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Rios DL, da Silva PCL, Moura CSS, Villanoeva CNBC, da Rocha Fernandes G, Bengoa AA, Garrote GL, Abraham AG, Nicoli JR, Neumann E, Nunes ÁC. Comparative metatranscriptome analysis of Brazilian milk and water kefir beverages. Int Microbiol 2024; 27:807-818. [PMID: 37759067 DOI: 10.1007/s10123-023-00431-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/06/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023]
Abstract
The present study compared bacterial and fungal diversity of kefir beverages produced using milk (MK) or sugared water (WK) as propagation matrices and grains from the cities of Curitiba (CU) or Salvador (SA), Brazil, by sequencing the complete set of RNA transcripts produced in four products. In Brazil, milk and sugared water are used as matrices to propagate kefir grains. In all beverages, the bacterial community was composed of Lactobacillaceae and Acetobacteraceae. Saccharomycetaceae was the yeast family more abundant in WK, and Dipodascaceae and Pichiaceae in MK. Regarding KEGG mapping of functional orthologs, the four kefir samples shared 70% of KO entries of yeast genes but only 36% of bacterial genes. Concerning main metabolic processes, the relative abundance of transcripts associated with metabolism (energy metabolism) and environmental information processing (membrane transport) had the highest water/milk kefir ratio observed in Firmicutes. In contrast, transcripts associated with genetic information processing (protein translation, folding, sorting, and degradation) oppositely had the lowest water/milk ratios. Concluding, milk and water kefir have quite different communities of microorganisms. Still, the main mapped functional processes are similar, with only quantitative variation in membrane transport and energy acquisition in the water kefir and protein synthesis and turnover in the milk kefir.
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Affiliation(s)
- Diego Lisboa Rios
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Campus Pampulha, Belo Horizonte, MG, 31270-901, Brazil
- EBTT - Informática, Instituto Federal do Amazonas (IFAM), São Gabriel da Cachoeira, Brazil
| | - Patrícia Costa Lima da Silva
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Campus Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - César Silva Santana Moura
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Campus Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | | | | | - Ana Agustina Bengoa
- Centro de Investigación y Desarrollo em Criotecnologia de Alimentos (CIDCA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Graciela Liliana Garrote
- Centro de Investigación y Desarrollo em Criotecnologia de Alimentos (CIDCA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Analía Graciela Abraham
- Centro de Investigación y Desarrollo em Criotecnologia de Alimentos (CIDCA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Jacques Robert Nicoli
- Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Elisabeth Neumann
- Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Álvaro Cantini Nunes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Campus Pampulha, Belo Horizonte, MG, 31270-901, Brazil.
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Sinha S, Elbaz‐Alon Y, Avinoam O. Ca 2+ as a coordinator of skeletal muscle differentiation, fusion and contraction. FEBS J 2022; 289:6531-6542. [PMID: 35689496 PMCID: PMC9795905 DOI: 10.1111/febs.16552] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/05/2022] [Accepted: 06/09/2022] [Indexed: 12/30/2022]
Abstract
Muscle regeneration is essential for vertebrate muscle homeostasis and recovery after injury. During regeneration, muscle stem cells differentiate into myocytes, which then fuse with pre-existing muscle fibres. Hence, differentiation, fusion and contraction must be tightly regulated during regeneration to avoid the disastrous consequences of premature fusion of myocytes to actively contracting fibres. Cytosolic calcium (Ca2+ ), which is coupled to both induction of myogenic differentiation and contraction, has more recently been implicated in the regulation of myocyte-to-myotube fusion. In this viewpoint, we propose that Ca2+ -mediated coordination of differentiation, fusion and contraction is a feature selected in the amniotes to facilitate muscle regeneration.
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Affiliation(s)
- Sansrity Sinha
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Yael Elbaz‐Alon
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Ori Avinoam
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
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Ji K, Jiao D, Yang G, Degen AA, Zhou J, Liu H, Wang W, Cong H. Transcriptome analysis revealed potential genes involved in thermogenesis in muscle tissue in cold-exposed lambs. Front Genet 2022; 13:1017458. [PMID: 36338953 PMCID: PMC9634817 DOI: 10.3389/fgene.2022.1017458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/05/2022] [Indexed: 11/28/2022] Open
Abstract
Cold tolerance is an important trait for sheep raised at high altitudes. Muscle tissue, comprising 30–40% of the total body mass, produces heat during cold exposure. However, little is known about the genetic mechanisms of this tissue and its role in thermogenesis in lambs. We examined genes in skeletal muscle tissue in a cold-adapted sheep breed, Altay, and a cold-intolerant sheep breed, Hu, when exposed to low air temperature. Three ewe-lambs of each breed were maintained at −5°C and three ewe-lambs of each breed were maintained at 20°C. After cold exposure for 25 days, the longissimus dorsi of each lamb was collected, and transcriptome profiles were sequenced and analyzed. The results of RNA-seq showed that the average reads among the four groups were 11.0 Gbase. The genome mapping rate averaged 88.1% and the gene mapping rate averaged 82.5%. The analysis of differentially expressed genes (DEGs) indicated that the peroxisome proliferator-activated receptors (PPAR), cAMP, and calcium signaling pathways and muscle contraction in muscle tissue were linked to thermogenesis in cold-exposed lambs. Furthermore, PCK1 (phosphoenolpyruvate carboxykinase1) increased glyceroneogenesis in cold-exposed Altay lambs, and APOC3 (apolipoprotein C3), LPL (lipoprotein lipase), and FABP4 (fatty acid binding protein 4, adipocyte) were involved in the intake and transport of free fatty acids. In Hu sheep, cAMP biosynthesis from ATP hydrolysis was regulated by ADCY10 (adenylate cyclase) and ADORA2a (adenosine A2a receptor). Skeletal muscle contraction was regulated by MYL2 (myosin light chain 2). In conclusion, cold exposure altered the expression level of genes involved in heat production in muscle tissue. Some potential mechanisms were revealed, including calcium ion transport in the calcium signaling pathway, fatty acid metabolism in the PPAR signaling pathway, and cAMP biosynthesis in the cAMP signaling pathway. This study implied that skeletal muscle plays an important role in thermoregulation in lambs.
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Affiliation(s)
- Kaixi Ji
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dan Jiao
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guo Yang
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- *Correspondence: Guo Yang,
| | - Abraham Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of Negev, Beer Sheva, Israel
| | - Jianwei Zhou
- State Key Laboratory of Grassland and Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Hu Liu
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Wenqiang Wang
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Haitao Cong
- Dongying Modern Animal Husbandry Development Service Center, Dongying, China
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Feng Z, Gong H, Fu J, Xu X, Song Y, Yan X, Mabrouk I, Zhou Y, Wang Y, Fu X, Sui Y, Liu T, Li C, Liu Z, Tian X, Sun L, Guo K, Sun Y, Hu J. In Ovo Injection of CHIR-99021 Promotes Feather Follicle Development via Modulating the Wnt Signaling Pathway and Transcriptome in Goose Embryos ( Anser cygnoides). Front Physiol 2022; 13:858274. [PMID: 35669574 PMCID: PMC9164139 DOI: 10.3389/fphys.2022.858274] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Feather performs important physiological functions in birds, and it is also one of the economic productions in goose farming. Understanding and modulating feather follicle development during embryogenesis are essential for bird biology and the poultry industry. CHIR-99021 is a potent Wnt/β-catenin signaling pathway activator associated with feather follicle development. In this study, goose embryos (Anser cygnoides) received an in ovo injection of CHIR-9902, which was conducted at the beginning of feather follicle development (E9). The results showed that feather growth and feather follicle development were promoted. The Wnt signaling pathway was activated by the inhibition of GSK-3β. Transcriptomic analyses showed that the transcription changes were related to translation, metabolism, energy transport, and stress in dorsal tissue of embryos that received CHIR-99021, which might be to adapt and coordinate the promoting effects of CHIR-99021 on feather follicle development. This study suggests that in ovo injection of CHIR-99021 is a potential strategy to improve feather follicle development and feather-related traits for goose farming and provides profiling of the Wnt signaling pathway and transcriptome in dorsal tissue of goose embryos for further understanding of feather follicle development.
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Affiliation(s)
- Ziqiang Feng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Haizhou Gong
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Jinhong Fu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xiaohui Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yupu Song
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xiaomin Yan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Ichraf Mabrouk
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yuxuan Zhou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yudong Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xianou Fu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yujian Sui
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Tuoya Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Chuanghang Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Zebei Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xu Tian
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Le Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Keying Guo
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yongfeng Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China,Key Laboratory of Animal Production, Product Quality and Security (Jilin Agricultural University), Ministry of Education, Changchun, China,*Correspondence: Yongfeng Sun, ; Jingtao Hu,
| | - Jingtao Hu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China,*Correspondence: Yongfeng Sun, ; Jingtao Hu,
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Subotić S, Višnjić-Jeftić Ž, Bojović S, Đikanović V, Krpo-Ćetković J, Lenhardt M. Seasonal variations of macro-, micro-, and toxic elements in tissues of vimba bream (Vimba vimba) from the Danube River near Belgrade, Serbia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:63087-63101. [PMID: 34216343 DOI: 10.1007/s11356-021-15073-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Vimba bream (Vimba vimba) individuals were collected from the Danube River near Belgrade, from May 2016 to May 2017. Samples of muscle and liver tissue were analyzed for concentrations of 25 elements (macro-, micro-, and toxic elements) using inductively coupled plasma optical emission spectrometry (ICP-OES). For both tissues, the highest concentrations of most elements were observed in late spring/early summer (months of May and June). Majority of statistically significant correlations between elements were positive in both tissues. Contributions of Ca, K, and Mg to human diet were in a similar range. The lowest contribution of all macroelements was observed for Na, while the contribution of Se was well above the recommended dietary allowance for this element. Levels of detected elements were well below MAC values prescribed by national and international regulations. The highest value of Hg liver/muscle index (>1) was observed in August, which could indicate a higher contamination of the sampling location in that month. Se:Hg molar ratio never drops below 1, which could indicate that Hg toxicity is prevented. THQ values showed little variation thought the year and were well below the threshold of 1, with the exception of THQ for Al in May (0.92). This element also strongly affects the hazard index.
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Affiliation(s)
- Srđan Subotić
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia.
| | - Željka Višnjić-Jeftić
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, Belgrade, 11000, Serbia
| | - Srđan Bojović
- Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, Belgrade, 11000, Serbia
| | - Vesna Đikanović
- Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, Belgrade, 11000, Serbia
| | - Jasmina Krpo-Ćetković
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
| | - Mirjana Lenhardt
- Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Despota Stefana 142, Belgrade, 11000, Serbia
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Yang T, Huang X, Ning Z, Gao T. Genome-Wide Survey Reveals the Microsatellite Characteristics and Phylogenetic Relationships of Harpadon nehereus. Curr Issues Mol Biol 2021; 43:1282-1292. [PMID: 34698106 PMCID: PMC8928995 DOI: 10.3390/cimb43030091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Harpadon nehereus forms one of the most important commercial fisheries along the Bay of Bengal and the southeast coast of China. In this study, the genome-wide survey dataset first produced using next-generation sequencing (NGS) was used to provide general information on the genome size, heterozygosity and repeat sequence ratio of H. nehereus. About 68.74 GB of high-quality sequence data were obtained in total and the genome size was estimated to be 1315 Mb with the 17-mer frequency distribution. The sequence repeat ratio and heterozygosity were calculated to be 52.49% and 0.67%, respectively. A total of 1,027,651 microsatellite motifs were identified and dinucleotide repeat was the most dominant simple sequence repeat (SSR) motif with a frequency of 54.35%. As a by-product of whole genome sequencing, the mitochondrial genome is a powerful tool to investigate the evolutionary relationships between H. nehereus and its relatives. The maximum likelihood (ML) phylogenetic tree was constructed according to the concatenated matrix of amino acids translated from the 13 protein-coding genes (PCGs). Monophyly of two species of the genus Harpadon was revealed in the present study and they formed a monophyletic clade with Saurida with a high bootstrap value of 100%. The results would help to push back the frontiers of genomics and open the doors of molecular diversity as well as conservation genetics studies on this species.
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Ducret V, Richards AJ, Videlier M, Scalvenzi T, Moore KA, Paszkiewicz K, Bonneaud C, Pollet N, Herrel A. Transcriptomic analysis of the trade-off between endurance and burst-performance in the frog Xenopus allofraseri. BMC Genomics 2021; 22:204. [PMID: 33757428 PMCID: PMC7986297 DOI: 10.1186/s12864-021-07517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Variation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and performance trade-offs remains poorly understood. In this study we identify the genes, signaling pathways, and regulatory processes possibly responsible for the trade-off between burst performance and endurance observed in Xenopus allofraseri, using a transcriptomic approach. RESULTS We obtained a total of about 121 million paired-end reads from Illumina RNA sequencing and analyzed 218,541 transcripts obtained from a de novo assembly. We identified 109 transcripts with a significant differential expression between endurant and burst performant individuals (FDR ≤ 0.05 and logFC ≥2), and blast searches resulted in 103 protein-coding genes. We found major differences between endurant and burst-performant individuals in the expression of genes involved in the polymerization and ATPase activity of actin filaments, cellular trafficking, proteoglycans and extracellular proteins secreted, lipid metabolism, mitochondrial activity and regulators of signaling cascades. Remarkably, we revealed transcript isoforms of key genes with functions in metabolism, apoptosis, nuclear export and as a transcriptional corepressor, expressed in either burst-performant or endurant individuals. Lastly, we find two up-regulated transcripts in burst-performant individuals that correspond to the expression of myosin-binding protein C fast-type (mybpc2). This suggests the presence of mybpc2 homoeologs and may have been favored by selection to permit fast and powerful locomotion. CONCLUSION These results suggest that the differential expression of genes belonging to the pathways of calcium signaling, endoplasmic reticulum stress responses and striated muscle contraction, in addition to the use of alternative splicing and effectors of cellular activity underlie locomotor performance trade-offs. Ultimately, our transcriptomic analysis offers new perspectives for future analyses of the role of single nucleotide variants, homoeology and alternative splicing in the evolution of locomotor performance trade-offs.
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Affiliation(s)
- Valérie Ducret
- UMR 7179 MECADEV, C.N.R.S/M.N.H.N., Département Adaptations du Vivant, 55 Rue Buffon, 75005, Paris, France.
| | - Adam J Richards
- Station d'Ecologie Expérimentale du CNRS, USR 2936, 09200, Moulis, France
| | - Mathieu Videlier
- Functional Ecology Lab, Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada
| | - Thibault Scalvenzi
- Evolution, Génomes, Comportement & Ecologie, Université Paris-Saclay, CNRS, IRD, 91198, Gif-sur-Yvette, France
| | - Karen A Moore
- Exeter Sequencing Service, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Konrad Paszkiewicz
- Exeter Sequencing Service, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Camille Bonneaud
- Station d'Ecologie Expérimentale du CNRS, USR 2936, 09200, Moulis, France
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, UK
| | - Nicolas Pollet
- Evolution, Génomes, Comportement & Ecologie, Université Paris-Saclay, CNRS, IRD, 91198, Gif-sur-Yvette, France
| | - Anthony Herrel
- Station d'Ecologie Expérimentale du CNRS, USR 2936, 09200, Moulis, France
- Evolutionary Morphology of Vertebrates, Ghent University, B-9000, Ghent, Belgium
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Ciezarek A, Gardner L, Savolainen V, Block B. Skeletal muscle and cardiac transcriptomics of a regionally endothermic fish, the Pacific bluefin tuna, Thunnus orientalis. BMC Genomics 2020; 21:642. [PMID: 32942994 PMCID: PMC7499911 DOI: 10.1186/s12864-020-07058-z] [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: 09/26/2019] [Accepted: 09/08/2020] [Indexed: 11/29/2022] Open
Abstract
Background The Pacific bluefin tuna (Thunnus orientalis) is a regionally endothermic fish that maintains temperatures in their swimming musculature, eyes, brain and viscera above that of the ambient water. Within their skeletal muscle, a thermal gradient exists, with deep muscles, close to the backbone, operating at elevated temperatures compared to superficial muscles near the skin. Their heart, by contrast, operates at ambient temperature, which in bluefin tunas can range widely. Cardiac function in tunas reduces in cold waters, yet the heart must continue to supply blood for metabolically demanding endothermic tissues. Physiological studies indicate Pacific bluefin tuna have an elevated cardiac capacity and increased cold-tolerance compared to warm-water tuna species, primarily enabled by increased capacity for sarcoplasmic reticulum calcium cycling within the cardiac muscles. Results Here, we compare tissue-specific gene-expression profiles of different cardiac and skeletal muscle tissues in Pacific bluefin tuna. There was little difference in the overall expression of calcium-cycling and cardiac contraction pathways between atrium and ventricle. However, expression of a key sarcoplasmic reticulum calcium-cycling gene, SERCA2b, which plays a key role maintaining intracellular calcium stores, was higher in atrium than ventricle. Expression of genes involved in aerobic metabolism and cardiac contraction were higher in the ventricle than atrium. The two morphologically distinct tissues that derive the ventricle, spongy and compact myocardium, had near-identical levels of gene expression. More genes had higher expression in the cool, superficial muscle than in the warm, deep muscle in both the aerobic red muscle (slow-twitch) and anaerobic white muscle (fast-twitch), suggesting thermal compensation. Conclusions We find evidence of widespread transcriptomic differences between the Pacific tuna ventricle and atrium, with potentially higher rates of calcium cycling in the atrium associated with the higher expression of SERCA2b compared to the ventricle. We find no evidence that genes associated with thermogenesis are upregulated in the deep, warm muscle compared to superficial, cool muscle. Heat generation may be enabled by by the high aerobic capacity of bluefin tuna red muscle.
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Affiliation(s)
- Adam Ciezarek
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK. .,Earlham Institute, Norwich Research Park, Norwich, UK.
| | - Luke Gardner
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Vincent Savolainen
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Barbara Block
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
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Hossain TJ, Chowdhury SI, Mozumder HA, Chowdhury MNA, Ali F, Rahman N, Dey S. Hydrolytic Exoenzymes Produced by Bacteria Isolated and Identified From the Gastrointestinal Tract of Bombay Duck. Front Microbiol 2020; 11:2097. [PMID: 32983064 PMCID: PMC7479992 DOI: 10.3389/fmicb.2020.02097] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
Bacteria producing hydrolytic exoenzymes are of great importance considering their contribution to the host metabolism as well as for their various applications in industrial bioprocesses. In this work hydrolytic capacity of bacteria isolated from the gastrointestinal tract of Bombay duck (Harpadon nehereus) was analyzed and the enzyme-producing bacteria were genetically characterized. A total of twenty gut-associated bacteria, classified into seventeen different species, were isolated and screened for the production of protease, lipase, pectinase, cellulase and amylase enzymes. It was found that thirteen of the isolates could produce at least one of these hydrolytic enzymes among which protease was the most common enzyme detected in ten isolates; lipase in nine, pectinase in four, and cellulase and amylase in one isolate each. This enzymatic array strongly correlated to the previously reported eating behavior of Bombay duck. 16S rRNA gene sequence-based taxonomic classification of the enzyme-producing isolates revealed that the thirteen isolates were grouped into three different classes of bacteria consisting of eight different genera. Staphylococcus, representing ∼46% of the isolates, was the most dominant genus. Measurement of enzyme-production via agar diffusion technique revealed that one of the isolates which belonged to the genus Exiguobacterium, secreted the highest amount of lipolytic and pectinolytic enzymes, whereas a Staphylococcus species produced highest proteolytic activity. The Exiguobacterium sp. expressing a maximum of four hydrolases, appeared to be the most promising isolate of all.
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Affiliation(s)
- Tanim J. Hossain
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Sumaiya I. Chowdhury
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Halima A. Mozumder
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Mohammad N. A. Chowdhury
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Ferdausi Ali
- Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
| | - Nabila Rahman
- Department of Biology, Chittagong Sunshine College, Chattogram, Bangladesh
| | - Sujan Dey
- Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
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Chen RY, Ngoc Hieu BT, Audira G, Lou B, Lin MD, Hsiao CD. Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles. Animals (Basel) 2020; 10:ani10071130. [PMID: 32635168 PMCID: PMC7401541 DOI: 10.3390/ani10071130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/20/2020] [Accepted: 06/27/2020] [Indexed: 11/20/2022] Open
Abstract
Simple Summary Oxygen-binding proteins that mediate oxygen-binding for storage and consumption, to reduce energy, are very diverse in fish, depending on their habitats. In the present study, oxygen-binding protein gene expression in the skeletal muscle of 25 diverse fish species was examined by a meta-transcriptomic approach. By using RNAseq data, this is the first study to examine the high level of myoglobin, one of the oxygen-binding proteins, transcripts in pacu and loach fish that might be related to their high tolerance for the oxygen-deficient environment. In addition, this study presents the power of the current method to compare the fish oxygen-binding protein expression and its putative gene expansion event. Abstract Oxygen-binding proteins, such as myoglobin, hemoglobin, neuroglobin, and cytoglobin, play a role in oxygen binding and delivery to tissues. In icefish, the loss of myoglobin and hemoglobin genes has been reported to be an adaptive evolution event. This interesting finding prompted us to exam oxygen-binding protein expression in diverse fish species. Taking advantage of substantial RNAseq data deposited in the NCBI (National Center for Biotechnology Information) database, we adopted a meta-transcriptomic approach to explore and compare four oxygen-binding protein gene expression levels in the skeletal muscle of 25 diverse fish species for the first time. RNAseq data were downloaded from the NCBI Sequence Read Archive (SRA) database, and de novo assembly was performed to generate transcript contigs. The genes encoding oxygen-binding proteins were then identified by the BLAST search, and the relative expression level of oxygen-binding protein genes was normalized by the RPKM (Reads per Kilobase Million) method. By performing expression profiling, hierarchy clustering, and principal component analysis, pacu and loach fish were noticed by their high myoglobin expression levels in skeletal muscle tissues among 25 diverse fish species. In conclusion, we demonstrated that meta-transcriptomic analysis of RNAseq data is an informative approach to compare the oxygen-binding protein expression and putative gene expansion event in fish.
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Affiliation(s)
- Rui-Yi Chen
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fisheries Research Institute of Zhejiang, Zhoushan 316100, China;
- Marine and Fishery Institute, Zhejiang Ocean University, Zhoushan 316100, China
| | - Bui Thi Ngoc Hieu
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan; (B.T.N.H.); (G.A.)
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 32023, Taiwan
| | - Gilbert Audira
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan; (B.T.N.H.); (G.A.)
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 32023, Taiwan
| | - Bao Lou
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Shiqiao Road 198, Hangzhou 310021, China
- Correspondence: (B.L.); (M.-D.L.); (C.-D.H.)
| | - Ming-Der Lin
- Department of Molecular Biology and Human Genetics, College of Medicine, Tzu Chi University, 701 Zhongyang Rd, Sec. 3, Hualien 97004, Taiwan
- Correspondence: (B.L.); (M.-D.L.); (C.-D.H.)
| | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan; (B.T.N.H.); (G.A.)
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 32023, Taiwan
- Center for Nanotechnology, Chung Yuan Christian University, Chung-Li 32023, Taiwan
- Correspondence: (B.L.); (M.-D.L.); (C.-D.H.)
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Sathish MN, Jeyasanta I, Patterson J. Occurrence of microplastics in epipelagic and mesopelagic fishes from Tuticorin, Southeast coast of India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137614. [PMID: 32143031 DOI: 10.1016/j.scitotenv.2020.137614] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/26/2020] [Accepted: 02/26/2020] [Indexed: 05/18/2023]
Abstract
This study investigated the microplastic (MP) contamination of seawater and fishes from different habitats so as to understand the level of human exposure to microplastics. Samples of Harpodon nehereus, Chirocentrus dorab, Sardinella albella, Rastrelliger kanagurta, Katsuwonus pelamis and Istiophorus platypterus were collected from Tuticorin, southeast coast of India. The MPs in seawater and the gastrointestinal tracts of fish were identified using Stereomicroscope and characterized by FTIR and SEM-EDAX analysis. The abundance of MPs varied from 3.1 ± 2.3 to 23.7 ± 4.2 items L-1 in water, from 0.11 ± 0.06 to 3.64 ± 1.7 items/individual, and from 0.0002 ± 0.0001 to 0.2 ± 0.03 items/g gut weight. The epipelagic fishes had higher levels of MP contamination than the mesopelagic ones. Most of the MPs identified were of blue color, of fiber type and with their size <500 μm. Polyethylene was the most commonly detected MP, followed by polyester and polyamide, and this fact could be attributed to the inflow of domestic sewage and to the intensive fisheries activities in the area. SEM-EDAX spectra revealed the weathered MP surfaces which could adsorb/leach inorganic elements (colorants and fillers) from/to the environment. We may conclude that the concentration of MPs in fishes is a function of the concentration of MPs in their environment.
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Affiliation(s)
- M Narmatha Sathish
- Suganthi Devadason Marine Research Institute, Affiliated to Manonmaniam Sundaranar University, Tirunelveli, India.
| | - Immaculate Jeyasanta
- Suganthi Devadason Marine Research Institute, Affiliated to Manonmaniam Sundaranar University, Tirunelveli, India
| | - Jamila Patterson
- Suganthi Devadason Marine Research Institute, Affiliated to Manonmaniam Sundaranar University, Tirunelveli, India
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Sun X, Wang W, Dong Y, Wang Y, Zhang M, Wang Z, Yu X, Huang J, Cai H. Relationship between calcium circulation-related factors and muscle strength in rat sciatic nerve injury model. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2020; 23:654-662. [PMID: 32742604 PMCID: PMC7375001 DOI: 10.22038/ijbms.2020.40915.9695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVES The purpose of this study is to investigate the indication function of the calcium circulation-related factors on the damage to muscle strength and contraction function after nerve injury. The target factors include ryanodine receptor (RyR), inositol-1,4,5-triphosphate receptor (IP3R), phospholamban (PLN), cryptocalcitonin (CASQ), ATPase and troponin C (TNNC). MATERIALS AND METHODS Sprague-Dawley (SD) rats were randomly divided into sham-operated group (SO), sciatic nerve injury group (SNI) and sciatic nerve disconnection group (SNT). Sciatic nerve function index and stretching test were used to examine the changes to muscle strength; bilateral gastrocnemius muscles were extracted after execution for gastrocnemius wet weight ratio test. HE staining slides and average cross-sectional area of muscle fibers were acquired to analyze the muscle atrophy. The transcription level of the factors was also measured. RESULTS Sciatic nerve damage in SNI group was significantly higher than that in SO group in the 6 weeks, but there was no significant difference between SNT and SO groups fallowing sciatic nerve damage. Sciatic nerve function in SNT group was worse than that in SNI group. The average cross-sectional area of gastrocnemius muscle fibers in SNI and SNT groups was significantly reduced compared to that in SO group. The transcriptional levels of RyR, PLN, CASQ, ATPase and TNNC in SNI and SNT groups were significantly different from those in SO group. CONCLUSION Calcium circulation-related factors could be used as potential indicators for assessment of damages to muscle strength.
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Affiliation(s)
- Xiaoming Sun
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China
| | - Wei Wang
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China
| | - Yangyi Dong
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China
| | - Yue Wang
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China
| | - Meixiang Zhang
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China
| | - Zhao Wang
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China
| | - Xiaowei Yu
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China
| | - Jiao Huang
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China
| | - Hongxing Cai
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China,Corresponding author: Hongxing Cai. Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, P. R. China. Tel: 0516-85748442
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