Influence of stocking density and environmental factors on the expression of insulin-like growth factors in cage-reared butter catfish (Ompok bimaculatus, Bloch 1794) within a large reservoir ecosystem

In vertebrates, insulin-like growth like factors (IGFs) play an important role in growth and other physiological processes. The GH-IGF axis is considered a valuable tool to monitor fish growth performance. Herein, we report the molecular characterization of igf-1, igf-2, and β-actin transcripts and relative expression of igf-1 and igf-2 in the liver and muscle tissue of cage-reared butter catfish, Ompok bimaculatus, in response to different stocking densities (T1, 15 fingerlings m-3; T2, 25 fingerlings m-3; and T3, 35 fingerlings m-3) over 180 days of culture duration. The length of the partial amplified transcript sequence of Obigf-1, Obigf-2, and Obβ-actin was 325, 438, and 924 bp, respectively. Phylogenetically, Obigf-1 and Obigf-2 were closely clustered with catfishes, viz., Clarias magur, Bagarius yarrelli, and Silurus asotus. The expression of igf-1 was significantly downregulated in the liver at higher densities after 120 days as biomass in the cages increased, while igf-2 expression did not change with the stocking densities over the culture period. Cortisol concentration was significantly elevated in T3 groups post 150 days of the culture period and correlated negatively with the expression of igf-1 (p < 0.05) and igf-2 (p > 0.05). Environmental parameters, pH, TDS, hardness, conductivity, and alkalinity showed a significant positive correlation with hepatic IGF expression. Our study indicates that the liver-derived igf-1 plays a more important role in the regulation of growth in response to culture density in the species studied, and thus, igf-1 can be used effectively as a biomarker for growth. Furthermore, this study will help in planning a proper harvest schedule and optimize the culture practices of O. bimaculatus in an open water cage system.

Identification of virulence-associated factors in Vibrio parahaemolyticus with special reference to moonlighting protein: a secretomics study

Vibrio parahaemolyticus causes seafood-borne gastroenteritis infection in human which can even lead to death. The pathogenic strain of V. parahaemolyticus secretes different types of virulence factors that are directly injected into the host cell by a different type of secretion system which helps bacteria to establish its own ecological niche within the organism. Therefore, the aim of this study was to isolate the extracellular secreted proteins from the trh positive strain of V. parahaemolyticus and identify them using two-dimensional gel electrophoresis and MALDI-TOFMS/MS. Seventeen different cellular proteins viz, Carbamoyl-phosphate synthase, 5-methyltetrahydropteroyltriglutamate, tRNA-dihydrouridine synthase, Glycerol-3-phosphate dehydrogenase, Orotidine 5'-phosphate decarboxylase, Molybdenum import ATP-binding protein, DnaJ, DNA polymerase IV, Ribosomal RNA small subunit methyltransferase G, ATP synthase subunit delta and gamma, Ribosome-recycling factor, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, tRNA pseudouridine synthase B, Ditrans, polycis-undecaprenyl-diphosphate synthase, Oxygen-dependent coproporphyrinogen-III oxidase, and Peptide deformylase 2 were identified which are mainly involved in different metabolic and biosynthetic pathways. Furthermore, the molecular function of the identified proteins were associated with catalytic activity, ligase activity, transporter, metal binding, and ATP synthase when they are intercellular. However, to understand the importance of these secreted proteins in the infection and survival of bacteria inside the host cell, pathogen-host protein-protein interactions (PPIs) were carried out which identified the association of eight secreted proteins with 41 human proteins involved in different cellular pathways, including ubiquitination degradation, adhesion, inflammation, immunity, and programmed cell death. The present study provides unreported strategies on host-cell environment's survival and adaptation mechanisms for the successful establishment of infections and intracellular propagation.

Identification of Potential Druggable Targets and Structure-Based Virtual Screening for Drug-like Molecules against the Shrimp Pathogen Enterocytozoon hepatopenaei

Enterocytozoon hepatopenaei (EHP) causes slow growth syndrome in shrimp, resulting in huge economic losses for the global shrimp industry. Despite worldwide reports, there are no effective therapeutics for controlling EHP infections. In this study, five potential druggable targets of EHP, namely, aquaporin (AQP), cytidine triphosphate (CTP) synthase, thymidine kinase (TK), methionine aminopeptidase2 (MetAP2), and dihydrofolate reductase (DHFR), were identified via functional classification of the whole EHP proteome. The three-dimensional structures of the proteins were constructed using the artificial-intelligence-based program AlphaFold 2. Following the prediction of druggable sites, the ZINC15 and ChEMBL databases were screened against targets using docking-based virtual screening. Molecules with affinity scores ≥ 7.5 and numbers of interactions ≥ 9 were initially selected and subsequently enriched based on their ADMET properties and electrostatic complementarities. Five compounds were finally selected against each target based on their complex stabilities and binding energies. The compounds CHEMBL3703838, CHEMBL2132563, and CHEMBL133039 were selected against AQP; CHEMBL1091856, CHEMBL1162979, and CHEMBL525202 against CTP synthase; CHEMBL4078273, CHEMBL1683320, and CHEMBL3674540 against TK; CHEMBL340488, CHEMBL1966988, and ZINC000828645375 against DHFR; and CHEMBL3913373, ZINC000016682972, and CHEMBL3142997 against MetAP2.The compounds exhibited high stabilities and low binding free energies, indicating their abilities to suppress EHP infections; however, further validation is necessary for determining their efficacy.

Effects of dietary supplementation of Pseudomonas aeruginosa FARP72 on the immunomodulation and resistance to Edwardsiella tarda in Pangasius pangasius

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Pseudomonas aeruginosa FARP72 (PA) supplemented diet impacts the innate immunity.

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Innate immune responses of P. pangasius are differentially stimulated by PA diet.

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It improved the resistance of P. pangasius against E. tarda infection significantly.

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IL-1β & C3 genes upregulated significantly in kidney of PA diet-fed challenged fish.

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Highest upregulation of transferrin seen in liver of PA diet-fed challenged fish.

Edwardsiella tarda is one of the serious bacterial pathogens infecting both cultured and wild catfish urging an immediate need for effective protection strategies. This study assessed the effects of dietary supplementation of Pseudomonas aeruginosa FARP72 at 10⁸ cells/g feed (PA diet) for 30 days on the innate immunity parameters, viz., respiratory oxidative burst (ROB) activity, lysozyme, ceruloplasmin, myeloperoxidase, in-vitro nitric oxide (NO) production in addition to the expression of immune genes encoding interleukin-1β, C3 and transferrin in yellowtail catfish Pangasius pangasius and their resistance to Edwardsiella tarda challenge at a sub-lethal dose of 1.50 × 10⁷ cells/fish. A significant increase in the innate immunity parameters was noted in PA diet-fed catfish on 30 dpf compared to the control. Post E. tarda challenge, the levels of immune parameters increased significantly and peaked at 5 dpi irrespective of feeding to confer protection against E. tarda. Their levels, however, decreased on and from 10 dpi. The results on the expression of immune genes encoding interleukin-1β, C3 and transferrin in the kidney and liver tissue samples of PA diet-fed P. pangasius upon challenge with E. tarda further confirmed the ability of P. aeruginosa to stimulate primary immune organs at the gene level. The effects of feeding P. aeruginosa FARP72 on the immune functions of catfish as examined by the functional immune assays, thus, demonstrating the innate immune responses of catfish that are differentially stimulated by the PA diet. The findings of our study would help evolve management strategies to confer protection against E. tarda infection in commercial catfish aquaculture.

Identification of novel salt tolerance-associated proteins from the secretome of Enterococcus faecalis

The ability of bacteria to adapt to the external environment is fundamental for their survival. A halotolerant microorganism Enterococcus faecalis able to grow under high salt stress conditions was isolated in the present study. The SDS-PAGE analysis of the secretome showed a protein band with a molecular weight of 28 kDa, gradually increased with an increase in salt concentration, and the highest intensity was observed at 15% salt stress condition. LC-MS/MS analysis of this particular band identified fourteen different proteins, out of which nine proteins were uncharacterized. Further, the function of uncharacterized proteins was predicted based on structure-function relationship using a reverse template search approach deciphering uncharacterized protein into type III polyketide synthases, stress-induced protein-1, Eed-h3k79me3, ba42 protein, 3-methyladenine DNA glycosylase, Atxa protein, membrane-bound respiratory hydrogenase, type-i restriction-modification system methylation subunit and ManxA. STRING network analysis further a showed strong association among the proteins. The processes predicted involvement of these proteins in signal transduction, ions transport, synthesis of the protective layer, cellular homeostasis and regulation of gene expression and different metabolic pathways. Thus, the fourteen proteins identified in the secretome play an essential role in maintaining cellular homeostasis in E. faecalis under high-salinity stress. This may represent a novel and previously unreported strategy by E. faecalis to maintain their normal growth and physiology under high salinity conditions.

Dietary therapeutic dose of oxytetracycline negatively influences the antioxidant capacity and immune-related genes expression in Nile tilapia Oreochromis niloticus (L.)

Effects of the dietary therapeutic dose of oxytetracycline (OTC) at 80 mg/kg biomass/day for consecutive 10 days on the behaviour, feed intake, mortality, residue accumulation and depletion, antioxidant capacity and immune-related genes expression in juvenile Nile tilapia Oreochromis niloticus were evaluated. OTC-dosing caused mortalities, reduced feed intake, and biomass reduction at 24.5-28.5 °C. OTC residues recorded on day 10 (161.40 ± 11.10 ng/g) were within the maximum residue limits of the Codex Alimentarius. The withdrawal period was 7 days as per the European Commission's regulation. Traces of residues were present even on day 42 post-OTC-dosing. Dietary OTC reduced the antioxidant capacity of the liver and muscle tissues and down-regulated the expression of tumour necrosis factor-α, interleukin-1β, and heat shock protein-70 genes in the liver significantly during the dosing period. The data generated on the biosafety of OTC-dosing may offer inputs for the development of management strategies in maintaining fish health and food safety.

Virulence factor genes and comparative pathogenicity study of tdh, trh and tlh positive Vibrio parahaemolyticus strains isolated from Whiteleg shrimp, Litopenaeus vannamei (Boone, 1931) in India

Vibrio parahaemolyticus is a gram-negative halophilic bacterium responsible for gastrointestinal infection in human and vibriosis in aquatic animals. The thermostable direct hemolysin (tdh), tdh-related hemolysin (trh) and thermolabile hemolysin (tlh) positive strains of V. parahaemolyticus were identified from brackishwater aquaculture farms of West Bengal and Andhra Pradesh, India. Moreover, the presence of other virulent genes like vcrD1, vopD, vp1680 under type three secretion system 1 (T3SS1) and vcrD2 vopD2, vopB2, vopC2 under type three secretion system 2 (T3SS2) were detected in tdh positive strain of V. parahaemolyticus. Furthermore, the study revealed that the tdh and trh positive isolates were resistant to β-lactam antibiotics and were able to lyse more than 95% of human Red Blood Cells (RBCs). In addition, both the isolates showed high cytotoxicity in Human Embryonic Kidney (HEK) cell line compared to tlh positive strain. Additionally, intraperitoneal and oral administration of tdh and trh positive strain of V. parahaemolyticus in Indian Major Carp, Labeo rohita caused 100% mortality at the level of 2.0 × 10⁸ CFU ml^-1 and 1.6 × 10⁸ CFU ml^-1, respectively. In contrast, only 10% mortality was observed in the case of tlh positive strain at the level of 2.5× 10⁸ CFU ml^-1. The histopathological changes like infiltration of blood cells and degenerated hepatic tissue in the liver of L. rohita were observed after the experimental challenge. The changes like degeneration of glomeruli, necrosis of renal tubules and Bowman's capsule were observed in the kidney section. Ragged, irregular shaped villi and necrosis of the villus were observed in the intestinal lumen. Overall, the study demonstrates that isolated V. parahaemolyticus is a potent aquatic microbial pathogen. Additionally, as V. parahaemolyticus is also a human pathogen and might pose a threat to the human population, proper management strategies are required to prevent the possible occurrence of disease.

The complete mitochondrial genome sequence of Osteobrama belangeri (Cyprinidae) and its comparison with other related Cypriniformes fish species

The complete mitogenome of Osteobrama belangeri is described using Ion Torrent (PGM sequencer), which was 16,609 bp in size comprising 13 mRNAs, teo rRNA genes, 22 tRNAs, and 926 bp as D-Loop control region, in addition to gene order and organization, being similar to most of the other related Cypriniformes fish mitogenome of NCBI databases. The all 22 tRNAs were packed into a typical clover-leaf structure. In the present study, the mitogenome has 99% similarity to the complete mitogenome sequence of O. belangeri mitogenome details previously and also would be helpful in understanding the phylogenetics, population genetics, and evolution of family Cyprinidae fishes.

Genetic diversity and multiple antibiotic resistance index study of bacterial pathogen, Klebsiella pneumoniae strains isolated from diseased Indian major carps

Intensive fish farming systems have led to increase in disease incidence, due to higher stocking density, high organic matter levels, and poor quality of the aquatic environment. Diseased fish samples showing hemorrhages and reddish lesions were collected from different freshwater fish farms located at three different districts of West Bengal, India (Burdwan, North 24 Parganas, and Nadia). The present study was conducted to evaluate the genetic diversity of ten different Klebsiella pneumoniae strains isolated from different infected freshwater fish samples based on 16S rRNA gene sequence analysis. Primarily, Klebsiella-specific media was used for the isolation and characterization of Klebsiella pneumoniae. Further, through a biochemical test, all the strains were confirmed as K. pneumoniae. PCR analysis of 16S-23S internal transcribed spacer (PCR ribotyping) was carried out to study the species variation within different Klebsiella pneumoniae isolates. For all the isolates, a conserved PCR ribotype pattern was observed while differing from other bacterial species. Phylogenetic study showed the high degree of homology with diverse source of other strains. The multiple antibiotic resistance (MAR) values of the present study for the isolates were found to be 0.468. MAR value above 0.2 indicates that the source of isolation was highly contaminated with antibiotics. Based on the 16S rRNA gene sequence analysis, the present study revealed the genetic diversity of Klebsiella pneumoniae isolated from the different diseased fish farms of West Bengal. All the strains were found to be hypermucoviscous and multidrug-resistant, thus making it pathogenic towards the host organisms. Further, the study revealed a high prevalence of K. pneumoniae in aquaculture farms, representing a risk towards successful aquaculture.

Computational characterization and molecular dynamics simulation of the thermostable direct hemolysin-related hemolysin (TRH) amplified from Vibrio parahaemolyticus

Vibrio parahaemolyticus is a major seafood-borne pathogen that causes life-threatening gastroenteric diseases in humans through the consumption of contaminated seafoods. V. parahaemolyticus produces different kinds of toxins, including thermostable direct hemolysin (TDH), TDH-related hemolysin (TRH), and some effector proteins belonging to the Type 3 Secretion System, out of which TDH and TRH are considered to be the major factors for virulence. Although TRH is one of the major virulent proteins, there is a dearth of understanding about the structural and functional properties of this protein. This study therefore aimed to amplify the full length trh gene from V. parahaemolyticus and perform sequence-based analyses, followed by structural and functional analyses of the TRH protein using different bioinformatics tools. The TRH protein shares significant conservedness with the TDH protein. A multiple sequence alignment of TRH proteins from Vibrio and non-Vibrio species revealed that the TRH protein is highly conserved throughout evolution. The three dimensional (3D) structure of the TRH protein was constructed by comparative modelling and the quality of the predicted model was verified. Molecular dynamics simulations were performed to understand the dynamics, residual fluctuations, and the compactness of the protein. The structure of TRH was found to contain 19 pockets, of which one (pocket ID: 2) was predicted to be important from the view of drug design. Eleven residues (E138, Y140, C151, F158, C161, K162, S163, and Q164), which are reported to actively participate in the formation of the tetrameric structure, were present in this pocket. This study extends our understanding of the structural and functional dynamics of the TRH protein and as well as provides new insights for the treatment and prevention of V. parahaemolyticus infections.

Population structure and genetic diversity of Indian Major Carp, Labeo rohita (Hamilton, 1822) from three phylo-geographically isolated riverine ecosystems of India as revealed by mtDNA cytochrome b region sequences

The population structure and genetic diversity of Rohu (Labeo rohita Hamilton, 1822) was studied by analysis of the partial sequences of mitochondrial DNA cytochrome b region. We examined 133 samples collected from six locations in three geographically isolated rivers of India. Analysis of 11 haplotypes showed low haplotype diversity (0.00150), nucleotide diversity (π) (0.02884) and low heterogeneity value (0.00374). Analysis of molecular variance (AMOVA) revealed the genetic diversity of L. rohita within population is very high than between the populations. The Fst scores (-0.07479 to 0.07022) were the indication of low genetic structure of L. rohita populations of three rivers of India. Conspicuously, Farakka-Bharuch population pair Fst score of 0.0000, although the sampling sites are from different rivers. The phylogenetic reconstruction of unique haplotypes revealed sharing of a single central haplotype (Hap_1) by all the six populations with a point mutations ranging from 1-25 nucleotides.

Population genetic structure of Indian shad, Tenualosa ilisha inferred from variation in mitochondrial DNA sequences

Indian shad, Tenualosa ilisha, is a commercially important anadromous fish representing major catch in Indo-pacific region. The present study evaluated partial Cytochrome b (Cyt b) gene sequence of mtDNA in T. ilisha for determining genetic variation from Bay of Bengal and Arabian Sea origins. The genomic DNA extracted from T. ilisha samples representing two distant rivers in the Indian subcontinent, the Bhagirathi (lower stretch of Ganges) and the Tapi was analyzed. Sequencing of 307 bp mtDNA Cytochrome b gene fragment revealed the presence of 5 haplotypes, with high haplotype diversity (Hd) of 0.9048 with variance 0.103 and low nucleotide diversity (π) of 0.14301. Three population specific haplotypes were observed in river Ganga and two haplotypes in river Tapi. Neighbour-joining tree based on Cytochrome b gene sequences of T. ilisha showed that population from Bay of Bengal and Arabian Sea origins belonged to two distinct clusters.

Chromosome-specific physical localisation of expressed sequence tag loci in Corchorus olitorius L

Jute (Corchorus spp.), as a natural fibre-producing species, ranks next only to cotton. Inadequate understanding of its genetic architecture is a major lacuna for genetic improvement of this crop in terms of yield and quality. Establishment of a physical map provides a genomic tool that helps in positional cloning of valuable genes. In this report, an attempt was initiated to study association and localisation of single copy expressed sequence tag (EST) loci in the genome of Corchorus olitorius. The chromosome-specific association of EST was determined based on the appearance of an extra signal for a single copy cDNA probe in mitotic interphase nuclei of specific trisomic(s) for fluorescence in situ hybridisation, and validated using a cDNA fragment of the 26S rRNA gene (600 bp) as molecular probe. The probe exhibited three signals in meiotic interphase nuclei of trisomic 5, instead of two as observed in diploids and other trisomics, indicating its association with chromosome 5. Subsequent hybridisation of the same probe on the pachytene chromosomes of diploids confirmed that 26S rRNA occupies the terminal end of the short arm of chromosome 5 in C. olitorius. Subsequently, chromosome-specific association of 63 single copy EST and their physical localisation were determined on chromosomes 2, 4, 5 and 7. The study describes chromosome-specific physical localisation of genes in jute. The approach used here could be a step towards construction of genome-wide physical maps for any recalcitrant plant species like jute.

Desynapsis and spontaneous trisomy in jute (Corchorus olitorius L.)

Cytological studies in desynaptic plants, isolated at the F6 generation of an intervarietal cross of Corchorus olitorius L., have shown variable numbers of bivalents and univalents in the PMC's at metaphase I, resulting in irregular distribution of chromosomes at anaphase I. The progenies of the desynaptic plants consisted of 9.24 percent of all possible primary trisomies except trisomie 6. The desynaptic condition is controlled by a pair of simple recessive genes.

Quantitative studies on the mating system of jute (Corchorus capsularis L.)

Nearly 35,000 individuals of C. capsularis were scored for selfing versus outcrossing in various populations. Different marker loci, such as anthocyanin pigmentation (C/c), serrated leaf (Sr/sr) and fasciated stem (Fs/fs), were used to determine the male gametes which had effected fertilization. The estimates of the outcrossing parameter, α were found to differ with years, locations and for the marker locus used in the estimation. The outcrossing for C/c was lowest, the outcrossing for Fs/fs was highest and that for Sr/sr was intermediate. The nature of outcrossing, in general, was nonrandom. Selfing predominated in this species.