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result(s) for
"Kumar, Vikash"
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Acute Hepatopancreatic Necrosis Disease (AHPND): Virulence, Pathogenesis and Mitigation Strategies in Shrimp Aquaculture
2021
Shrimp, as a high-protein animal food commodity, are one of the fastest growing food producing sectors in the world. It has emerged as a highly traded seafood product, currently exceeding 8 MT of high value. However, disease outbreaks, which are considered as the primary cause of production loss in shrimp farming, have moved to the forefront in recent years and brought socio-economic and environmental unsustainability to the shrimp aquaculture industry. Acute hepatopancreatic necrosis disease (AHPND), caused by Vibrio spp., is a relatively new farmed penaeid shrimp bacterial disease. The shrimp production in AHPND affected regions has dropped to ~60%, and the disease has caused a global loss of USD 43 billion to the shrimp farming industry. The conventional approaches, such as antibiotics and disinfectants, often applied for the mitigation or cure of AHPND, have had limited success. Additionally, their usage has been associated with alteration of host gut microbiota and immunity and development of antibiotic resistance in bacterial pathogens. For example, the Mexico AHPND-causing V. parahaemolyticus strain (13-306D/4 and 13-511/A1) were reported to carry tetB gene coding for tetracycline resistance gene, and V. campbellii from China was found to carry multiple antibiotic resistance genes. As a consequence, there is an urgent need to thoroughly understand the virulence mechanism of AHPND-causing Vibrio spp. and develop novel management strategies to control AHPND in shrimp aquaculture, that will be crucially important to ensure food security in the future and offer economic stability to farmers. In this review, the most important findings of AHPND are highlighted, discussed and put in perspective, and some directions for future research are presented.
Journal Article
Identification of lead molecules against potential drug target protein MAPK4 from L. donovani: An in-silico approach using docking, molecular dynamics and binding free energy calculation
by
Dubey, Vikash Kumar
,
Saudagar, Prakash
,
Sasidharan, Santanu
in
Amino Acid Sequence - genetics
,
Amino acids
,
Angiogenesis inhibitors
2019
Leishmaniasis caused by obligate intracellular parasites of genus Leishmania is one of the most neglected tropical diseases threatening 350 million people worldwide. Protein kinases have drawn much attention as potential drug targets due to their important role in various cellular processes. In Leishmania sp. mitogen-activated protein kinase 4 is essential for the parasite survival because of its involvement in various regulatory, apoptotic and developmental pathways. The current study reveals the identification of natural inhibitors of L. donovani mitogen-activated protein kinase-4 (LdMPK4). We have performed in silico docking of 110 natural inhibitors of Leishmania parasite that have been reported earlier and identified two compounds Genistein (GEN) and Chrysin (CHY). The homology model of LdMPK4 was developed, followed by binding affinity studies, and pharmacokinetic properties of the inhibitors were calculated by maintaining ATP as a standard molecule. The modelled structure was deposited in the protein model database with PMDB ID: PM0080988. Molecular dynamic simulation of the enzyme-inhibitor complex along with the free energy calculations over 50 ns showed that GEN and CHY are more stable in their binding. These two molecules, GEN and CHY, can be considered as lead molecules for targeting LdMPK4 enzyme and could emerge as potential LdMPK4 inhibitors.
Journal Article
Disability and its sociodemographic correlates among older people in Nepal: evidence from the 2022 Nepal Demographic Health Survey
by
Subedi, Govind
,
Thapa, Naba Raj
,
KC, Vikash Kumar
in
Activities of daily living
,
Aged
,
Aged, 80 and over
2025
Background
Older people are more vulnerable and have a higher risk of having a disability. There are very few studies on disability among older people in Nepal. To fill this knowledge and research gap, this study examines the prevalence and analyzes sociodemographic correlates of disability among older people in Nepal.
Methods
The 2022 Nepal Demographic and Health Survey data was used for this study. The study included 3014 older people aged 60 years and above. The Washington Group Short Set Questions were used to measure disability. Disability was categorized as ‘with disability’ and ‘without disability’. Descriptive statistics were used to assess the prevalence of disability while multivariate logistic regression was used as inferential statistics to analyze sociodemographic correlates of disability.
Results
The results show that more than a quarter (27%) of older people had disabilities. The prevalence of disability was higher among older people aged 80 years and above (54%), females (31%), no education (31%), widowed (40%), residing in Karnali province (39%), and those who belonged to poor household wealth (31%). This pattern was consistent in both older males and females. Older people aged 70–79 or 80 years and above, those who had no education or primary education and who were widowed, were more likely to have a disability. Older people from rich household wealth and from Koshi, Madhesh, Bagmati, Gandaki, Lumbini and Sudurpashchim provinces were less likely to have a disability.
Conclusions
The burden of disability among older people in Nepal is considerable. Therefore, there is a need for health interventions targeting the identified groups at risk of disability to improve the well-being of older people.
Journal Article
Heat Shock Proteins (Hsps) in Cellular Homeostasis: A Promising Tool for Health Management in Crustacean Aquaculture
2022
Heat shock proteins (Hsps) are a family of ubiquitously expressed stress proteins and extrinsic chaperones that are required for viability and cell growth in all living organisms. These proteins are highly conserved and produced in all cellular organisms when exposed to stress. Hsps play a significant role in protein synthesis and homeostasis, as well as in the maintenance of overall health in crustaceans against various internal and external environmental stresses. Recent reports have suggested that enhancing in vivo Hsp levels via non-lethal heat shock, exogenous Hsps, or plant-based compounds, could be a promising strategy used to develop protective immunity in crustaceans against both abiotic and biotic stresses. Hence, Hsps as the agent of being an immune booster and increasing disease resistance will present a significant advancement in reducing stressful conditions in the aquaculture system.
Journal Article
Dual-target drugs against Leishmania donovani for potential novel therapeutics
by
Sarma, Manash
,
Dubey, Vikash Kumar
,
Kanaujia, Shankar Prasad
in
631/114
,
631/154
,
Antioxidants
2023
Antioxidant defense mechanisms are important for a parasite to overcome oxidative stress and survive within host macrophage cells. Mitochondrial iron superoxide dismutase A (FeSODA) and trypanothione reductase (TR) are critical enzymes in the antioxidant defense mechanism of
Leishmania donovani
. FeSODA is responsible for neutralizing reactive oxygen species in mitochondria, while TR is responsible for reducing trypanothione, the molecules that help the parasite fight oxidative stress in Leishmania. In this study, we used multitarget ligands to inhibit both the FeSODA and TR enzymes. We combined structure-based drug design using virtual screening approach to find inhibitors against both the targets. The ZINC15 database of biogenic compounds was utilized to extract drugs-like molecules against leishmaniasis. The compounds were screened by standard precision (SP) and extra precision (XP) docking methods. Two compounds, ZINC000008876351 and ZINC000253403245, were selected based on molecular docking based on the binding affinity for both the targets. The screened molecules ZINC000008876351 and ZINC000253403245 showed strong hydrogen bonding with the target proteins according to the Molecular mechanics with generalised Born and surface area solvation (MM-GBSA) techniques. These two compounds were also experimentally investigated on promastigotes stage of
L. donovani
. Under in vitro condition, the compounds show inhibitory effects on
L. donovani
promastigotes with IC
50
values of 24.82 ± 0.61 µM for ZINC000008876351 and 7.52 ± 0.17 µM for ZINC000253403245. Thus, the screened compounds seem to have good potential as therapeutic candidates for leishmaniasis.
Journal Article
Ecytonucleospora hepatopenaei (EHP) disease prevalence and mortality in Litopenaeus vannamei: a comparative study from Eastern India shrimp farms
by
Kumar, Vikash
,
Parida, Satya Narayan
,
Das, Basanta Kumar
in
Animal models
,
Animals
,
Aquaculture
2024
Ecytonucleospora hepatopenaei
(EHP), a microsporidian parasite first named and characterized from the
Penaeus monodon
(black or giant tiger shrimp), causes growth retardation and poses a significant threat to shrimp farming. We observed shrimp farms associated with disease conditions during our fish disease surveillance and health management program in West Bengal, India. Shrimp exhibited growth retardation and increased size variability, particularly in advanced stages, exhibiting soft shells, lethargy, reduced feeding and empty midguts. Floating white feces were observed on the surface of the pond water. Suspecting a microbial infection, the shrimp samples were collected and aseptically brought to the ICAR-CIFRI laboratory for molecular confirmation. A nested PCR was used to screen shrimp tissue, feces, feed and environmental samples for the possible presence of hepatopancreatic microsporidiosis caused by
Ecytonucleospora hepatopenaei
. The results confirmed that the shrimp samples were positive for EHP. Histopathological investigation revealed mature spores in the HP tubule lumen and epithelial cells along with necrotic tubule in the symptomatic group. Further, the transcription analysis revealed that ProPO, Hsp70 and α2-macroglobulin genes were significantly upregulated, while decreased expression of LGBP, PXN and Integrin ß was observed in shrimp infected with Hepatopancreatic microsporidiosis. Furthermore, compared with the healthy group, significant intestinal bacteria changes were observed in the EHP-infected group. The in vivo survival assay, using crustacean animal model
Artemia franciscana
, suggests that symptomatic shrimp gut samples harbour pathogenic
Vibrio parahaemolyticus
,
V. harveyi
and
V. campbellii
. These results significantly advance our understanding of the molecular and ecological aspects of EHP pathobiology.
Journal Article
Accurate extraction of electrical parameters in three-diode photovoltaic systems through the enhanced mother tree methodology: A novel approach for parameter estimation
by
Loulijat, Azeddine
,
Makhad, Mohamed
,
El Ouanjli, Najib
in
Accuracy
,
Algorithms
,
Alternative energy
2025
Accurately simulating photovoltaic (PV) modules requires precise parameter extraction, a complex task due to the nonlinear nature of these systems. This study introduces the Mother Tree Optimization with Climate Change (MTO-CL) algorithm to address this challenge by enhancing parameter estimation for a solar PV three-diode model. MTO-CL improves optimization performance by incorporating climate change-inspired adaptations, which affect two key phases: elimination (refreshing 20% of suboptimal solutions) and distortion (slight adjustments to 80% of remaining solutions). This balance between exploration and exploitation allows the algorithm to dynamically and effectively identify optimal parameters. Compared to seven alternative methods, MTO-CL shows superior performance in parameter estimation for various solar modules, including ST40 and SM55, across different irradiances and temperatures. It achieves exceptionally low Root Mean Square Error (RMSE) values from 0.0025A to 0.0165A and Mean Squared Error (MSE) values between 6.2 × 10^−6 and 2.7 × 10^−4, while also significantly minimizing power errors, ranging from 22.86 mW to 239.40 mW. These results demonstrate MTO-CL’s effectiveness in improving the accuracy and reliability of PV system modeling, offering a robust tool for enhanced solar energy applications.
Journal Article
Phloroglucinol Treatment Induces Transgenerational Epigenetic Inherited Resistance Against Vibrio Infections and Thermal Stress in a Brine Shrimp (Artemia franciscana) Model
2019
Emerging, infectious diseases in shrimp like acute hepatopancreatic necrosis disease (AHPND) caused by
and mortality caused by other
species such as
are worldwide related to huge economic losses in industrial shrimp production. As a strategy to prevent disease outbreaks, a plant-based phenolic compound could be used as a biocontrol agent. Here, using the brine shrimp (
) as a model system, we showed that phloroglucinol treatment of the parental animals at early life stages resulted in transgenerational inherited increased resistance in their progeny against biotic stress, i.e., bacteria (
AHPND strain and
) and abiotic stress, i.e., lethal heat shock. Increased resistance was recorded in three subsequent generations. Innate immune-related gene expression profiles and potential epigenetic mechanisms were studied to discover the underlying protective mechanisms. Our results showed that phloroglucinol treatment of the brine shrimp parents significantly (
< 0.05) enhanced the expression of a core set of innate immune genes (
, and
) in subsequent generations. We also demonstrated that epigenetic mechanisms such as DNA methylation, m6A RNA methylation, and histone acetylation and methylation (active chromatin marker i.e., H3K4Me3, H3K4me1, H3K27me1, H3 hyperacetylation, H3K14ac and repression marker, i.e., H3K27me3, H4 hypoacetylation) might play a role in regulation of gene expression leading toward the observed transgenerational inheritance of the resistant brine shrimp progenies. To our knowledge, this is the first report on transgenerational inheritance of a compound-induced robust protected phenotype in brine shrimp, particularly protected against AHPND caused by
and vibriosis caused by
. Results showed that epigenetic reprogramming is likely to play a role in the underlying mechanism.
Journal Article
Comparative metagenomic analysis from Sundarbans ecosystems advances our understanding of microbial communities and their functional roles
by
Kumar, Vikash
,
Das, Basanta Kumar
,
Patra, Biswanath
in
631/326/171
,
631/326/2565
,
Alcaligenes
2024
The Sundarbans mangrove, located at the mouth of the Ganges and Brahmaputra Rivers, is the world’s largest tidal mangrove forest. These mangroves are also one of the most striking sources of microbial diversity, essential in productivity, conservation, nutrient cycling, and rehabilitation. Hence, the main objective of this study was to use metagenome analysis and provide detailed insight into microbial communities and their functional roles in the Sundarbans mangrove ecosystem. A comparative analysis was also done with a non-mangrove region of the Sundarbans ecosystem to assess the capability of the environmental parameters to explain the variation in microbial community composition. The study found several dominant bacteria, viz.,
Alphaproteobacteria
,
Actinomycetota
,
Bacilli
,
Clostridia
,
Desulfobacterota
,
Gammaproteobacteria
, and
Nitrospira,
from the mangrove region. The mangrove sampling site reports several salt-tolerant bacteria like
Alkalibacillus haloalkaliphilus
,
Halomonas anticariensis
, and
Salinivibrio socompensis
. We found some probiotic species, viz.,
Bacillus clausii, Lactobacillus curvatus, Vibrio mediterranei
and
Vibrio fluvialis,
from the Sundarbans mangrove. Nitrifying bacteria in Sundarbans soils were
Nitrococcus mobilis
,
Nitrosococcus oceani, Nitrosomonas halophila, Nitrospirade fluvii,
and others. Methanogenic archaea, viz.,
Methanoculleus marisnigri
,
Methanobrevibacter gottschalkii,
and
Methanolacinia petrolearia,
were highly abundant in the mangroves as compared to the non-mangrove soils. The identified methanotrophic bacterial species, viz.,
Methylobacter tundripaludum, Methylococcus capsulatus, Methylophaga thiooxydans,
and
Methylosarcina lacus
are expected to play a significant role in the degradation of methane in mangrove soil. Among the bioremediation bacterial species identified,
Pseudomonas alcaligenes
,
Pseudomonas mendocina
,
Paracoccus denitrificans,
and
Shewanella putrefaciens
play a significant role in the remediation of environmental pollution. Overall, our study shows for the first time that the Sundarbans, the largest mangrove ecosystem in the world, has a wide range of methanogenic archaea, methanotrophs, pathogenic, salt-tolerant, probiotic, nitrifying, and bioremediation bacteria.
Journal Article