Browsing by Author "Singh P.P."
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Item Assessment of Trachyspermum ammi essential oil against Aspergillus flavus, aflatoxin B1 contamination, and post-harvest quality of Sorghum bicolor(Elsevier Ltd, 2024) Singh P.P.; Jaiswal A.K.; Singh R.; Kumar A.; Gupta V.; Raghuvanshi T.S.; Sharma A.; Prakash B.The present investigation explored the antifungal effectiveness of Trachyspermum ammi essential oil (TAEO) against Aspergillus flavus, aflatoxin B1 (AFB1) contamination, and its mechanism of action using biochemical and computational approaches. The GC�MS result revealed the chemical diversity of TAEO with the highest percentage of ?-terpinene (39 %). The TAEO exhibited minimum inhibitory concentration against A. flavus growth (0.5 �L/mL) and AFB1 (0.4 �L/mL) with radical scavenging activity (IC50 = 2.13 �L/mL). The mechanism of action of TAEO was associated with the alteration in plasma membrane functioning, antioxidative defense, and carbon source catabolism. The molecular dynamic result shows the multi-regime binding of ?-terpinene with the target proteins (Nor1, Omt1, and Vbs) of AFB1 biosynthesis. Furthermore, TAEO exhibited remarkable in-situ protection of Sorghum bicolor seed samples against A. flavus and AFB1 contamination and protected the nutritional deterioration. Hence, the study recommends TAEO as a natural antifungal agent for food protection against A. flavus mediated biodeterioration. � 2024 Elsevier LtdItem Correction to: Genetic evidence for a single founding population of the Lakshadweep Islands (Molecular Genetics and Genomics, (2024), 299, 1, (8), 10.1007/s00438-024-02110-z)(Springer Science and Business Media Deutschland GmbH, 2024) Kumar S.; Singh P.P.; Pasupuleti N.; Shendre S.S.; Sequeira J.J.; Babu I.; Mustak M.S.; Rai N.; Chaubey G.In this article the author name Mohammed S. Mustak was incorrectly written as Mohammed S. Mutak. The original article has been corrected. � The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024.Item Correction to: Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations (Scientific Reports, (2024), 14, 1, (7822), 10.1038/s41598-024-54607-7)(Nature Research, 2024) Pandey R.K.; Srivastava A.; Mishra R.K.; Singh P.P.; Chaubey G.Correction to: Scientific Reportshttps://doi.org/10.1038/s41598-024-54607-7, published online 03 April 2024 The original version of this Article contained errors in the Material and Methods section and in the legend of Figure�3 (A, B, C). In the Material and Methods section, under the subheading �Insilco analysis�, �To analyse the TMPRSS2 expression in various human tissues, the GTEx portal database (http://www.gtexportal.org/home/) was used.� now reads: �To analyse the FURIN expression in various human tissues, the GTEx portal database (http://www.gtexportal.org/home/) was used.� In the legend of Figure�3, �(A) and (B) display the allele frequency distribution of rs2070788 across Indian populations in a frequency map and the corresponding COVID-19 Case Fatality Rate (CFR) as of August 30th, 2021.� now reads: �(A) and (B) display the allele frequency distribution of rs1981458 across Indian populations in a frequency map and the corresponding COVID-19 Case Fatality Rate (CFR) as of August 30th, 2021.� �The linear regression graph depicts the association between the rs1981458 allele frequency of the TMPRSS2 gene with COVID-19 CFR.� now reads: �The linear regression graph depicts the association between the rs1981458 allele frequency of the FURIN gene with COVID-19 CFR.� The original Article has been corrected. � The Author(s) 2024.Item Essential oils as green promising alternatives to chemical preservatives for agri-food products: New insight into molecular mechanism, toxicity assessment, and safety profile(Elsevier Ltd, 2024) Prakash B.; Singh P.P.; Gupta V.; Raghuvanshi T.S.Microbial food spoilage caused by food-borne bacteria, molds, and associated toxic chemicals significantly alters the nutritional quality of food products and makes them unpalatable to the consumer. In view of potential adverse effects (resistance development, residual toxicity, and negative effects on consumer health) of some of the currently used preservative agents and consumer preferences towards safe, minimally processed, and chemical-free products, food industries are looking for natural alternatives to the chemical preservatives. In this context, essential oils (EOs) showed broad-range antimicrobial effectiveness, low toxicity, and diverse mechanisms of action, and could be considered promising natural plant-based antimicrobials. The existing technical barriers related to the screening of plants, extraction methods, characterization, dose optimization, and unpredicted mechanism of toxicity in the food system, could be overcome using recent scientific and technological advancements, especially bioinformatics, nanotechnology, and mathematical approaches. The review focused on the potential antimicrobial efficacy of EOs against food-borne microbes and the role of recent scientific technology and social networking platform in addressing the major obstacles with EOs-based antimicrobial agents. In addition, a detailed mechanistic understanding of the antimicrobial efficacy of EOs, safety profile, and risk assessment using bioinformatics approaches are summarized to explore their potential application as food preservatives. � 2023 Elsevier LtdItem Genetic evidence for a single founding population of the Lakshadweep Islands(Springer Science and Business Media Deutschland GmbH, 2024) Kumar S.; Singh P.P.; Pasupuleti N.; Shendre S.S.; Sequeira J.J.; Babu I.; Mutak M.S.; Rai N.; Chaubey G.Lakshadweep is an archipelago of 36 islands located in the Southeastern Arabian Sea. In the absence of a detailed archaeological record, the human settlement timing of this island is vague. Previous genetic studies on haploid DNA makers suggested sex-biased ancestry linked to North and South Indian populations. Maternal ancestry suggested a closer link with the Southern Indian, while paternal ancestry advocated the Northern Indian genetic�affinity. Since the haploid markers are more sensitive to genetic drift, which is evident for the Island populations, we have used the biparental high-resolution single-nucleotide polymorphic markers to reconstruct the population history of Lakshadweep Islands. Using the fine-scaled analyses, we specifically focused on (A) the ancestry components of Lakshadweep Islands populations; (B) their relation with East, West Eurasia and South Asia; (C) the number of founding lineages and (D) the putative migration from Northern India as the paternal ancestry was closer to the North Indian populations. Our analysis of ancestry components confirmed relatively higher North Indian ancestry among the Lakshadweep population. These populations are closely related to the South Asian populations. We identified mainly�a single founding population for these Islands, geographically divided into two sub-clusters. By examining the population�s genetic composition and analysing the gene flow from different source populations, this study contributes to our understanding of Lakshadweep Island�s evolutionary history and population dynamics. These findings shed light on the complex interactions between ethnic groups and their genetic contributions in making the Lakshadweep population. � The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024.Item Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations(Nature Research, 2024) Pandey R.K.; Srivastava A.; Mishra R.K.; Singh P.P.; Chaubey G.SARS CoV-2, the causative agent for the ongoing COVID-19 pandemic, it enters the host cell by activating the ACE2 receptor with the help of two proteasesi.e., Furin and TMPRSS2. Therefore, variations in these genes may account for differential susceptibility and severity between populations. Previous studies have shown that the role of ACE2 and TMPRSS2 gene variants in understanding COVID-19 susceptibility among Indian populations. Nevertheless, a knowledge gap exists concerning the COVID-19 susceptibility of Furin gene variants among diverse South Asian ethnic groups. Investigating the role of Furin gene variants and their global phylogeographic structure is essential to comprehensively understanding COVID-19 susceptibility in these populations. We have used 450 samples from diverse Indian states and performed linear regression to analyse the Furin gene variant's with COVID-19 Case Fatality Rate (CFR) that could be epidemiologically associated with disease severity outcomes. Associated genetic variants were further evaluated for their expression and regulatory potential through various Insilco analyses. Additionally, we examined the Furin gene using next-generation sequencing (NGS) data from 393 diverse global samples, with a particular emphasis on South Asia, to investigate its Phylogeographic structure among�diverse world populations. We found a significant positive association for the SNP rs1981458 with COVID-19 CFR (p < 0.05) among diverse Indian populations at different timelines of the first and second waves. Further, QTL and other regulatory analyses showed various significant associations for positive regulatory roles of rs1981458 and Furin gene, mainly in Immune cells and virus infection process, highlighting their role in host immunity and viral assembly and processing. The Furin protein�protein interaction suggested that COVID-19 may contribute to Pulmonary arterial hypertension via a typical inflammation mechanism. The phylogeographic architecture of the Furin gene demonstrated a closer genetic affinity of South Asia with West Eurasian populations. Therefore, it is worth proposing that for the Furin gene, the COVID-19 susceptibility of South Asians will be more similar to the West Eurasian population. Our previous studies on the ACE2 and TMPRSS2 genes showed genetic affinity of South Asian with East Eurasians and West Eurasians, respectively. Therefore, with the collective information from these three important genes (ACE2, TMPRSS2 and Furin) we modelled COVID-19 susceptibilityof South Asia in between these two major ancestries with an inclination towards West Eurasia. In conclusion, this study, for the first time, concluded the role of rs1981458 in COVID-19 severity among the Indian population and outlined its regulatory potential.This study also highlights that the genetic structure for COVID-19 susceptibilityof South Asia is distinct, however, inclined to the West Eurasian population. We believe this insight may be utilised as a genetic biomarker to identify vulnerable populations, which might be directly relevant for developing policies and allocating resources more effectively during an epidemic. � The Author(s) 2024.Item Reconstructing the population history of the�Nicobarese(Springer Nature, 2024) Mishra R.K.; Singh P.P.; Rai N.; Desai S.; Pandey P.; Tiwary S.K.; Tamang R.; Suravajhala P.; Shrivastava P.; Thangaraj K.; van Driem G.; Chaubey G.The Nicobarese are the major tribal groups in the Nicobar district, situated south of the Andaman group of Islands. Linguistic phylogeny suggests that the linguistic ancestors of the Nicobarese settled the Nicobar archipelago in the early Holocene. So far, genetic research on them is low-resolution and restricted to the haploid DNA markers. Therefore, in the present analysis, we have used the high-resolution biparental (1554 published and 5 newly genotyped Nicobarese individuals) and uniparental genetic markers and looked at the genetic association of Nicobarese with the South and Southeast Asian populations. We report a common ancestral component shared among the Austroasiatic of South and Southeast Asia. Our analyses have suggested that the Nicobarese peoples retain this ancestral Austroasiatic predominant component in their genomes in the highest proportion. On the Southeast Asian mainland, the Htin Mal, who speak an Austroasiatic language of the Khmuic branch, represent a population that has preserved their ethnic distinctness from other groups over time and consequently shown the highest drift with the Nicobarese. The analysis based on haplotypes indicated a significant level of genomic segment sharing across linguistic groups, indicating an ancient broader distribution of Austroasiatic populations in Southeast Asia. Based on the temporal analyses of haploid DNA, it is suggested that the forebears of the Nicobarese people may have arrived on the Nicobar Islands in the last 5000 YBP. Therefore, among the modern populations, the Nicobarese peoples and the Htin Mal language community represent good genetic proxies for ancient Austroasiatics. � The Author(s), under exclusive licence to European Society of Human Genetics 2024.Item The genetic admixture and assimilation of Ahom: a historic migrant from Thailand to India(Oxford University Press, 2024) Kumar S.; Singh P.P.; Pasupuleti N.; Tripathy V.M.; Chauley M.K.; Chaubey G.; Rai N.The Northeastern region of India is considered a gateway for modern humans' dispersal throughout Asia. This region is a mixture of various ethnic and indigenous populations amalgamating multiple ancestries. One reason for such amalgamation is that, South Asia experienced multiple historic migrations from various parts of the world. A few examples explored genetically are Jews, Parsis and Siddis. Ahom is a dynasty that historically migrated to India during the 12th century. However, this putative migration has not been studied genetically at high resolution. Therefore, to validate this historical evidence, we genotyped autosomal data of the Modern Ahom population residing in seven sister states of India. Principal Component and Admixture analyses haave suggested a substantial admixture of the Ahom population with the local Tibeto-Burman populations. Moreover, the haplotype-based analysis has linked these Ahom individuals mainly with the Kusunda (a language isolated from Nepal) and Khasi (an Austroasiatic population of Meghalaya). Such unexpected presence of widespread population affinities suggests that Ahom mixed and assimilated a wide variety of Trans-Himalayan populations inhabiting this region after the migration. In summary, we observed a significant deviation of Ahom from their ancestral homeland (Thailand) and extensive admixture and assimilation with the local South Asian populations. � 2024 The Author(s). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
