited. Consequently, the present study aimed to investigate the structures, target genes, and expressions of miR-155 and miR-181 in various porcine cells and tissues. Materials and Methods: Five healthy male pigs from a porcine reproductive and respiratory syndrome virus-negative farm were studied. Before slaughter, blood samples were collected for peripheral blood mononuclear cell isolation. After slaughter, samples of spleen, lymph nodes, and forelimb muscles were collected. Both miR-155 and miR-181 were investigated for their structures with RNAfold web server, for their target genes from three online web servers, and for their expressions using polymerase chain reaction (PCR). Results: The structures of miR-155 and miR-181 contained hairpins with free energies of −35.27 and −35.29 kcal/mole, respectively. Target gene prediction revealed that miR-155 had perfect complementarity with Socs1 and Mapk3k14, while miR-181 had perfect complementarity with Ddx3x, Nfat5, Foxp1, and Mpp5. PCR showed that both miRNAs were detectable from all investigated cells and tissues. Moreover, the highest expression of both miRNAs was found from the lymph node of the pigs. Conclusion: Both miR-155 and miR-181 might be involved with the regulation of porcine immune functions as both miRNAs were detected in several cells and tissues of the pigs. In addition, they had very high complementarities with the seed regions of several immune-related genes.
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Affiliation(s)
- Jirapat Ninsuwon
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies for Agriculture and Food, Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
| | - Pitchaporn Waiyamitra
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Atthaporn Roongsitthichai
- Veterinary Clinic Research Unit, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham, Thailand.,Office of Academic Affairs, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham, Thailand
| | - Win Surachetpong
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies for Agriculture and Food, Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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Lee HE, Huh JW, Kim HS. Bioinformatics Analysis of Evolution and Human Disease Related Transposable Element-Derived microRNAs. Life (Basel) 2020; 10:life10060095. [PMID: 32630504 PMCID: PMC7345915 DOI: 10.3390/life10060095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/22/2022] Open
Abstract
Transposable element (TE) has the ability to insert into certain parts of the genome, and due to this event, it is possible for TEs to generate new factors and one of these factors are microRNAs (miRNA). miRNAs are non-coding RNAs made up of 19 to 24 nucleotides and numerous miRNAs are derived from TE. In this study, to support general knowledge on TE and miRNAs derived from TE, several bioinformatics tools and databases were used to analyze miRNAs derived from TE in two aspects: evolution and human disease. The distribution of TEs in diverse species presents that almost half of the genome is covered with TE in mammalians and less than a half in other vertebrates and invertebrates. Based on selected evolution-related miRNAs studies, a total of 51 miRNAs derived from TE were found and analyzed. For the human disease-related miRNAs, total of 34 miRNAs derived from TE were organized from the previous studies. In summary, abundant miRNAs derived from TE are found, however, the function of miRNAs derived from TE is not informed either. Therefore, this study provides theoretical understanding of miRNAs derived from TE by using various bioinformatics tools.
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Affiliation(s)
- Hee-Eun Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (H.-E.L.); (J.-W.H.)
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (H.-E.L.); (J.-W.H.)
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2259; Fax: +82-51-581-2962
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Choi SY, Han EC, Hong SH, Kwon TG, Lee Y, Lee HJ. Regulating Osteogenic Differentiation by Suppression of Exosomal MicroRNAs. Tissue Eng Part A 2020; 25:1146-1154. [PMID: 30520703 DOI: 10.1089/ten.tea.2018.0257] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
IMPACT STATEMENT We investigated the role of exosomes in osteogenesis and the use of miRNA inhibitor-transfected exosomes to control osteogenic differentiation. RNA-sequencing (RNA-seq) of exosomal miRNAs revealed that growth condition of milieu of preosteoblast exosomes harbors high levels of let-7, which plays a critical role in osteogenesis regulation. We modified exosomes by transfecting let-7 inhibitor into exosomes under growth condition in MC3T3-E1 cells and revealed that exosomes whose let-7 was inactivated by engineering lost the ability to recover osteogenic differentiation. Genetically modified exosomes may serve as powerful biomaterials for developmental control, including of osteogenesis regulation.
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Affiliation(s)
- Song-Yi Choi
- 1Department of Microbiology and Immunology, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Eun-Chong Han
- 1Department of Microbiology and Immunology, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Su-Hyung Hong
- 1Department of Microbiology and Immunology, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Tae-Geon Kwon
- 2Department of Oral and Maxillofacial Surgery, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Youngkyun Lee
- 3Department of Biochemistry, School of Dentistry, Kyungpook National University, Daegu, Korea
| | - Heon-Jin Lee
- 1Department of Microbiology and Immunology, School of Dentistry, Kyungpook National University, Daegu, Korea.,4Brain Science and Engineering Institute, Kyungpook National University, Daegu, Korea
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7
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Im J, Kim WR, Lee HE, Kim A, Kim DH, Choi YH, Cha HJ, Kim S, Kim HS. Expression analysis of LTR-derived miR-1269a and target gene, KSR2 in Sebastes schlegelii. Genes Genomics 2019; 42:55-65. [PMID: 31721105 DOI: 10.1007/s13258-019-00880-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/24/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND Sebastes schlegelii are an important species of fish found in the coastal areas of the Korea with significant commercial importance. Most studies thus far have been primarily focused on environmental factors; behavioural patterns, aquaculture, diseases and limited genetic studies with little to none related to either microRNAs (miRNAs) or transposable elements (TE). OBJECTIVES In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii. Also, we performed luciferase reporter assay in HINAE cells. METHODS UCSC Genome Browser (https://genome.ucsc.edu/) was used to examine which TE is associated with miR-1269a. For the target genes for miR-1269a, the target genes associated with the miRNA were identified using miRDB (http://www.mirdb.org/) and TargetScan 7.1 (http://www.targetscan.org/vert_71/). A two-step miRNA kit, HB miR Multi Assay Kit™ System. I was used for the analysis of TE-derived miRNA expression patterns. The 3'UTR of KSR2 gene was cloned into the psiCHECK-2 vector. Subsequently co-transfected with miR-1269a mimics to HINAE cells for luciferase reporter assay. RESULTS MiR-1269a was found to be derived from LTR retrotransposon, MLT2B. LTR-derived miR-1269a was highly expressed in the muscle, liver and gonad tissues of Sebastes schlegelii, but KSR2 revealed high expression in the brain. Co-transfection of KSR2 and miR-1269a mimic to HINAE cells showed high activity of miR-1269a in relation to KSR2. CONCLUSION LTR-derived miR-1269a showed enhancer activity with relation to KSR2 in Sebastes schlegelii. The data may be used as a foundation for further investigation regarding correlation of miRNA and target genes in addition to other functional studies of biological significance in Sebastes schlegelii.
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Affiliation(s)
- Jennifer Im
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Woo Ryung Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Ahran Kim
- Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea
| | - Yung Hyun Choi
- Department of Biochemistry, College of Korean Medicine, Dong-eui University, Busan, 47340, Republic of Korea
| | - Hee-Jae Cha
- Department of Parasitology and Genetics, College of Medicine, Kosin University, Busan, 49267, Republic of Korea
| | - Suhkmann Kim
- Department of Chemistry, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea. .,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea.
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8
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Kim SW, Jo A, Im J, Lee HE, Kim HS. Expression analysis of miR-221-3p and its target genes in horses. Genes Genomics 2019; 41:459-465. [PMID: 30604147 DOI: 10.1007/s13258-018-00778-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/17/2018] [Indexed: 11/25/2022]
Abstract
BACKGROUND A microRNA (miRNA) is a small non-coding RNA (ncRNA) approximately 20 nucleotides long and it affects gene expression through mRNA cleavage or translational repression. Horses (Equus caballus) have been domesticated and bred to enhance their speed for racing. It has been studied extensively with genetic diversity, origins and evolution. OBJECTIVES We examined expression patterns of miR-221-3p and its target gene CDKN1C in various horse tissues. METHODS We used bioinformatic tools to examine target gene, seed region and evolutionary conservation of miR-221-3p. The expression patterns of miR-221-3p and its target gene CDKN1C were analyzed by quantitative polymerase chain reaction (qPCR). RESULTS Among eight tissues of horse, miR-221-3p was highly expressed in cerebellum and spleen. On the other hand, only medulla was highly expressed in CDKN1C gene. CONCLUSION Our study provides expression data of miR-221-3p and CDKN1C gene in horse and suggests the fundamental information for future studies in relation to functional importance.
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Affiliation(s)
- So-Won Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Ara Jo
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Jennifer Im
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea. .,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea.
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9
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Jo A, Lee HE, Kim HS. Identification and expression analysis of a novel miRNA derived from ERV-E1 LTR in Equus caballus. Gene 2018; 687:238-245. [PMID: 30453070 DOI: 10.1016/j.gene.2018.11.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022]
Abstract
Horses (Equus caballus) have been domesticated and bred to enhance speed, strength, and agility. Members of the Equus caballus Endogenous Retrovirus (EqERV) family affect several of these abilities in horses. EqERV elements have been integrated in the horse genome during evolution and generate repeat elements such as long terminal repeats (LTRs). LTR sequences are involved in retrovirus replication and play an essential function in post-transcriptional control mechanisms, such as by providing binding sites for microRNAs (miRNAs) or generating miRNA precursors. In this study, we identified a novel miRNA derived from EqERV-E1 LTR using various bioinformatics tools. To examine the relationship between EqERV-E1 LTR and similar elements, we used BLAST2seq and phylogenetic analysis. LTR sequences were located in the untranslated region (UTR) of mRNAs and also formed the stem-loop secondary structure. The sequence was registered in the DDBJ database as LTR derived miRNA under the accession number corresponding to LC383797 (referred to eca-miR-1804). Quantitative polymerase chain reaction (qPCR) to confirm the expression of eca-miR-1804 and the similar miR-1255a, showed an almost identical expression pattern in eight different equine tissues. Therefore, these data imply that the LTR could function as an miRNA, which is expressed in the examined equine tissues. In addition, the current study provides inputs for additional functional studies concerning the LTR of other EqERV families.
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Affiliation(s)
- Ara Jo
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea.
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10
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Gotesman M, Menanteau-Ledouble S, Saleh M, Bergmann SM, El-Matbouli M. A new age in AquaMedicine: unconventional approach in studying aquatic diseases. BMC Vet Res 2018; 14:178. [PMID: 29879957 PMCID: PMC5992843 DOI: 10.1186/s12917-018-1501-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/24/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Marine and aquaculture industries are important sectors of the food production and global trade. Unfortunately, the fish food industry is challenged with a plethora of infectious pathogens. The freshwater and marine fish communities are rapidly incorporating novel and most up to date techniques for detection, characterization and treatment strategies. Rapid detection of infectious diseases is important in preventing large disease outbreaks. MAIN TEXT One hundred forty-six articles including reviews papers were analyzed and their conclusions evaluated in the present paper. This allowed us to describe the most recent development research regarding the control of diseases in the aquatic environment as well as promising avenues that may result in beneficial developments. For the characterization of diseases, traditional sequencing and histological based methods have been augmented with transcriptional and proteomic studies. Recent studies have demonstrated that transcriptional based approaches using qPCR are often synergistic to expression based studies that rely on proteomic-based techniques to better understand pathogen-host interactions. Preventative therapies that rely on prophylactics such as vaccination with protein antigens or attenuated viruses are not always feasible and therefore, the development of therapies based on small nucleotide based medicine is on the horizon. Of those, RNAi or CRISPR/Cas- based therapies show great promise in combating various types of diseases caused by viral and parasitic agents that effect aquatic and fish medicine. CONCLUSIONS In our modern times, when the marine industry has become so vital for feed and economic stability, even the most extreme alternative treatment strategies such as the use of small molecules or even the use of disease to control invasive species populations should be considered.
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Affiliation(s)
- Michael Gotesman
- Department of Biology, New York City College of Technology of the City University of New York, Brooklyn, New York, USA
| | - Simon Menanteau-Ledouble
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Mona Saleh
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Sven M Bergmann
- Institute of Infectology, Friedrich-Loffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
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11
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Jo A, Lee HE, Kim HS. Genomic Analysis of miR-21-3p and Expression Pattern with Target Gene in Olive Flounder. Genomics Inform 2017; 15:98-107. [PMID: 29020725 PMCID: PMC5637345 DOI: 10.5808/gi.2017.15.3.98] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/08/2017] [Accepted: 08/15/2017] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) act as regulators of gene expression by binding to the 3’ untranslated region (UTR) of target genes. They perform important biological functions in the various species. Among many miRNAs, miR-21-3p is known to serve vital functions in development and apoptosis in olive flounder. Using genomic and bioinformatic tools, evolutionary conservation of miR-21-3p was examined in various species, and expression pattern was analyzed in olive flounder. Conserved sequences (5’-CAGUCG-3’) in numerous species were detected through the stem-loop structure of miR-21-3p. Thus, we analyzed target genes of miR-21-3p. Among them, 3’ UTR region of PPIL2 gene indicated the highest binding affinity with miR-21-3p based on the minimum free energy value. The PPIL2 gene showed high expression levels in testis tissue of the olive flounder, whereas miR-21-3p showed rather ubiquitous expression patterns except in testis tissue, indicating that miR-21-3p seems to control the PPIL2 gene expression in a complementary repression manner in various tissues of olive flounder. Taken together, this current study contributes to infer the target gene candidates for the miR-21-3p using bioinformatics tools. Furthermore, our data offers important information on the relationship between miR-21-3p and target gene for further functional study.
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Affiliation(s)
- Ara Jo
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea.,Genetic Engineering Institute, Pusan National University, Busan 46241, Korea
| | - Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea.,Genetic Engineering Institute, Pusan National University, Busan 46241, Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea.,Genetic Engineering Institute, Pusan National University, Busan 46241, Korea
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