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A K Singh

Publications and source records attributed to A K Singh.

At least 19 recordsLinked to original sources
PubMed2025

Development and validation of a high-density 'Amahysnp' genotyping array in grain amaranth (Amaranthus hypochondriacus).

BACKGROUND: Grain amaranth has recently gained global attention as a promising crop alternative to traditional cereals due to its nutritional value and adaptability to various growing conditions. Although gene banks conserve extensive collections of amaranth germplasm, the genomic and phenotypic characterization of these resources is limited, which hinders their full utilization in breeding programs. A major challenge is the lack of high-throughput genotyping assays essential for comprehensive genomic characterization and trait mapping. High-density SNP arrays have become standard tools for genome-wide analysis across multiple loci, enabling molecular breeding across a range of crop species. RESULTS: In this study, we developed a 64 K high-throughput SNP genotyping array named "AmahySNP", using Affymetrix® Axiom® technology. The array contains 64,069 high-density SNPs distributed across both genic (55.17%) and non-genic (44.83%) regions of the Amaranthus hypochondriacus genome. The genic region includes 8,879 genes, which consist of 4,830 single-copy genes and 4,049 multi-copy genes distributed across 16 scaffolds. These genes cover various functional regions, including exons (10.5%), introns (40.1%), 5'UTRs (1.6%), and 3'UTRs (2.9%), respectively. The AmahySNP array was effectively utilized for population structure analysis, genetic diversity studies, core development, and genome wide association studies (GWAS) in amaranth germplasm. A representative core set of 112 accessions was identified, which includes two released varieties (Annapurna and Suvarna) and 100 diverse accessions from 12 different regions, representing 12% of the total 917 accessions evaluated. Phylogenetic analysis revealed three major genetic clusters, independent of their geographical origins. GWAS conducted using 22,763 polymorphic SNPs from 540 genotypes identified 13 novel loci associated days to flowering (DTF) trait, seven of which were located within annotated genes. CONCLUSIONS: The AmahySNP 64 K SNP chip a valuable genomic tool for amaranth research and breeding with a strong potential to accelerate its genetic improvement. It enables high-throughput genotyping for a wide range of applications, including GWAS and other genomic studies, and will significantly advance the exploration of natural genetic variations. Ultimately, this resource will empower amaranth breeders to develop improved amaranth cultivars with enhanced crop yield, resilience, and nutritional quality, contributing to global food security and sustainable agriculture.

Amaranthus↗
PubMed2006

Coat protein gene diversity among Chrysanthemum virus B isolates from India.

The complete coat protein (CP) sequences from 29 Indian isolates of Chrysanthemum virus B (CVB) were determined and analysed in relation to other previously characterized carlaviruses. The CP genes of the Indian CVB isolates were highly heterogeneous, sharing nucleotide sequence identities of 74-98%. Based on phylogenetic analyses, the isolates formed three groups potentially representing either two or three major CVB strain groupings. Recombination analysis revealed at least one definite recombination event involving the exchange of sequences between members of different groups. To our knowledge this is the first reported evidence of homologous recombination in carlaviruses.

Amino Acid Sequence↗
PubMed2006

Proteomic analyses of murine macrophages treated with Bacillus anthracis lethal toxin.

Bacillus anthracis is the etiological agent of anthrax and the bacterium produces a tripartite anthrax toxin composed of protective antigen (PA), lethal factor (LF) and edema factor (EF). PA represents the binding domain of the toxin and acts in concert with either LF, a metalloprotease, or EF, an adenylate cyclase, to form lethal toxin (LeTx) or edema toxin (EdTx), respectively. We analyzed the proteomics response of two murine macrophage cell lines (J774.1A and RAW264.7) following B. anthracis LeTx treatment to detect unique host proteins involved in anthrax infection using difference in-gel electrophoresis (DIGE) followed by nanoLC-MS for identification of the proteins. The comparative proteomics approach identified a set of proteins in each cell line that was consistently upregulated when the two macrophage cell lines were treated with LeTx. The upregulated proteins include those involved in energy metabolism, cytoskeleton structure and stress response. A subset of five proteins (ATP synthase beta subunit, beta-actin, Hsp70, vimentin, and Hsp60 homolog) was identified that were commonly upregulated in both cell lines. The proteomic data suggest the involvement of reactive oxygen species (ROS) in cell lysis as seen by the upregulation of proteins that lead to the production of ROS in both the cell lines used in our study. However, proteins that afford protection against ROS may play an important role in the survival of the macrophage to LeTx infection as shown by the differences in proteomic responses of the two cell lines to the action of LeTx. These identified proteins may have the potential to be used as biomarkers for diagnostics and therapeutics.

Animals↗
PubMed2006

Vibrational assignment of the normal modes of 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one via FTIR and Raman spectra, and ab inito calculations.

Raman and FTIR spectra of 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one were recorded in the regions, 100-3300 and 400-4000 cm(-1), respectively. Vibrational frequencies and intensities of the fundamental modes of this hetrocyclic organic molecule were computed using ab initio as well as AM1 semiempirical molecular orbital methods. Ab initio calculations were carried out with basis set up to RHF/6-311G. Conformational studies regarding the effect of moving the methoxy group in the 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one molecule to a different position on the ring was also carried out. Observed vibrational wavenumbers were found to be mostly consistent with ab initio values. The most intense mode of vibration observed at 1250 cm(-1) in Raman spectra, also observed as a strong band in FTIR, was assigned as C-O stretching vibration in the methoxy group. Asymmetric stretching vibrations between CC and CN bonds was predicted as most intense mode by our ab initio calculation.

Benzylidene Compounds↗
PubMed2006

Investigations of the possible pharmacological effects of organotin(II) complexes.

Antitumour, antifertility and histopathological investigations were carried out on male rats by the use of organotin complexes. The organotin complexes were synthesized by the alkylation of [Sn(TAML(n))Cl(2)] (n=1-4 and TAML(n) represents the tetraazamacrocyclic ligands) in the presence of CH(3)I or C(2)H(5)Br. The structures of all the complexes have been established on the basis of elemental analyses, conductivity measurements, IR, (1)H NMR, (13)C NMR, (119)Sn NMR and X-ray spectral data. The antitumour effect of the compounds was examined on swiss mice. The results obtained clearly indicated that the compounds, [C(2)H(5)Sn(TAML(3))C(5)H(5)N] and [C(2)H(5)Sn(TAML(4))C(5)H(5)N] display effective antitumour activity. The emphasis has been given on in vivo study on male albino rats (Rattus norvegicus) by performing serum analyses, blood analyses and fertility test.

Animals↗
PubMed2006

Dynamics of organic carbon and microbial biomass in alluvial soil with tillage and amendments in rice-wheat systems.

Rice-wheat cropping systems of the Indo-Gangetic plains (IGP) occupying 12 million ha of productive land are important for the food security of South Asia. There are, however, concerns that yield and factor productivity trends in these systems are declining/stagnating in recent years. Decrease in soil organic carbon is often suggested as a reason for such trends. A field experiment was conducted to study the soil organic carbon (SOC) and soil microbial biomass carbon (MBC) dynamics in the rice-wheat systems. Use of organic amendments and puddling of soil before rice transplanting increased SOC and MBC contents. Microbial biomass carbon showed a seasonal pattern. It was low initially, reached its peak during the flowering stages in both rice and wheat and declined thereafter. Microbial biomass carbon was linearly related to SOC in both rice and wheat indicating that SOC could be used as a proxy for MBC.

Biomass↗
PubMed2006

Process development for the removal and recovery of hazardous dye erythrosine from wastewater by waste materials-Bottom Ash and De-Oiled Soya as adsorbents.

Erythrosine is a water-soluble xanthene class of dye. It is widely used as colorant in foods, textiles, drugs and cosmetics. It is highly toxic, causes various types of allergies, thyroid activities, carcinogenicity, DNA damage behaviour, neurotoxicity and xenoestrogen nature in the humans and animals. The photochemical and biochemical degradation of the erythrosine is not recommended due to formation of toxic by-products. The present paper is an attempt to remove erythrosine from wastewater using adsorption over Bottom Ash-a power plant waste and De-Oiled Soya-an agricultural waste. Under the batch studies, effect of concentration of dye, temperature, pH of the solution, dosage of adsorbents, sieve size of adsorbents, etc., have been studied for the uptake of the dye over both adsorbents. The adsorption process verifies Langmuir and Freundlich adsorption isotherms in both the cases and based on the data different thermodynamic parameters have been evaluated. Batch studies also include kinetic measurements, rate constant study, mass transfer behaviour and establishment of mechanistic pathway for both the cases. For the bulk removal of the dye column operations have been carried out and breakthrough capacities of the Bottom Ash and De-Oiled Soya columns have been calculated. Attempts have also been made for the recovery of the adsorbed dye from exhausted columns by eluting dilute NaOH and more than 90% of the dye was recovered.

Adsorption↗
PubMed2006

Krabbe disease: psychosine-mediated activation of phospholipase A2 in oligodendrocyte cell death.

Globoid cell leukodystrophy (Krabbe disease) is an inherited neurological disorder caused by the pathogenomic accumulation of psychosine (galactosylsphingosine), a substrate for the deficient enzyme galactocerebroside beta-galactosidase. This study underscores the mechanism of action of psychosine in the regulation of oligodendrocyte cell death via the generation of lysophosphatidylcholine (LPC) and arachidonic acid (AA) by the activation of secretory phospholipase A2 (sPLA2). There was a significant increase in the level of LPC, indicating a phospholipase A2 (PLA2)-dependent pathobiology, in the brains of Krabbe disease patients and those of twitcher mice, an animal model of Krabbe disease. In vitro studies of the treatment of primary oligodendrocytes and the oligodendrocyte MO3.13 cell line with psychosine also showed the generation of LPC and the release of AA in a dose- and time-dependent manner, indicating psychosine-induced activation of PLA2. Studies with various pharmacological inhibitors of cytosolic phospholipase A2 and sPLA2 and psychosine-mediated induction of sPLA2 enzymatic activity in media supernatant suggest that psychosine-induced release of AA and generation of LPC is mainly contributed by sPLA2. An inhibitor of sPLA2, 7,7-dimethyl eicosadienoic acid, completely attenuated the psychosine-mediated accumulation of LPC levels, release of AA, and generation of reactive oxygen species, and blocked oligodendroyte cell death, as evident from cell survival, DNA fragmentation, and caspase 3 activity assays. This study documents for the first time that psychosine-induced cell death is mediated via the sPLA2 signaling pathway and that inhibitors of sPLA2 may hold a therapeutic potential for protection against oligodendrocyte cell death and resulting demyelination in Krabbe disease.

Animals↗
PubMed2006

Omental infarct: CT imaging features.

BACKGROUND: The aim of this study is to describe contrast-enhanced computed tomographic (CT) features of acute omental infarction and to study the evolutionary changes on follow-up CT imaging. METHODS: Fifteen cases of omental infarction were evaluated for their initial CT imaging features. The imaging features evaluated included size of the fatty lesion, location, peripheral rim, and relation to colon. CT findings were correlated with etiology, clinical presentation, and leukocytosis. Follow-up CT images were available in eight patients and the imaging features were studied. RESULTS: Eight omental infarcts were of unknown etiology and seven were secondary to abdominal surgery. In 53% of patients (eight of 15), the location of the omental infarct was in the right lower, mid, or upper quadrants. These eight right-side infarcts occurred in six patients with primary omental infarcts. In 13 of 14 patients who underwent CT within 15 days of onset of omental infarct, the margin of the lesion was ill defined. Primary omental (n = 8) infarcts were seen in younger patients (p = 0.02) and were larger on CT (p = 0.02) compared with secondary omental infarcts. CT findings evolved from an ill-defined, heterogeneous fat-density lesion to a well-defined, heterogeneous fat-density lesion with a peripheral hyperdense rim in all six secondary omental infarctions for which acute stage and follow-up CT images were available for interpretation. CONCLUSION: There is a significant difference in the age distribution and CT findings in terms of size of the omental infarction between primary and secondary etiologies. On follow-up CT, secondary omental infarcts progressively shrank and developed a well-defined, hyperdense rim around a fatty core.

Abdomen, Acute↗
PubMed2006

Rho/ROCK pathway as a target of tumor therapy.

This study emphasizes the importance of Rho/ROCK pathway in lovastatin-induced apoptosis as replenishment with exogenous isoprenoid, geranylgeranylpyrophosphate (GGPP), resulted in inhibition of apoptosis in cultured tumor cells. Treatment of C6 glioma cells with Toxin B and exoenzyme C3 resulted in cell death suggesting the role of geranylgeranylated protein(s) in the survival of glioma cells. Relative apoptotic death observed in cells transfected with dominant negative constructs of RhoA, Rac, and cdc42 imply Rho A as playing the major role in cell survival. Furthermore, the inhibition of Rho A kinase (ROCK), a direct downstream effector of Rho A, by Y-27632 or dominant negative of ROCK, induced apoptosis in glioma cells. These findings indicate that RhoA/ROCK pathway is involved negatively in the regulation of glioma cell death pathway. Moreover, in vivo studies of lovastatin treatment in animals implanted with C6 glioma cell tumors also resulted in smaller tumor size and induced apoptosis in the tumor tissue. The implantation of stably transfected C6 glioma cells with expression vector of C3 exoenzyme, dominant negative of RhoA and ROCK, resulted in significant smaller tumor mass, further establishing the importance of geranylgeranylated proteins, specifically RhoA and its downstream effecter ROCK, in cell survival and tumor genesis.

Amides↗
PubMed2006

Evaluation of proteinuria in healthy living kidney donor candidates.

BACKGROUND: Evaluation of living kidney donor candidates includes careful assessment for the presence or absence of kidney disease. Kidney donation has been considered to be at least relatively contraindicated if urinary total protein excretion is above the normal range. However, at the present time, there is no uniformly accepted level of urine total protein excretion that would exclude donation. Albumin excretion instead of total protein excretion as a criterion has not previously been evaluated. MATERIALS AND METHODS: This was a prospective observational study over a 3-year period in a single tertiary care center designed to assess current selection criteria for kidney donation with respect to urine total protein and albumin excretion. RESULTS: Twenty four percent (25 of 105) of healthy adult kidney donor candidates had elevated urinary total protein excretion rates (150 to 292 mg/24 h). Of these 105 candidates, 39 had simultaneous measurements of both urinary total protein and albumin. Although one-third (13/39) had elevated 24-hour urine total protein values, none had elevated urine albumin excretion. CONCLUSION: Measurement of albumin, the most common single protein found in urine, appears to be helpful in the evaluation of proteinuria in donor candidates. Many healthy adult kidney donor candidates have mildly elevated total protein excretion but normal albumin excretion. We believe that such patients should not be excluded from donation.

Adult↗
PubMed2006

Beware! Fungal urosepsis may follow endoscopic intervention for prolonged indwelling ureteral stent.

We present a 38-year-old lady with a prolonged indwelling ureteral stent that had been placed for pain relief after development of Steinstrasse following extracorporeal lithotripsy for a 2.5-cm left renal calculus. The patient developed candidal urosepsis within 6 hours after ureteroscopy and percutaneous nephrolithotomy (PCNL) for the removal of residual fragments. She subsequently recovered on systemic antifungal therapy in the form of intravenous amphotericin B and achieved complete stone clearance after repeat ureteroscopy and PCNL. Fungal urosepsis is known to complicate the postoperative course in chronically debilitated patients with poor nutritional status or those with diabetes or other significant comorbities. To our knowledge, this is the first reported case of a patient with no significant comorbities developing fungal urosepsis after endoscopic intervention for a long-term indwelling ureteral stent.

Adult↗
PubMed2006

Dynamic, equilibrium and human studies of adsorption of 201Tl by Prussian blue.

Prussian blue is the recommended but infrequently required antidote for radiocesium and thallium chemical poisoning. Conceivably, its most frequent application will be the decontamination of radiothallium (thallous chloride) from human body following myocardial scintigraphy. Dosage schedule and physicochemical parameters of interaction with radiothallium, however, need to be defined, as the known data is inadequate on this account. The objective of the present study is to create physiologically relevant and mathematically rigorous data on interaction of Prussian blue with Tl, to estimate dosage schedule of Prussian blue suitable for myocardial scintigraphy, and to perform preliminary human studies to evaluate the efficacy of the antidote in reducing the considerable radiation burden imparted by this radiotracer. Adsorption efficacy of Prussian blue for radiothallium was found to be more than 95% at basic (intestinal) pH even at low concentrations and in presence of the physiological cations, potassium and sodium. Isotherm analysis and derivations using Langmuir, Bajpai, Lagergreen, and Freundlich equations suggest a favorable adsorption of Tl on Prussian blue with qmax being 5,000 MBq g. Based on these findings and clinical considerations, particularly preferential gall bladder excretion and enterohepatic recycling of radioactive thallous chloride, a dose of 100 mg Prussian blue with every major meal for 3 days was considered adequate for the purpose. Our experience with the first two patients (serving as their own self-controls) suggests that Prussian blue therapy is a safe and effective method to significantly reduce radiation burden imparted by thallium myocardial scintigraphy.

Adsorption↗
PubMed2006

Allergenicity assessment of transgenic mustard (Brassica juncea) expressing bacterial codA gene.

BACKGROUND: Assessing the allergenicity and toxicity of genetically modified (GM) crops is essential before they become a regular part of our food supply. The present study aimed to assess the allergenicity of Brassica juncea (mustard) expressing choline oxidase (codA) gene from Arthrobacter globiformis that provides resistance against abiotic stresses. METHODS: SDAP, Farrp, and Swiss-Prot databases were used to study allergenicity of choline oxidase. Digestibility of choline oxidase was assessed in simulated gastric fluid (SGF). Specific immunoglobulin E (IgE) reactivity of native and GM mustard was compared by using enzyme-linked immunosorbent assay (ELISA) and skin tests in respiratory-allergic patients. Allergenicity of GM and native mustard proteins was compared in Balb/c mice. RESULTS: Choline oxidase showed no significant homology with allergenic proteins in SDAP and Farrp databases. Cross-reactive epitope search showed a stretch similar to Hev b 6 having some antigenic properties. Purified choline oxidase showed complete degradation with SGF. Skin prick test of native and GM mustard extract on respiratory allergic patients showed significant correlation (P < 0.05). ELISA with 96 patients' sera showed comparable IgE reactivity. Balb/c mice immunized with native and GM mustard proteins showed low IgE response. Presensitized mice on intravenous challenge with Brassica extract showed no anaphylactic symptoms unlike ovalbumin (OVA) sensitization that showed anaphylactic reaction in mice. Lung histology of OVA-sensitized mice showed narrowing of airway and large eosinophilic infiltration, whereas native and GM Brassica extract showed normal airway. CONCLUSION: Genetically modified mustard with the codA gene possessed allergenicity similar to that of native mustard and no enhancement of IgE binding was observed due to genetic manipulation.

Adolescent↗