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"Khan, Mohd"
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Mapping and Validation of the Major Sex-Determining Region in Nile Tilapia (Oreochromis niloticus L.) Using RAD Sequencing
Sex in Oreochromis niloticus (Nile tilapia) is principally determined by an XX/XY locus but other genetic and environmental factors also influence sex ratio. Restriction Associated DNA (RAD) sequencing was used in two families derived from crossing XY males with females from an isogenic clonal line, in order to identify Single Nucleotide Polymorphisms (SNPs) and map the sex-determining region(s). We constructed a linkage map with 3,802 SNPs, which corresponded to 3,280 informative markers, and identified a major sex-determining region on linkage group 1, explaining nearly 96% of the phenotypic variance. This sex-determining region was mapped in a 2 cM interval, corresponding to approximately 1.2 Mb in the O. niloticus draft genome. In order to validate this, a diverse family (4 families; 96 individuals in total) and population (40 broodstock individuals) test panel were genotyped for five of the SNPs showing the highest association with phenotypic sex. From the expanded data set, SNPs Oni23063 and Oni28137 showed the highest association, which persisted both in the case of family and population data. Across the entire dataset all females were found to be homozygous for these two SNPs. Males were heterozygous, with the exception of five individuals in the population and two in the family dataset. These fish possessed the homozygous genotype expected of females. Progeny sex ratios (over 95% females) from two of the males with the \"female\" genotype indicated that they were neomales (XX males). Sex reversal induced by elevated temperature during sexual differentiation also resulted in phenotypic males with the \"female\" genotype. This study narrows down the region containing the main sex-determining locus, and provides genetic markers tightly linked to this locus, with an association that persisted across the population. These markers will be of use in refining the production of genetically male O. niloticus for aquaculture.
Journal Article
CRISPR/Cas9-mediated knock-in of alligator cathelicidin gene in a non-coding region of channel catfish genome
CRISPR/Cas9-based gene knockout in animal cells, particularly in teleosts, has proven to be very efficient with regards to mutation rates, but the precise insertion of exogenous DNA or gene knock-in via the homology-directed repair (HDR) pathway has seldom been achieved outside of the model organisms. Here, we succeeded in integrating with high efficiency an exogenous alligator cathelicidin gene into a targeted non-coding region of channel catfish (
Ictalurus punctatus
) chromosome 1 using two different donor templates (synthesized linear dsDNA and cloned plasmid DNA constructs). We also tested two different promoters for driving the gene, zebrafish ubiquitin promoter and common carp β-actin promoter, harboring a 250-bp homologous region flanking both sides of the genomic target locus. Integration rates were found higher in dead fry than in live fingerlings, indicating either off-target effects or pleiotropic effects. Furthermore, low levels of mosaicism were detected in the tissues of P
1
individuals harboring the transgene, and high transgene expression was observed in the blood of some P
1
fish. This can be an indication of the localization of cathelicidin in neutrophils and macrophage granules as also observed in most antimicrobial peptides. This study marks the first use of CRISPR/Cas9 HDR for gene integration in channel catfish and may contribute to the generation of a more efficient system for precise gene integration in catfish and other aquaculture species, and the development of gene-edited, disease-resistant fish.
Journal Article
Microbiological Control of Xanthomonas Induced Bacterial Leaf Streak Disease of Wheat via Phytocompounds and ROS Processing Enzymes Produced Under Biotic Stress
Common wheat, consumed widely as a human food is severely affected by biotic stresses. The use of plant beneficial bacteria in the management of biotic stresses is increasing due to its abundance, low inoculant production cost and no environmental risks. This study assessed the impact of bacterial phytopathogen,
Xanthomonas
sp. on the performance of wheat including phytocompound production and evaluated the biocontrol potential of beneficial rhizobacteria against
Xanthomonas
induced bacterial leaf streak (BLS) disease. The rhizobacteria,
Azotobacter chroococcum
Beijerinck,
Bacillus megaterium,
and
Pseudomonas fluorescens
produced biocontrol related antimicrobial compounds (ammonia and hydrogen cyanide) and hydrolytic enzymes (cellulase and amylase).
In-planta
, infected plants had visible BLS symptoms which included yellowing of leaves and necrotic lesions etc. Upon foliar inoculation,
Xanthomonas
sp. adversely affected growth and significantly reduced dry biomass, plant length, total chlorophyll content and seed yield by 42%, 26%, 59%, and 16%, respectively, over uninfected control. The
Xanthomonas
infection significantly enhanced the secretion of non-enzymatic and enzymatic phytocompounds, proline, malondialdehyde and reactive oxygen species (ROS) processing enzymes, catalase, superoxide dismutase and glutathione reductase in BLS wheat. Scanning electron microscope (SEM) and confocal laser scanning microscope (CLSM) showed cellular damage in
Xanthomonas
infected leaf tissues. The bacterial inoculations profoundly enhanced the biological and physiological growth of stressed wheat plants but significantly declined the production of phytocompounds and the activity of the three ROS processing enzymes. These findings demonstrate that microbial antagonists,
A. chroococcum
,
B. megaterium,
and
P. fluorescens
, endowed with potential biocontrol activity provides a promising option for the long-term management of BLS disease, optimize wheat production and fulfil human food demands.
Journal Article
A DFT study of vibrational spectra of 5-chlorouracil with molecular structure, HOMO–LUMO, MEPs/ESPs and thermodynamic properties
The density functional theory calculation has been carried out for the analysis of 5-chlorouracil using DFT/Gaussian 09 with GAR2PED. Recorded experimental spectra for Raman and IR of 5-chlorouracil have been analyzed all fundamental vibrational modes using the outcome results of DFT at 6-311++G** of Gaussian 09 calculations and the GaussView 5.09. To help the analysis of vibrational modes, GAR2PED program has been used in the calculation of PEDs. The charge transfer properties of 5-chlorouracil have been analyzed using HOMO and LUMO level energy analysis. HOMO and LUMO energy gap study supports the charge transfer possibility in molecule. These have been made to study for reactivity and stability of
heterocyclic molecules
for the analysis of antiviral drugs against the new corona virus: COVID-19. Here, the
smaller energy gap
of 5-chlorouracil is more responsible for charge transfer interaction in the
heterocyclic drug molecules
and a reason of more bioactivity. The electron density mapping within molecular electrostatic potential plot and electrostatic potential plotting within iso-surface plot have been evaluated the charge distribution concept in the molecule as the nucleophilic reactions and electrophilic sites. These computations have been used to produce the molecular charges, structure and thermodynamic functions of biomolecule. This study has been made to all internal modes of chloro group substituent at pyrimidine ring of C
5
atom. The splitting of frequencies has arisen in the two species for the normal distribution modes.
Graphical abstract
Journal Article
Nutrient uptake under combined drought and salinity stress in hexaploid wheat species
Wheat is an important crop that often suffers from combined drought and salinity stress in agricultural fields, which adversely affects its growth, yield, and nutrient uptake. Understanding the response of genotypes to this combined stress is crucial to developing resilient cultivars. Nutrient uptake patterns in plants under stress not only reveal the physiological effects but also reflect their adaptive strategy and tolerance potential. Neglected and underutilized wheat species with high genetic diversity offer a valuable resource to explore different traits under combined stresses. Notably, no study has thoroughly assessed nutrient uptake in different hexaploid wheat species under combined drought and salinity stress. Thus, this study provides new insights into the individual and combined effects of drought and salinity stresses on nutrient uptake and accumulation of 30 hexaploid wheat genotypes of seven different species grown in a hydroponic system. The combined stress had a synergistic negative effect on nutrient accumulation in wheat genotypes as compared to single stresses. While species-based genetic variability was observed in individual stresses, a greater genotypic diversity was noticed under combined stress. A considerable genotypic variation ranging from 33.6% to 62.6% was observed in traits such as root-shoot phosphorus, manganese, zinc, as well as root copper, iron, and dry weight, while traits like shoot calcium, iron, potassium, and dry weight showed lower genotypic variation (8.3% to 25.8%). Among the studied genotypes, Tc4 (PI 164160, Kanak, India) was the best performing genotype across all three stress conditions, followed by Ta3 (CItr 17028, CAR 1101, Chile) and Tsh2 (PI 42013, India). The patterns of nutrient accumulation proposed that combined stress encompasses a complex interaction of multiple stress pathways. The results yielded valuable insights underscoring the significance of nutrient profiling as a critical component of breeding frameworks for climate-resilient wheat.
Journal Article
Dynamic linkages among energy consumption, urbanization and ecological footprint: empirical evidence from NARDL approach
PurposeThe primary purpose is to investigate the dynamic relationships among urbanization, energy use and environmental pollution in the context of India from 1971 to 2018. The paper also examines the validity of Environmental Kuznets Curve (EKC) hypothesis in the present Indian context.Design/methodology/approachThe study uses a nonlinear autoregressive distributed lag cointegration test (Shin et al., 2014) to investigate the dynamic relationship among the mentioned variables. The Wald test is also used to statistically check the presence of asymmetry. Additionally, the VECM test is applied to examine the causality among the variables.FindingsThis study documents that urbanization in India is good for environment in the long run, whereas energy consumption is bad for the environment. It also finds that positive and negative shocks of energy and urbanization exert asymmetric impacts on ecological footprint. Furthermore, the results could not validate the EKC hypothesis for India.Practical implicationsThe outcome of the study suggests designing an environmental policy which considers the nonlinearity of the investigated relationships and bearing in mind the use of comprehensive indicator like ecological footprint is equally important to address the wide-ranging problem of the environment. Policy reorientation towards the production and consumption of green energy, investment in research and development, and use of efficient technology is very crucial to achieve sustainable outcomes in the long run.Originality/valueIn this study, the researchers use the ‘ecological footprint’ variable to obtain a more accurate and comprehensive assessment of environmental deterioration. The mentioned dynamic relationships are investigated using an improved methodology of the NARDL model, which assumes the asymmetric impact of the explanatory variables on the response variable. The novelty of this study lies in examining the non-linear impact of urbanization and energy on ecological footprint which is inadequately addressed in the context of Indian economy.
Journal Article
Next-Generation Intelligent MXene-Based Electrochemical Aptasensors for Point-of-Care Cancer Diagnostics
HighlightsShed light on MXene-based electrochemical aptasensors for the detection of cancer biomarkers.Strategies for the design and synthesis of biomarker-specific aptamer are presented.The properties such as electrical conductivity, chemical stability, mechanical properties, and the hydrophilic–hydrophobic nature of MXenes are discussed.Brief insight on futuristic sensing applications along with challenges are highlighted.Delayed diagnosis of cancer using conventional diagnostic modalities needs to be addressed to reduce the mortality rate of cancer. Recently, 2D nanomaterial-enabled advanced biosensors have shown potential towards the early diagnosis of cancer. The high surface area, surface functional groups availability, and excellent electrical conductivity of MXene make it the 2D material of choice for the fabrication of advanced electrochemical biosensors for disease diagnostics. MXene-enabled electrochemical aptasensors have shown great promise for the detection of cancer biomarkers with a femtomolar limit of detection. Additionally, the stability, ease of synthesis, good reproducibility, and high specificity offered by MXene-enabled aptasensors hold promise to be the mainstream diagnostic approach. In this review, the design and fabrication of MXene-based electrochemical aptasensors for the detection of cancer biomarkers have been discussed. Besides, various synthetic processes and useful properties of MXenes which can be tuned and optimized easily and efficiently to fabricate sensitive biosensors have been elucidated. Further, futuristic sensing applications along with challenges will be deliberated herein.
Journal Article
High-performance visible light photodetectors based on inorganic CZT and InCZT single crystals
Herein, the optoelectrical investigation of cadmium zinc telluride (CZT) and indium (In) doped CZT (InCZT) single crystals-based photodetectors have been demonstrated. The grown crystals were configured into photodetector devices and recorded the current-voltage (
I-V
) and current-time (
I-t
) characteristics under different illumination intensities. It has been observed that the photocurrent generation mechanism in both photodetector devices is dominantly driven by a photogating effect. The CZT photodetector exhibits stable and reversible device performances to 632 nm light, including a promotable responsivity of 0.38 AW
−1
, a high photoswitch ratio of 152, specific detectivity of 6.30 × 10
11
Jones, and fast switching time (rise time of 210 ms and decay time of 150 ms). When doped with In, the responsivity of device increases to 0.50 AW
−1
, photoswitch ratio decrease to 10, specific detectivity decrease to 1.80 × 10
11
Jones, rise time decrease to 140 ms and decay time increase to 200 ms. Moreover, these devices show a very high external quantum efficiency of 200% for CZT and 250% for InCZT. These results demonstrate that the CZT based crystals have great potential for visible light photodetector applications.
Journal Article
Fungi for Sustainable Pharmaceutical Remediation: Enzymatic Innovations, Challenges, and Applications—A Review
The extensive use of pharmaceuticals in human and veterinary medicine has led to their persistent environmental release, posing ecological and public health risks. Major sources include manufacturing effluents, excretion, aquaculture, and improper disposal, contributing to bioaccumulation and ecotoxicity. Mycoremediation is the fungal-mediated biodegradation of pharmaceuticals, offers a promising and sustainable approach to mitigate pharmaceutical pollution. Studies have reported that certain fungal species, including Trametes versicolor and Pleurotus ostreatus, can degrade up to 90% of pharmaceutical contaminants, such as diclofenac, carbamazepine, and ibuprofen, within days to weeks, depending on environmental conditions. Fungi produce a range of extracellular enzymes, such as laccases and peroxidases, alongside intracellular enzymes like cytochrome P450 monooxygenases, which catalyze the transformation of complex pharmaceutical compounds. These enzymes play an essential role in modifying, detoxifying, and mineralizing xenobiotics, thereby reducing their environmental persistence and toxicity. The effectiveness of fungal biotransformation is influenced by factors such as substrate specificity, enzyme stability, and environmental conditions. Optimal degradation typically occurs at pH 4.5–6.0 and temperatures of 20–30 °C. Recent advancements in enzyme engineering, immobilization techniques, and bioreactor design have improved catalytic efficiency and process feasibility. However, scaling up fungal-based remediation systems for large-scale applications remains a challenge. Addressing these limitations with synthetic biology, metabolic engineering, and other biotechnological innovations could further enhance the enzymatic degradation of pharmaceuticals. This review highlights the enzymatic innovations, applications, and challenges of pharmaceutical mycoremediation, emphasizing the potential of fungi as a transformative solution for sustainable pharmaceutical waste management.
Journal Article