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Zhang Q, Lu B. The mRNA and microRNA Landscape of the Blastema Niche in Regenerating Newt Limbs. Int J Mol Sci 2024; 25:9225. [PMID: 39273174 PMCID: PMC11395517 DOI: 10.3390/ijms25179225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/18/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
Newts are excellent vertebrate models for investigating tissue regeneration due to their remarkable regenerative capabilities. To investigate the mRNA and microRNAs (miRNAs) profiles within the blastema niche of regenerating newt limbs, we amputated the limbs of Chinese fire belly newts (Cynops orientalis) and conducted comprehensive analyses of the transcriptome and microRNA profiles at five distinct time points post-amputation (0 hours, 1 day, 5 days 10 days and 20 days). We identified 24 significantly differentially expressed (DE) genes and 20 significantly DE miRNAs. Utilizing weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) enrichment analysis, we identified four genes likely to playing crucial roles in the early stages of limb regeneration: Cemip, Rhou, Gpd2 and Pcna. Moreover, mRNA-miRNA integration analysis uncovered seven human miRNAs (miR-19b-1, miR-19b-2, miR-21-5p, miR-127-5p, miR-150-5p, miR-194-5p, and miR-210-5p) may regulate the expression of these four key genes. The temporal expression patterns of these key genes and miRNAs further validated the robustness of the identified mRNA-miRNA landscape. Our study successfully identified candidate key genes and elucidated a portion of the genetic regulatory mechanisms involved in newt limb regeneration. These findings offer valuable insights for further exploration of the intricate processes of tissue regeneration.
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Affiliation(s)
- Qi Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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2
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ÇAKAR B, TOMRUK C, ÇELİK S, UYANIKGİL Y. Rejeneratif tıpta model organizma; Aksolotl (Ambystoma Mexicanum). EGE TIP DERGISI 2022. [DOI: 10.19161/etd.1086385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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3
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Li R, Xiao Y, Li K, Tian L. Transcription and Post-translational Regulation of Autophagy in Insects. Front Physiol 2022; 13:825202. [PMID: 35283796 PMCID: PMC8916536 DOI: 10.3389/fphys.2022.825202] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/19/2022] [Indexed: 01/18/2023] Open
Abstract
Autophagy attracts great attention, and numerous progresses have been obtained in the last two decades. Autophagy is implicated in mammalian neurodegenerative diseases, tumorigenesis, as well as development in insects. The regulatory mechanism of autophagy is well documented in yeast and mammals, whereas it is not fully illustrated in insects. Drosophila melanogaster and Bombyx mori are the two well-studied insects for autophagy, and several insect-mammalian evolutionarily conserved or insect-specific mechanisms in regulating autophagy are reported. In this review, we summarize the most recent studies of autophagy regulated at both transcriptional and post-translational levels by insect hormone in cooperation with other signals, such as nutrient, which will provide a reference and deep thinking for studies on autophagy in insects.
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Affiliation(s)
- Rongsong Li
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Sericulture and Mulberry Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yang Xiao
- Department of Sericulture and Southern Medicine Resources Utilization, The Sericultural and Agri-Food Research Institute of the Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Kang Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ling Tian
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Sericulture and Mulberry Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
- *Correspondence: Ling Tian,
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Ribeiro AO, de Oliveira AC, Costa JM, Nachtigall PG, Herkenhoff ME, Campos VF, Delella FK, Pinhal D. MicroRNA roles in regeneration: Multiple lessons from zebrafish. Dev Dyn 2021; 251:556-576. [PMID: 34547148 DOI: 10.1002/dvdy.421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/23/2021] [Accepted: 09/07/2021] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs with pivotal roles in the control of gene expression. By comparing the miRNA profiles of uninjured vs. regenerating tissues and structures, several studies have found that miRNAs are potentially involved in the regenerative process. By inducing miRNA overexpression or inhibition, elegant experiments have directed regenerative responses validating relevant miRNA-to-target interactions. The zebrafish (Danio rerio) has been the epicenter of regenerative research because of its exceptional capability to self-repair damaged tissues and body structures. In this review, we discuss recent discoveries that have improved our understanding of the impact of gene regulation mediated by miRNAs in the context of the regeneration of fins, heart, retina, and nervous tissue in zebrafish. We compiled what is known about the miRNA control of regeneration in these tissues and investigated the links among up-regulated and down-regulated miRNAs, their putative or validated targets, and the regenerative process. Finally, we briefly discuss the forthcoming prospects, highlighting directions and the potential for further development of this field.
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Affiliation(s)
- Amanda Oliveira Ribeiro
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
| | - Arthur Casulli de Oliveira
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
| | - Juliana Mara Costa
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
| | - Pedro Gabriel Nachtigall
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil.,Laboratório Especial de Toxicologia Aplicada (LETA), CeTICS, Instituto Butantan, São Paulo, SP, Brazil
| | - Marcos Edgar Herkenhoff
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil.,Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Vinicius Farias Campos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Flávia Karina Delella
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
| | - Danillo Pinhal
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
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Abdo SE, Gewaily MS, Abo-Al-Ela HG, Almeer R, Soliman AA, Elkomy AH, Dawood MAO. Vitamin C rescues inflammation, immunosuppression, and histopathological alterations induced by chlorpyrifos in Nile tilapia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:28750-28763. [PMID: 33548043 DOI: 10.1007/s11356-021-12711-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Chlorpyrifos (CPF) is an extensive environmental contaminant and disrupts the physiological status of living organisms. CPF is found to hinder the health of aquatic organisms and ecological function in aquatic systems. The current study aimed at evaluating the protective effects of vitamin C (VC) on the immune response, hematological parameters, and histopathological alterations in Nile tilapia exposed to CPF. Nile tilapia were exposed to waterborne CPF (15 μg/L) for 30 days. Fish were divided into control group: received basal diet; CPF group: received basal diet and exposed to waterborne CPF; VC group: received basal diet plus 0.8 mg VC/kg; and CPF/VC group: received basal diet plus 0.8 mg VC/kg and exposed to waterborne CPF. Blood samples were taken after 15 days and 30 days of the treatment. Liver, gills, and intestine tissues were collected on the 30th day of treatment. CPF showed a deleterious effect on fish's growth performance; it decreased the weight gain by 6%, while VC increased it by 17-23% compared to the control group. CPF group recorded the lowest survival rate (83%), while VC achieved survivability of 96.7% and 93.3% in VC and CPF/VC groups, respectively. The blood picture revealed moderate changes in the CPF group, where the marked alteration was in the hemoglobin concentration and white blood cells. CPF disrupted the hepatic and renal function. Serum lysozyme activity, phagocytic activity, and phagocytic index displayed a dramatic decline in the CPF group but enhanced in VC and CPF/VC groups. An upregulation was observed in antioxidant genes (catalase and glutathione peroxidase), heat shock protein 70, caspase-3, and the cytokines interleukin 1β, interleukin 8, and interferon-gamma in the CPF group. Simultaneously, moderate or normal levels were shown in the VC and CPF/VC groups. CPF altered the histoarchitecture of gills, intestine, and hepatopancreas with apparent degenerative changes possibly resulted from the oxidative stress. At the same time, VC retained the normal structure of the studied tissues. This study raises concerns about the safety of CPF and its impact on the aquatic environment. VC has a high potential to restore the normal physiology of fish exposed to CPF.
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Affiliation(s)
- Safaa E Abdo
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Mahmoud S Gewaily
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Haitham G Abo-Al-Ela
- Genetics and Biotechnology, Department of Aquaculture, Faculty of Fish Resources, Suez University, Suez, Egypt
| | - Rafa Almeer
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Ali A Soliman
- Fish Nutrition Laboratory, Aquaculture Division, National Institute of Oceanography and Fisheries, Alexandria, Egypt
| | - Azza H Elkomy
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Mahmoud A O Dawood
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt.
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Abo-Al-Ela HG, El-Kassas S, El-Naggar K, Abdo SE, Jahejo AR, Al Wakeel RA. Stress and immunity in poultry: light management and nanotechnology as effective immune enhancers to fight stress. Cell Stress Chaperones 2021; 26:457-472. [PMID: 33847921 PMCID: PMC8065079 DOI: 10.1007/s12192-021-01204-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Accepted: 04/04/2021] [Indexed: 02/07/2023] Open
Abstract
The poultry industry plays a significant role in boosting the economy of several countries, particularly developing countries, and acts as a good, cheap, and affordable source of animal protein. A stress-free environment is the main target in poultry production. There are several stressors, such as cold stress, heat stress, high stocking density, and diseases that can affect birds and cause several deleterious changes. Stress reduces feed intake and growth, as well as impairs immune response and function, resulting in high disease susceptibility. These effects are correlated with higher corticosteroid levels that modulate several immune pathways such as cytokine-cytokine receptor interaction and Toll-like receptor signaling along with induction of excessive production of reactive oxygen species (ROS) and thus oxidative stress. Several approaches have been considered to boost bird immunity to overcome stress-associated effects. Of these, dietary supplementation of certain nutrients and management modifications, such as light management, are commonly considered. Dietary supplementations improve bird immunity by improving the development of lymphoid tissues and triggering beneficial immune modulators and responses. Since nano-minerals have higher bioavailability compared to inorganic or organic forms, they are highly recommended to be included in the bird's diet during stress. Additionally, light management is considered a cheap and safe approach to control stress. Changing light from continuous to intermittent and using monochromatic light instead of the normal light improve bird performance and health. Such changes in light management are associated with a reduction of ROS production and increased antioxidant production. In this review, we discuss the impact of stress on the immune system of birds and the transcriptome of oxidative stress and immune-related genes, in addition, how nano-minerals supplementations and light system modulate or mitigate stress-associated effects.
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Affiliation(s)
- Haitham G Abo-Al-Ela
- Genetics and Biotechnology, Department of Aquaculture, Faculty of Fish Resources, Suez University, Suez, 43518, Egypt.
| | - Seham El-Kassas
- Animal, Poultry and Fish Breeding and Production, Department of Animal Wealth Development, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt.
| | - Karima El-Naggar
- Department of Nutrition and Veterinary Clinical Nutrition, Faculty of Veterinary Medicine, Alexandria University, Edfina, 22758, Egypt
| | - Safaa E Abdo
- Genetics and Genetic Engineering, Department of Animal Wealth Development, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ali Raza Jahejo
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Rasha A Al Wakeel
- Department of Physiology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
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Abo-Al-Ela HG. The emerging regulatory roles of noncoding RNAs in immune function of fish: MicroRNAs versus long noncoding RNAs. Mol Genet Genomics 2021; 296:765-781. [PMID: 33904988 DOI: 10.1007/s00438-021-01786-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/12/2021] [Indexed: 02/06/2023]
Abstract
The genome could be considered as raw data expressed in proteins and various types of noncoding RNAs (ncRNAs). However, a large portion of the genome is dedicated to ncRNAs, which in turn represent a considerable amount of the transcriptome. ncRNAs are modulated on levels of type and amount whenever any physiological process occurs or as a response to external modulators. ncRNAs, typically forming complexes with other partners, are key molecules that influence diverse cellular processes. Based on the knowledge of mammalian biology, ncRNAs are known to regulate and control diverse trafficking pathways and cellular activities. Long noncoding RNAs (lncRNAs) notably have diverse and more regulatory roles than microRNAs. Expanding these studies on fish has derived the same conclusion with relevance to other species, including invertebrates, explored the potentials to harness such types of RNA to further understand the biology of such organisms, and opened gates for applying recent technologies, such as RNA interference and delivering micromolecules as microRNAs to living cells and possibly to target organs. These technologies should improve aquaculture productivity and fish health, as well as help understand fish biology.
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Affiliation(s)
- Haitham G Abo-Al-Ela
- Genetics and Biotechnology, Department of Aquaculture, Faculty of Fish Resources, Suez University, 43518, Suez, Egypt.
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Abo-Al-Ela HG. RNA Interference in Aquaculture: A Small Tool for Big Potential. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4343-4355. [PMID: 33835783 DOI: 10.1021/acs.jafc.1c00268] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
For decades, the tight regulatory functions of DNA and RNA have been the focus of extensive research with the goal of harnessing RNA molecules (e.g., microRNA and small interfering RNA) to control gene expression and to study biological functions. RNA interference (RNAi) has shown evidence of mediating gene expression, has been utilized to study functional genomics, and recently has potential in therapeutic agents. RNAi is a natural mechanism and a well-studied tool that can be used to silence specific genes. This method is also used in aquaculture as a research tool and to enhance immune responses. RNAi methods do have their limitations (e.g., immune triggering); efficient and easy-to-use RNAi methods for large-scale applications need further development. Despite these limitations, RNAi methods have been successfully used in aquaculture, in particular shrimp. This review discusses the uses of RNAi in aquaculture, such as immune- and production-related issues and the possible limitations that may hinder the application of RNAi in the aquaculture industry. Our challenge is to develop a highly potent in vivo RNAi delivery platform that could complete the desired action with minimal side effects and which can be applied on a large-scale with relatively little expense in the aquaculture industry.
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Affiliation(s)
- Haitham G Abo-Al-Ela
- Genetics and Biotechnology, Department of Aquaculture, Faculty of Fish Resources, Suez University, Suez 43518, Egypt
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