African catfish transcriptome
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Project description:Antimicrobial peptides (AMPs) constitute a broad range of bioactive compounds in diverse organisms, including fish. They are effector molecules for the innate immune response, against pathogens, tissue damage and infections. Still, AMPs from African Catfish, Clarias gariepinus skin mucus are largely unexplored despite their possible therapeutic role in combating antimicrobial resistance. In this study, African Catfish Antimicrobial peptides (ACAPs) were identified from the skin mucus of African Catfish, C. gariepinus. Native peptides were extracted from fish mucus scrapings in 10% acetic acid (v/v) and ultra-filtered using 5kDa molecular cut-off membrane. The extract was purified using C18 Solid Phase Extraction. The antibacterial activity was determined using the Agar Well Diffusion method and broth-dilution method utilizing Staphylococcus aureus (ATCC 25923) and Escherichia coli (ATCC 25922). Thereafter, Sephadex G-25 gel filtration was further utilized in bio-guided isolation of the most active fractions prior to peptide identification using Orbitrap Fusion Lumos Tribrid Mass Spectrometry. The skin mucus extracted from African Catfish from all the three major lakes of Uganda exhibited antimicrobial activity on E. coli and S. aureus. Lake Albert’s C. gariepinus demonstrated the best activity with the lowest MIC of 2.84 µg/mL and 0.71 µg/mL on S. aureus and E. coli respectively. Sephadex G-25 peak I mass spectrometry analysis alongside in silico analysis revealed seven short peptides (11-15 amino acid residues) of high antimicrobial scores (0.561-0.905 units). In addition, these peptides had a low molecular weight (1005.57-1622.05 Da), and had percentage hydrophobicity above 54%. Up to four of these antimicrobial peptides demonstrated α-helix structure conformation, rendering them amphipathic. The findings of this study indicate that novel antimicrobial peptides can be sourced from the skin mucus of C. gariepinus. Such antimicrobial peptides are potential alternatives to the traditional antibiotics and can be of great application to food and pharmaceutical industries; however, further studies are still needed to establish their drug-likeness and safety profiles.
2021-12-01 | PXD029193 | Pride
Project description:The global surge in multi-drug resistant bacteria, including extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has led to a growing need for new antibacterial compounds. Despite being promising, the potential of fish-derived antimicrobial peptides (AMPs) in combating ESBL-E. coli is largely unexplored. In this study, native peptides were extracted from the skin mucus of farmed African Catfish, Clarias gariepinus, using a combination of 10 % acetic acid solvent hydrolysis, 5 kDa ultrafiltration, and C18 hydrophobic interactions. Peptides were then sequenced using Orbitrap Fusion Lumos Tribrid Mass Spectrometry. The identified peptides were screened for potential antibacterial activity using Random Forest and AdaBoost machine learning algorithms. The most promising peptide was then chemically synthesized and evaluated in vitro for safety on Rabbit red blood cells and activity against ESBL-E. coli (ATCC 35218) utilizing the spot-on-lawn and broth dilution methods. Eight short peptides were identified with 13 - 22 amino acid residues and molecular weight range of 968.42 to 2434.11 Da. Peptide, FACAP-II was non-hemolytic to rabbit erythrocytes (p>0.05), with Zone of Inhibition (ZOI) of 22.7 mm and Minimum Inhibitory concentration (MIC) of 91.3 μg/mL. The peptide is thus a candidate antibacterial compound with enormous potential applications in the pharmaceutical industry. However, further studies are still required to establish the upscale production strategy and optimize its activity and safety in vivo.
2024-06-25 | PXD049239 | Pride
Project description:Walking catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater fish species of the Siluriformes order. C. macrocephalus has both gills and modified gill structures serving as an air breathing organ (ABO) which allows them aerial breathing (AB), while I. punctatus does not possess an air-breathing organ (ABO), and thus cannot breathe in air. These two species provide an excellent model for studying the molecular basis of accessory air-breathing organ development in teleost fish. In this study, seven development stages in C. macrocephalus were selected for RNA-seq analysis to compare with channel catfish as the time when air breathing organ developed and became functional. Through comparative genetic contents analysis, 1,458 genes were identified to be present in C. macrocephalus, but absent from I. punctatus. Gene expression analysis and protein-protein intersection (PPI) analysis were performed, 26 genes were selected in C. macrocephalus, including mb, ngb, hbae genes, which are mainly associated with oxygen carrier activity, oxygen binding and heme binding activities. Our work provides a large data resource for exploring the genomic basis of air breathing function in C. macrocephalus and offers an insight into the adaption of aquatic organisms to hypoxia and high ammonia environment.
2020-12-09 | GSE151993 | GEO
Project description:Channel catfish (Ictalurus punctatus) and tra catfish (Pangasianodon hypophthalmus) both belong to the order Siluriformes. Channel catfish does not possess an air-breathing organ (ABO), and thus cannot breathe in the air, while tra catfish is a facultative air-breather and use the swim bladder as its air-breathing organ, which provides for aerial breathing in low oxygen conditions. Tra and channel catfish serve as a great comparative model for studying the transition of life from water to terrestrial living, as well as for understanding genes that are crucial for development of the swim bladder and the function of air-breathing in tra catfish. We selected seven developmental stages in tra catfish for RNA-Seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated in tra catfish, and a total of 21, 448 unique genes were detected. A comparative genomic analysis was conducted between channel catfish and tra catfish. Gene expression analysis was performed for these tra catfish specific genes. Hypoxia challenge and microtomy experiments collectively suggested that there are critical timepoints for the development of the air-breathing function and swim bladder development stages in tra catfish. Key genes were identified to be the best candidates of genes related to the air-breathing ability in tra catfish. This study provides a large data resource for functional genomic studies in air-breathing function in tra catfish, and sheds light on the adaption of aquatic organisms to the terrestrial environment.
2021-01-12 | GSE154904 | GEO
Project description:Channel catfish and blue catfish represent two economically important freshwater aquaculture species in the United States. Our study aims to investigate the gene expression differences between these two catfish species by high-throughput RNA sequencing to understand their associated phenotypic differences in growth and disease resistant. Our transcriptomic analyses provide some insights into gene function differences between the two species and the molecular basis of channel catfish growth advantage in the tank culture environment.
2023-11-20 | GSE247918 | GEO
Project description:The hybrid between female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) is superior in feed conversion, disease resistance, carcass yield, and harvestability compared to both parental species. However, heterosis and heterobeltiosis only occur in pond culture, and channel catfish grow much faster than the other genetic types in small culture units. This environment-dependent heterosis is intriguing, but the underlying genetic mechanisms are not well understood. In this study, phenotypic characterization and transcriptomic analyses were performed in the channel catfish, blue catfish, and their reciprocal F1s reared in tanks. The results showed that the channel catfish is superior in growth-related morphometrics, presumably due to significantly lower innate immune function, as investigated by reduced lysozyme activity and alternative complement activity. RNA-seq analysis revealed that genes involved in fatty acid metabolism/transport are significantly upregulated in channel catfish compared to blue catfish and hybrids, which also contributes to the growth phenotype. Interestingly, hybrids have a 40-80% elevation in blood glucose than the parental species, which can be explained by a phenomenon called transgressive expression (overexpression/underexpression in F1s than the parental species). A total of 1,140 transgressive genes were identified in F1 hybrids, indicating that 8.5% of the transcriptome displayed transgressive expression. Transgressive genes upregulated in F1s are enriched for glycan degradation function, directly related to the increase in blood glucose level. This study is the first to explore molecular mechanisms of environment-dependent hetero-sis/heterobeltiosis in a vertebrate species and sheds light on the regulation and evolution of heterosis vs. hybrid incompatibility.
2022-01-05 | GSE186603 | GEO
Project description:Seven early developmental stages in channel catfish, Ictalurus punctatus, were selected for transcriptome sequencing and analysis, Differential expression analysis and WGCNA approach was applied. The genes that play vital roles in embryogenesis and regulation of early development in channel catfish were detected. Our work reveals new insights for exploring the underlying mechanisms of channel catfish early development.
2020-08-26 | GSE152002 | GEO