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BACKGROUND: DNA N6-methyladenosine (6mA), as an important epigenetic modification, widely exists in bacterial genomes and participates in the regulation of toxicity, antibiotic resistance, and antioxidant. With the continuous development of sequencing technology, more 6mA sites have been identified in bacterial genomes, but few studies have focused on the distribution characteristics of 6mA at the whole-genome level and its association with gene expression and function. RESULTS: This study conducted an in-depth analysis of the 6mA in the genomes of two pathogenic bacteria, Aeromonas veronii and Helicobacter pylori. The results showed that the 6mA was widely distributed in both strains. In A. veronii, 6mA sites were enriched at 3' end of protein-coding genes, exhibiting a certain inhibitory effect on gene expression. Genes with low 6mA density were associated with cell motility. While in H. pylori, 6mA sites were enriched at 5' end of protein-coding genes, potentially enhancing gene expression. Genes with low 6mA density were closely related to defense mechanism. CONCLUSIONS: This study elucidated the distribution characteristics of 6mA in A. veronii and H. pylori, highlighting the effects of 6mA on gene expression and function. These findings provide valuable insights into the epigenetic regulation and functional characteristics of A. veronii and H. pylori.
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Helicobacter pylori , Helicobacter pylori/genética , Epigênese Genética , Aeromonas veronii/genética , DNA/metabolismo , Adenosina/genética , Adenosina/metabolismo , Metilação de DNARESUMO
In this study, Penaeus monodon were gave basic feed supplemented with three levels of Enterococcus faecium. Then, the expression of non-specific immunity-related genes, and the activities of total antioxidant capacity (T-AOC), superoxide dismutase (SOD), malondialdehyde (MDA), acid phosphatase (ACP), alkaline phosphatase (AKP), phenol oxidase (PO) were evaluated. Meanwhile, the disease resistance test and intestinal flora determination were conducted. The results showed that the MDA levels of 2% and 5% E. faecium groups were significantly lower than that of the control group (P < 0.05). While the SOD and T-AOC and ACP and AKP of experimental groups were significantly higher (P < 0.05), the PO of experimental groups were significantly lower than that of the control group (P < 0.05). In addition, the expressions of immunity-related genes (tlr22, dorsal, lysozyme, crustin, imd, and relish) in the 2% and 5% E. faecalis groups were significantly greater than those in the control group (P < 0.05). After P. monodon was challenged with Vibrio parahaemolyticus for 7 days, the average cumulative mortality of P. monodon in the 2% and 5% groups were significantly lower than that in the 0% group (P < 0.05). With the increase of feeding time, the number of effective OTUs in each group showed a downward trend. At the 14th d, Proteobacteria, Bacteroidetes and Firmicutes, the dominant flora in the intestinal tract of P. monodon. In summary, supplied with E. faecium could increase the expression of non-specific immunity-related genes, enhance the immune capacity of P. monodon.
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Enterococcus faecium , Microbioma Gastrointestinal , Penaeidae , Animais , Enterococcus faecium/metabolismo , Antioxidantes/metabolismo , Monofenol Mono-Oxigenase/metabolismo , Superóxido Dismutase/metabolismo , Expressão Gênica , Imunidade InataRESUMO
Clostridium perfringens type A is the main cause of necrotic enteritis (NE) in chickens. Since the use of antibiotics in feed is withdrawn, it is imperative to find out suitable alternatives to control NE. Baicalin-aluminum complex is synthesized from baicalin, a flavonoid isolated from Scutellaria baicalensis Georgi. The present study investigated the effects of baicalin-aluminum on the virulence-associated traits and virulence genes expression of C. perfringens CVCC2030, it also evaluated the in vivo therapeutic effect on NE. The results showed that baicalin-aluminum inhibited bacterial hemolytic activity, diminished biofilm formation, attenuated cytotoxicity to Caco-2 cells, downregulated the expression of genes encoding for clostridial toxins and extracellular enzymes such as alpha toxin (CPA), perfringolysin O (PFO), collagenase (ColA), and sialidases (NanI, NanJ). Additionally, baicalin-aluminum was found to negatively regulate the expression of genes involved in quorum sensing (QS) communication, including genes of Agr QS system (agrB, agrD) and genes of VirS/R two-component regulatory system (virS, virR). In vivo experiments, baicalin-aluminum lightened the intestinal lesions and histological damage, it inhibited pro-inflammatory cytokines (TNF-α, IL-1ß, IL-6) expression in the jejunal and ileal tissues. Besides, baicalin-aluminum alleviated the upregulation of C. perfringens and Escherichia coli and raised the relative abundance of Lactobacillus in the ileal digesta. This study suggests that baicalin-aluminum may be a potential candidate against C. perfringens infection by inhibiting the virulence-associated traits and virulence genes expression.
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Infecções por Clostridium , Enterite , Doenças das Aves Domésticas , Humanos , Animais , Clostridium perfringens/genética , Fatores de Virulência/genética , Fatores de Virulência/metabolismo , Infecções por Clostridium/tratamento farmacológico , Infecções por Clostridium/veterinária , Infecções por Clostridium/microbiologia , Galinhas , Alumínio/metabolismo , Células CACO-2 , Flavonoides/farmacologia , Enterite/tratamento farmacológico , Enterite/veterinária , Doenças das Aves Domésticas/microbiologiaRESUMO
Aeromonas veronii is an opportunistic pathogen that affects both fish and mammals, including humans, leading to bacteraemia, sepsis, meningitis and even death. The increasing virulence and drug resistance of A. veronii are of significant concern and pose a severe risk to public safety. The Type I restriction-modification (RM) system, which functions as a bacterial defence mechanism, can influence gene expression through DNA methylation. However, little research has been conducted to explore its origin, evolutionary path, and relationship to virulence and drug resistance in A. veronii. In this study, we analysed the pan-genome of 233 A. veronii strains, and the results indicated that it was 'open', meaning that A. veronii has acquired additional genes from other species. This suggested that A. veronii had the potential to adapt and evolve rapidly, which might have contributed to its drug resistance. One Type I methyltransferase (MTase) and two complete Type I RM systems were identified, namely AveC4I, AveC4II and AveC4III in A. veronii strain C4, respectively. Notably, AveC4I was exclusive to A. veronii C4. Phylogenetic analysis revealed that AveC4I was derived from horizontal gene transfer from Thiocystis violascens and exchanged genes with the human pathogen Comamonas kerstersii. Single molecule real-time sequencing was applied to identify the motif methylated by AveC4I, which was unique and not recognized by any reported MTases in the REBASE database. We also annotated the functions and pathways of the genes containing the motif, revealing that AveC4I may control drug resistance in A. veronii C4. Our findings provide new insight on the mechanisms underlying drug resistance in pathogenic bacteria. By identifying the specific genes and pathways affected by AveC4I, this study may aid in the development of new therapeutic approaches to combat A. veronii infections.
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As one of the most open and economically dynamic regions in China, the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) is at the forefront of low-carbon development and has an exemplary and leading role for other regions. This study provides a research framework based on the Logarithmic Mean Divisia Index (LMDI) and system dynamics (SD) by first compiling an inventory of CO2 emissions in the GBA and surrounding cities from 2000 to 2019 and then systematically and comprehensively analyzing the driving factors, future trends and policy implications of CO2 emissions in the GBA and surrounding cities. The results show that (a) CO2 emissions in the GBA and surrounding cities grew from 253.39 Mt in 2000 to 627.86 Mt in 2019, with an average annual growth rate of 4.89 %. The per capita CO2 emissions showed a continuous decreasing trend, and the overall carbon intensity of each sector showed a decreasing trend. (b) GDP per capita growth has the greatest effect on CO2 emissions, followed by the number of transport vehicles and population. The negative effects are energy intensity, average output of transportation vehicles, and residential energy intensity, with energy intensity being the most critical. (c) In the baseline scenario, regional CO2 emissions in 2030 are 1.25 times higher than those in 2019 and continue to grow. (d) Technological innovation measures are the most effective among individual emission reduction policies, followed by optimization of industrial structure. Furthermore, energy structure adjustment, vehicle licensing restrictions, and residents' green living are less effective. (e) Under comprehensive emission reduction measures, the region can achieve carbon emissions peaking in 2026 and reduce the regional carbon intensity by 66.24 % in 2030 compared with 2005. This study provides effective data support for the GBA and surrounding cities to formulate low carbon policies, promote carbon emission reduction and achieve carbon emissions peaking early.
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Dióxido de Carbono , Carbono , Hong Kong , Macau , Dióxido de Carbono/análise , Cidades , China , Carbono/análiseRESUMO
For solving the global shortage of fish meal (FM) supplies from fisheries, the black soldier fly (Hermetia illucens) has become a new protein alternative in aquatic feeds. The present study investigated the effects of dietary inclusion of defatted H. illucens larvae meal (DBLM) on growth, serum biochemical parameters, digestive function, and muscle quality of tongue sole (Cynoglossus semilaevis). The feeding experiment consisted of five experimental diets: a control diet based on FM protein (H0) and four DBLM diets, substituting 25% (H25), 50% (H50), 75% (H75), and 100% (H100) of FM. C. semilaevis (initial weight 563.48 ± 22.81 g) were randomly allocated over five treatments in quadruplicate. After 65 days of feeding, the weight gain rate (WGR), specific growth rate (SGR), and protein efficiency ratio (PER) were significantly higher in H0 and H25 groups with less feed conversion ratio (FCR) and feed intake (FI). The concentrations of serum ALT, TG, T-CHO, ALB, and GLO and their ratio (i.e., A/G) in the H25 group were also significantly higher than those in the other DBLM diet-feeding groups. The digestive enzyme activities first increased (from 25% to 75%) and then decreased (from 75%) with the increased level of DBLM in diets. Meanwhile, there were significant improvements in the thickness of the intestinal longitudinal muscle (LM), circular muscle (CM), columnar epithelium (CE), and lamina propria (LP) in H25 C. semilaevis compared to the control group (p < 0.05). The fish from the other DBLM diets groups presented significant reductions in the thicknesses of LM, CM, CE, and LP, as well as the length of microvilli (ML) in a dose-dependent manner (p < 0.05). However, the substitution of FM increased up to 50% would result in intestinal structural damage. Moreover, the proximate compositions, antioxidant and water holding capacity, and muscular structures of C. semilaevis fillets were all significantly affected after substituting 25% FM with DBLM (p < 0.05). Except for the dry matter, moisture, ash, crude fat, and protein contents were significantly higher in H25 C. semilaevis muscles. The SOD activity in the H0 group was significantly lower than that in the H25 group. The CAT activity in C. semilaevis muscles prominently reduced along with the increase in DBLM content in feeding diets (p < 0.05). The water holding capacity of C. semilaevis fillets was best in the H25 group. In summary, the optimum proportion of DBLM with FM for feeding C. semilaevis may be around 25%.
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Salinity is an important environmental factor that affects fish growth, development, and reproduction. As euryhaline fish, half-smooth tongue sole (Cynoglossus semilaevis) are a suitable species for deciphering the salinity adaptation mechanism of fish; however, the molecular mechanisms underlying low- and high-salinity responses remain unclear. In this study, RNA-seq was applied to characterize the genes and regulatory pathways involved in C. semilaevis gill responses to high- (32 ppt), low- (8 ppt), and control-salinity (24 ppt) water. Gills were rich in mitochondria-rich cells (MRCs) in high salinity. Compared with control, 2137 and 218 differentially expressed genes (DEGs) were identified in low and high salinity, respectively. The enriched functions of most DEGs were metabolism, ion transport, regulation of cell cycle, and immune response. The DEGs involved in oxidative phosphorylation, citrate cycle, and fatty acid metabolism were down-regulated in low salinity. For ion transport, high and low salinity significantly altered the expressions of prlr, ca12, and cftr. In cell cycle arrest and cellular repair, gadd45b, igfbp5, and igfbp2 were significantly upregulated in high and low salinity. For immune response, il10, il34, il12b, and crp increased in high and low salinity. Our findings suggested that alterations in material and energy metabolism, ions transport, cell cycle arrest, cellular repair, and immune response, are required to maintain C. semilaevis gill homeostasis under high and low salinity. This study provides insight into the divergence of C. semilaevis osmoregulation mechanisms acclimating to high and low salinity, which will serve as reference for the healthy culture of C. semilaevis.
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Linguado , Brânquias , Animais , Peixes , Linguado/fisiologia , Brânquias/metabolismo , Homeostase , Salinidade , Transcriptoma , Água/metabolismoRESUMO
Due to the marked increase in the prevalence of overweight and obesity worldwide and an environment leading to a series of chronic diseases, physical exercise is an important way to prevent chronic diseases. Additionally, a good exercise smart bracelet can bring convenience to physical exercise. Quick and accurate evaluation of smart sports bracelets has become a hot topic and draws attention from both academic researchers and public society. In the literature, the analytic hierarchy process (AHP) and entropy weight method (EWM) were used to obtain the weights from both subjective and objective perspectives, which were integrated by the comprehensive weighting method, and furthermore the performance of sports smart bracelet was evaluated through fuzzy comprehensive evaluation. Also, to avoid complex weight calculations caused by the comprehensive weighting method, machine learning methods are used to model the structure and contribute to the comprehensive evaluation process. However, few studies have investigated all previous elements in the comprehensive evaluation process. In this study, we consider all previous parts when evaluating smart sports bracelets. In particular, we use the sparrow search algorithm (SSA) to optimize the backpropagation (BP) neural network for constructing the comprehensive score prediction model of the sports smart bracelet. Results show that the sparrow search algorithm-optimized backpropagation (SSA-BP) neural network model has good predictive ability and can quickly obtain evaluation results on the premise of effectively ensuring the accuracy of the evaluation results.
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Redes Neurais de Computação , Esportes , Algoritmos , Entropia , Lógica Fuzzy , Aprendizado de MáquinaRESUMO
Ionic liquids (ILs) are acknowledged as green chemicals and favorable substitutes for volatile organic solvents, which are currently used. However, previous studies have shown that these compounds had toxicological impacts on aquatic organisms. To investigate the effects of 1-hexyl-3- methylimidazolium bromide ionic liquid ([C6mim]Br) on embryonic development and reproduction in water flea (Daphnia magna), a series of exposure experiments were conducted, including acute toxicity, maternal exposure, and chronic exposure tests. In acute toxicity experiment, D. magna neonates exhibited developmental abnormalities in the shell spine and the second antennae in a concentration-dependent manner after exposure to [C6mim]Br. The results in maternal exposure test also revealed a certain embryo-toxicity in response to [C6mim]Br in D. magna. However, the toxicity was lower than that conveyed by direct acute exposure, this indicated that the IL could act directly on organism. During the 21 days chronic exposure, the 1.6 mg/L exposure caused marked drop in the survival, molts and the number of the first brood of D. magna. Meanwhile, the total number of offspring was significantly declined in 1.6 mg/L concentration treatment groups, whereas increased in 0.2 mg/L groups. Generally, abnormalities in the offspring were significantly increased across all of the treatment groups in contrast to the control. No effect on sex differentiation was found during the experiments. These findings suggested that [C6mim]Br could affect embryonic development and reproduction in D. magna, and provided references for further study on the mechanisms underlying toxicological effects of ILs and the assessment of their potential environmental risks.
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Boratos/toxicidade , Daphnia/fisiologia , Imidazóis/toxicidade , Poluentes Químicos da Água/toxicidade , Animais , Organismos Aquáticos , Brometos/farmacologia , Daphnia/efeitos dos fármacos , Daphnia/embriologia , Embrião não Mamífero/efeitos dos fármacos , Desenvolvimento Embrionário , Feminino , Humanos , Líquidos Iônicos/toxicidade , Muda , Reprodução/efeitos dos fármacos , SolventesRESUMO
In this study, a two-component lattice Boltzmann method (TLBM) in combination with a discrete element approach (DEA) based on a representative volume element (RVE) with respect to a bidisperse magnetorheological fluid (MRF) was performed to simulate the behavior and microstructure formation of magnetic particles in a carrier liquid. The bidisperse MRF reported herein is a suspension dispersed by soft micron carbonyl iron (CI) particles and Fe3O4 nanoparticles dual-coated with gelatin and multi-walled carbon nanotubes (MWCNTs) in the carrier liquid. In the TLBM of two-component liquid and particle simulation, the inter-particle interactions were completely ignored; on the other hand, the DEA was just employed for calculating the dynamic behavior of particles. Therefore, due to the explicit nature of the combination of TLBM and DEA, it is a more efficient and accurate strategy for the simulation and calculation of complex MRF systems. Moreover, the immersed boundary method (IBM) was used to describe the interactions between the magnetic particles and the carrier liquid. The RVE of the bidisperse MRF was selected to eliminate specific operational conditions and reduce the calculation costs. New numerical results were obtained for the motion velocities, microstructure evolution and kinetic energy of bidisperse magnetic particles (BMPs) under the effect of a magnetic field; when the mass fraction of the nanoparticles was 0.1, the bidisperse MRF exhibited an improved response time in terms of the particle motion and microstructure formation. In addition, the effects of the Reynolds (Re) and Hartmann (Ha) numbers on the fluid-particle interaction and flow velocity were illustrated.
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The magnetorheology and dispersion stability of bidisperse magnetic particles (BMP)-based magnetorheological (MR) fluids were improved by applying a novel functional coating composed of gelatin and graphite oxide (GO) to the surfaces of the micron-sized carbonyl iron (CI) and nanoparticles Fe3O4. Gelatin acted as a grafting agent to reduce the aggregation and sedimentation of CI particles and prevent nanoparticles Fe3O4 from oxidation. In addition, a dense GO network on the surface of gelatin-coated BMP was synthesized by self-assembly to possess a better MR performance and redispersibility. The rheological properties of MR fluids containing dual-coated BMP were measured by a rotational rheometer under the presence of magnetic field and their dispersion stability was examined through sedimentation tests. The results showed that CI@Fe3O4@Gelatin@GO (CI@Fe3O4@G@GO) particles possessed enhanced MR properties and dispersion stability. In addition, the nanoparticle-enhancing effects on the dispersion stability of BMP-based MR fluids were investigated using Monte Carlo simulations.
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Background: The ultrahigh density intensive farming model of grass carp (Ctenopharyngodon idellus) may elicit growth inhibition, decrease flesh quality, and increase disease susceptibility of fish. The degradation in quality and excessive fat accumulation in cultured C. idellus have long been attributed to possible alterations in the lipid metabolism of fish muscle tissues as a result of overnutrition from artificial diets. To investigate the effects of different diets on fish muscle quality, a large-scale metabolomics study was performed on 250 tails of C. idellus. Findings: The experimental fish were divided into four groups based on sex and diet-female artificial feed (FAF), female grass feed, male artificial feed (MAF), and male grass feed (MGF). After a 113-day rearing period, the artificial feed (AF) group showed a significantly higher total mass of muscle fat (P < 0.01), with the FAF group being the highest. Metabolomics profiling based on liquid chromatography-mass spectrometry revealed distinctive patterns of clustering according to the four groups. Overall, artificial feeding was associated with higher concentrations of docosapentaenoic acid, dihomo-gamma-linolenic acid, and arachidonic acid, whereas grass feeding was associated with elevated n-3 unsaturated fatty acids (UFAs) such as eicosapentaenoic acid, alpha-linolenic acid, and gamma-linolenic acid. Artificial feeding also resulted in significant increased docosahexaenoic acid in MAF muscle than in MGF fish, whereas there was no significance in the comparison of female samples. Metabolic pathway analyses using both targeted and untargeted approaches consistently revealed that arachidonic acid metabolism and steroid hormone biosynthesis pathways were significantly different between AF and grass fed groups. Conclusions: Our results suggest that grass is a better source of dietary fatty acid and protein when compared to artificial feed. Grass feeding could effectively lower triglycerides in serum, reduce fat accumulation, and alter lipid compositions in fish muscle by increasing the concentrations of n-3 UFAs, leading to better nutrition and health.
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Ração Animal , Carpas/metabolismo , Metaboloma , Metabolômica , Animais , Biomarcadores , Cromatografia Líquida , Biologia Computacional/métodos , Feminino , Metabolismo dos Lipídeos , Masculino , Espectrometria de Massas , Metabolômica/métodos , Músculos/metabolismoRESUMO
Fish muscle, the main edible parts with high protein level and low fat level, is consumed worldwide. Diet contributes greatly to fish growth performance and muscle quality. In order to elucidate the correlation between diet and muscle quality, the same batch of juvenile grass carp (Ctenopharyngodon idellus) were divided into two groups and fed with either grass (Lolium perenne, Euphrasia pectinata and Sorghum sudanense) or artificial feed, respectively. However, the different two diets didn't result in significant differences in all the detected water quality parameters (e.g., Tm, pH, DO, NH3/[Formula: see text]-N, [Formula: see text]-N, [Formula: see text], TN, TP, and TOC) between the two experimental groups. After a 4-month culture period, various indexes and expression of myogenic regulatory factor (MRFs) and their related genes were tested. The weight gain of the fish fed with artificial feed (AFG) was nearly 40% higher than the fish fed with grass (GFG). Significantly higher alkaline phosphatase, total cholestrol, high density cholestrol and total protein were detected in GFG as compared to AFG. GFG also showed increased hardness, resilience and shear force in texture profile analysis, with significantly bigger and compact muscle fibers in histologic slices. The fat accumulation was most serious in the abdomen muscle of AFG. Additionally, the expression levels of MyoG, MyoD, IGF-1, and MSTNs were higher, whereas Myf-5, MRF4, and IGF-2 were lower in most positional muscles of GFG as compared to AFG. Overall, these results suggested that feeding grass could promote muscle growth and development by stimulating muscle fiber hypertrophy, as well as significantly enhance the expression of CoL1As. Feeding C. idellus with grass could also improve flesh quality by improving muscle characteristics, enhancing the production of collagen, meanthile, reducing fat accumulation and moisture in muscle, but at the cost of a slower growth.
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To investigate the leptin related genes expression patterns and their possible function during the gonadal development in fish, the cDNA and genomic sequences of leptin, leptin receptor (leptinR), and leptin receptor overlapping transcript like-1 (leprotl1) were cloned and their expression levels were quantified in the different gonadal development stages of Megalobrama amblycephala. The results showed that the full length cDNA sequences of leptin, leptinR and leprotl1 were 953, 3432 and 1676 bp, coding 168, 1082, and 131 amino acid polypeptides, and the genomic sequences were 1836, 28,528 and 5480 bp, which respectively had 3, 15 and 4 exons, respectively. The phylogenetic analysis revealed that three genes were relatively conserved in fish species. Quantitative real-time PCR results showed that the three genes were ubiquitously expressed in all examined tissues during the different gonadal development stages. The leptin and leptinR took part in the onset of puberty, especially in female M. amblycephala, by increasing the expression levels in brain during the stage I to III of ovary. The expression levels of leptin and leptinR had significant differences between male and female in hypothalamic-pituitary-gonadal (HPG) axis tissues (p < 0.05). The leptinR had the same variation tendency with leptin, but the opposite changes of expression levels were found in leprotl1, which may resist the expression of leptinR for inhibiting the function of leptin in target organ. These findings revealed details about the possible role of these genes in regulating gonadal maturation in fish species.
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Peixes/genética , Leptina/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Clonagem Molecular , DNA Complementar/química , DNA Complementar/genética , Evolução Molecular , Feminino , Peixes/classificação , Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Gônadas/metabolismo , Leptina/química , Masculino , Dados de Sequência Molecular , Organogênese/genética , FilogeniaRESUMO
The blunt snout bream, Megalobrama amblycephala, is a herbivorous freshwater fish species native to China and a major aquaculture species in Chinese freshwater polyculture systems. In recent years, the bacterium Aeromonas hydrophila has been reported to be its pathogen causing great losses of farmed fish. To understand the immune response of the blunt snout bream to A. hydrophila infection, we used the Solexa/Illumina technology to analyze the transcriptomic profile after artificial bacterial infection. Two nonnormalized cDNA libraries were synthesized from tissues collected from control blunt snout bream or those injected with A. hydrophila. After assembly, 155,052 unigenes (average length 692.8 bp) were isolated. All unigenes were annotated using BLASTX relative to several public databases: the National Center for Biotechnology Information nonreduntant (Nr) database, SwissProt, Eukaryotic Orthologous Groups of proteins (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO). The sequence similarity (86%) of the assembled unigenes was to zebrafish based on the Nr database. A number of unigenes (n = 30,482) were assigned to three GO categories: biological processes (25,242 unigenes), molecular functions (26,096 unigenes), and cellular components (22,778 unigenes). 20,909 unigenes were classified into 25 KOG categories and 28,744 unigenes were assigned into 315 specific signaling pathways. In total, 238 significantly differentially expressed unigenes (mapped to 125 genes) were identified: 101 upregulated genes and 24 downregulated genes. Another 303 unigenes were mapped to unknown or novel genes. Among the known expressed genes identified, 53 were immune-related genes and were distributed in 71 signaling pathways. The expression patterns of selected up- and downregulated genes from the control and injected groups were determined with reverse transcription-quantitative PCR (RT-qPCR). Microsatellites (n = 10,877), including di-to pentanucleotide repeat motifs, were also identified in the blunt snout bream transcriptome profiles. This study extends our understanding of the immune defense mechanisms of the blunt snout bream against A. hydrophila and provides useful data for further studies of the immunogenetics of this species.
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Aeromonas hydrophila/fisiologia , Cyprinidae , Doenças dos Peixes/genética , Proteínas de Peixes/genética , Infecções por Bactérias Gram-Negativas/veterinária , Transcriptoma , Animais , Cyprinidae/genética , Cyprinidae/metabolismo , Doenças dos Peixes/microbiologia , Proteínas de Peixes/metabolismo , Biblioteca Gênica , Infecções por Bactérias Gram-Negativas/genética , Infecções por Bactérias Gram-Negativas/microbiologia , Repetições de Microssatélites , Reação em Cadeia da Polimerase Via Transcriptase Reversa/veterinária , Análise de Sequência de DNA/veterináriaRESUMO
BACKGROUND: Blunt snout bream (Megalobrama amblycephala) is an economically important fish species in the Chinese freshwater polyculture system for its delicacy and high economic value. MicroRNAs (miRNAs) play important roles in regulation of almost all biological processes in eukaryotes. Although previous studies have identified thousands of miRNAs from many species, little information is known for miRNAs of M. amblycephala. To investigate functions of miRNAs associated with growth of M. amblycephala, we adopted the Solexa sequencing technology to sequence two small RNA libraries prepared from four growth related tissues (brain, pituitary, liver and muscle) of M. amblycephala using individuals with relatively high and low growth rates. RESULTS: In this study, we have identified 347 conserved miRNAs (belonging to 123 families) and 22 novel miRNAs in M. amblycephala. Moreover, we observed sequence variants and seed edits of the miRNAs. Of the 5,166 single nucleotide substitutions observed in two libraries, the most abundant were G-to-U (15.9%), followed by U-to-C (12.1%), G-to-A (11.2%), and A to G (11.2%). Subsequently, we compared the expression patterns of miRNAs in the two libraries (big-size group with high growth rate versus small-size group with low growth rate). Results indicated that 27 miRNAs displayed significant differential expressions between the two libraries (p < 0.05). Of these, 16 were significantly up-regulated and 11 were significantly down-regulated in the big-size group compared to the small-size group. Furthermore, stem-loop RT-PCR was applied to validate and profile the expression of the differentially expressed miRNAs in ten tissues, and the result revealed that the conserved miRNAs expressed at higher levels than the novel miRNAs, especially in brain, liver and muscle. Also, targets prediction of differentially expressed miRNAs and KEGG pathway analysis suggested that differentially expressed miRNAs are involved in growth and metabolism, signal transduction, cell cycle, neural development and functions. CONCLUSIONS: The present study provides the first large-scale characterization of miRNAs in M. amblycephala and miRNA profile related to different growth performances. The discovery of miRNA resource from this study is expected to contribute to a better understanding of the miRNAs roles playing in regulating the growth biological processes and the study of miRNA function and phenotype-associated miRNA identification in fish.