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Article ; Online: Correction to: The immunogenetics of COVID-19.

Srivastava, Anshika / Hollenbach, Jill A

2023 Volume 75, Issue 3, Page(s) 321

Language	English
Publishing date	2023-02-23
Publishing country	United States
Document type	Published Erratum
ZDB-ID	186560-2
ISSN	1432-1211 ; 0093-7711
ISSN (online)	1432-1211
ISSN	0093-7711
DOI	10.1007/s00251-023-01300-0
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Article ; Online: Author Correction: Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations.

Pandey, Rudra Kumar / Srivastava, Anshika / Mishra, Rahul Kumar / Singh, Prajjval Pratap / Chaubey, Gyaneshwer

Scientific reports

2024 Volume 14, Issue 1, Page(s) 9523

Language	English
Publishing date	2024-04-25
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-60182-8
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Article ; Online: The immunogenetics of COVID-19.

Srivastava, Anshika / Hollenbach, Jill A

Immunogenetics

2022 Volume 75, Issue 3, Page(s) 309–320

Abstract: The worldwide coronavirus disease 2019 pandemic was sparked by the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) that first surfaced in December 2019 (COVID-19). The effects of COVID-19 differ substantially not just between ... ...

Abstract	The worldwide coronavirus disease 2019 pandemic was sparked by the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) that first surfaced in December 2019 (COVID-19). The effects of COVID-19 differ substantially not just between patients individually but also between populations with different ancestries. In humans, the human leukocyte antigen (HLA) system coordinates immune regulation. Since HLA molecules are a major component of antigen-presenting pathway, they play an important role in determining susceptibility to infectious disease. It is likely that differential susceptibility to SARS-CoV-2 infection and/or disease course in COVID-19 in different individuals could be influenced by the variations in the HLA genes which are associated with various immune responses to SARS-CoV-2. A growing number of studies have identified a connection between HLA variation and diverse COVID-19 outcomes. Here, we review research investigating the impact of HLA on individual responses to SARS-CoV-2 infection and/or progression, also discussing the significance of MHC-related immunological patterns and its use in vaccine design.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Immunogenetics ; Histocompatibility Antigens Class I/genetics
Chemical Substances	Histocompatibility Antigens Class I
Language	English
Publishing date	2022-12-19
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	186560-2
ISSN	1432-1211 ; 0093-7711
ISSN (online)	1432-1211
ISSN	0093-7711
DOI	10.1007/s00251-022-01284-3
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Article ; Online: Atomistic nonlinear carrier dynamics in Ge.

Srivastava, Anshika / Srivastava, Pankaj / Srivastava, Anchal / Saxena, P K

Scientific reports

2023 Volume 13, Issue 1, Page(s) 5630

Abstract: An atomistic technique to successfully demonstrate the ultrafast carrier dynamics in Ge photoconductive samples is reported here. The technique is validated against the experimental findings and with the Drude conductivities. The impact of the various ... ...

Abstract	An atomistic technique to successfully demonstrate the ultrafast carrier dynamics in Ge photoconductive samples is reported here. The technique is validated against the experimental findings and with the Drude conductivities. The impact of the various different scattering mechanisms is used to calibrate the experimental results. It is observed that the total scattering rate is not a constant parameter as contrast to Drude model which uses constant scattering rate as the fitting parameter to demonstrate the ultrafast carrier dynamics, but strongly dependent on the applied peak THz field strength. It also contradicts with the relaxation time approximation (RTA) method which uses scattering rate chosen on the empirical basis as the fitting parameter to demonstrate the ultrafast carrier dynamics. On the other hand the limitations and challenges offered by various types of density functional theories (DFT) pose lot of challenges. In current manuscript various types of scattering mechanisms i.e. acoustic, intervalley, Coulomb and impact ionization on the behavior of carrier conductivity are studied in details. The proposed technique has shown capability to extract low and high frequency conductivities accurately which is impossible through the Drude model or DFT based theories. It is observed that the free carrier absorption coefficient depends on the refractive index of the material at low THz frequencies. The solution of Boltzmann transport equation through Monte Carlo technique provides valuable insights for better understanding of ultrafast carrier transportation mechanism. The free carrier absorption spectra are found to be in good agreement with the experimental results at various THz field strengths.
Language	English
Publishing date	2023-04-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-32732-z
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Article ; Online: Atomistic nonlinear carrier dynamics in Ge

Anshika Srivastava / Pankaj Srivastava / Anchal Srivastava / P. K. Saxena

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 9

Abstract: Abstract An atomistic technique to successfully demonstrate the ultrafast carrier dynamics in Ge photoconductive samples is reported here. The technique is validated against the experimental findings and with the Drude conductivities. The impact of the ... ...

Abstract	Abstract An atomistic technique to successfully demonstrate the ultrafast carrier dynamics in Ge photoconductive samples is reported here. The technique is validated against the experimental findings and with the Drude conductivities. The impact of the various different scattering mechanisms is used to calibrate the experimental results. It is observed that the total scattering rate is not a constant parameter as contrast to Drude model which uses constant scattering rate as the fitting parameter to demonstrate the ultrafast carrier dynamics, but strongly dependent on the applied peak THz field strength. It also contradicts with the relaxation time approximation (RTA) method which uses scattering rate chosen on the empirical basis as the fitting parameter to demonstrate the ultrafast carrier dynamics. On the other hand the limitations and challenges offered by various types of density functional theories (DFT) pose lot of challenges. In current manuscript various types of scattering mechanisms i.e. acoustic, intervalley, Coulomb and impact ionization on the behavior of carrier conductivity are studied in details. The proposed technique has shown capability to extract low and high frequency conductivities accurately which is impossible through the Drude model or DFT based theories. It is observed that the free carrier absorption coefficient depends on the refractive index of the material at low THz frequencies. The solution of Boltzmann transport equation through Monte Carlo technique provides valuable insights for better understanding of ultrafast carrier transportation mechanism. The free carrier absorption spectra are found to be in good agreement with the experimental results at various THz field strengths.
Keywords	Medicine ; R ; Science ; Q
Subject code	541
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: In Silico Characterization of RNASEH2A Pathogenic Variants and Identification of Novel Splice Site Donor Variant c.549+1G>T in Indian Population.

Nanjundagowda, Vykuntaraju K / Paikaraya, Swabhiman / Srinivasan, Varunvenkat M / Srivastava, Anshika

Cureus

2023 Volume 15, Issue 6, Page(s) e40366

Abstract: Background Aicardi-Goutieres syndrome (AGS) is a genetic disorder that has variable manifestations including neurological, immunological, and sometimes other system involvement in various combinations. Considering the high genetic and clinical diversity ... ...

Abstract	Background Aicardi-Goutieres syndrome (AGS) is a genetic disorder that has variable manifestations including neurological, immunological, and sometimes other system involvement in various combinations. Considering the high genetic and clinical diversity of AGS and the importance of RNASEH2 complex in the biological system, it is important to take a systematic approach to delineate the genetic diagnosis and impact of missense mutations. Methods Clinical targeted gene sequencing followed by Sanger validation was performed in an individual with the clinical features of AGS. Protein modeling studies of all the reported
Language	English
Publishing date	2023-06-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.40366
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Article: In silico

Gowda, Vykuntaraju K / Srinivasan, Varunvenkat M / Srivastava, Sudhanshu / Ghali, Noor / Kinhal, Uddhav / Shamnur, Asha / Srivastava, Anshika

Journal of family medicine and primary care

2024 Volume 13, Issue 1, Page(s) 208–220

Abstract: Background: H/ACA small nucleolar ribonucleoproteins (snoRNP) form a complex with multiple proteins to accomplish the pseudouridylation of rRNA. The assembly of H/ACA small nucleolar ribonucleoproteins (snoRNP) is initiated by H/ACA ribonucleoprotein ... ...

Abstract	Background: H/ACA small nucleolar ribonucleoproteins (snoRNP) form a complex with multiple proteins to accomplish the pseudouridylation of rRNA. The assembly of H/ACA small nucleolar ribonucleoproteins (snoRNP) is initiated by H/ACA ribonucleoprotein Assembly factor, that is, SHQ1. Mutations in Methods: Whole exome sequencing followed by Sanger validation was performed in an individual with the clinical features of neurodevelopmental disorder with seizures and dystonia (OMIM619922). Protein modeling studies of all the reported Results and discussion:* We identified compound heterozygous variants, one known frameshift deletion c. 828_831del, p.(Asp277Serfs27) and the other novel missense variant c. 1157A>C, p.(Tyr386Ser) found in an individual with neurodevelopmental disorder, seizures, movement disorder, and hypomyelination leukodystrophy on neuroimaging. Protein-interactome studies identified potential genetic interactors that include Conclusion:* In conclusion, a sophisticated genotype and phenotype correlation followed by linking the genes to the key biological pathways opens new avenues to understand disease pathology and plan for therapeutic interventions.
Language	English
Publishing date	2024-02-08
Publishing country	India
Document type	Journal Article
ZDB-ID	2735275-4
ISSN	2278-7135 ; 2249-4863
ISSN (online)	2278-7135
ISSN	2249-4863
DOI	10.4103/jfmpc.jfmpc_979_23
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Article ; Online: Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations.

Pandey, Rudra Kumar / Srivastava, Anshika / Mishra, Rahul Kumar / Singh, Prajjval Pratap / Chaubey, Gyaneshwer

Scientific reports

2024 Volume 14, Issue 1, Page(s) 7822

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Humans ; Angiotensin-Converting Enzyme 2/genetics ; COVID-19/epidemiology ; COVID-19/genetics ; Furin/genetics ; Pandemics ; Polymorphism, Genetic
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Furin (EC 3.4.21.75) ; FURIN protein, human (EC 3.4.21.75)
Language	English
Publishing date	2024-04-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-54607-7
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Article ; Online: Discovering targeted inhibitors for Escherichia coli efflux pump fusion proteins using computational and structure-guided approaches.

Chauhan, Shweta Singh / Gupta, Anshika / Srivastava, Aashna / Parthasarathi, Ramakrishnan

Journal of computational chemistry

2023 Volume 45, Issue 1, Page(s) 13–24

Abstract: Multidrug resistance pathogens causing infections and illness remain largely untreated clinically. Efflux pumps are one of the primary processes through which bacteria develop resistance by transferring antibiotics from the interior of their cells to the ...

Abstract	Multidrug resistance pathogens causing infections and illness remain largely untreated clinically. Efflux pumps are one of the primary processes through which bacteria develop resistance by transferring antibiotics from the interior of their cells to the outside environment. Inhibiting these pumps by developing efficient derivatives appears to be a promising strategy for restoring antibiotic potency. This investigation explores literature-reported inhibitors of E. coli efflux pump fusion proteins AcrB-AcrA and identify potential chemical derivatives of these inhibitors to overcome the limitations. Using computational and structure-guided approaches, a study was conducted with the selected inhibitors (AcrA:25-AcrB:59) obtained by data mining and their derivatives (AcrA:857-AcrB:3891) to identify their inhibitory effect on efflux pump using virtual screening, molecular docking and density functional theory (DFT) calculations. The finding indicates that Compound 2 (ZINC000072136376) has shown better binding and a significant inhibitory effect on AcrA, while Compound 3 (ZINC000072266819) has shown stronger binding and substantial inhibition effect on both non-mutant and mutated AcrB subunits. The identified derivatives could exhibit a better inhibitor and provide a potential approach for restoring the actions of resistant antibiotics.
MeSH term(s)	Escherichia coli Proteins/chemistry ; Escherichia coli/metabolism ; Molecular Docking Simulation ; Multidrug Resistance-Associated Proteins/chemistry ; Multidrug Resistance-Associated Proteins/metabolism ; Multidrug Resistance-Associated Proteins/pharmacology ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/chemistry
Chemical Substances	Escherichia coli Proteins ; Multidrug Resistance-Associated Proteins ; Anti-Bacterial Agents ; AcrB protein, E coli
Language	English
Publishing date	2023-09-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1479181-X
ISSN	1096-987X ; 0192-8651
ISSN (online)	1096-987X
ISSN	0192-8651
DOI	10.1002/jcc.27215
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Article ; Online: Effects of diclofenac sodium gel phonophoresis in sports activities induced grade-l ankle sprain

Anshika Singh / Sumit Raghav / Latika Gulyani / Gunjan Chaudhary / Anirudh Srivastava

Фізична реабілітація та рекреаційно-оздоровчі технології, Vol 8, Iss 4, Pp 203-

2023 Volume 210

Abstract: Purpose: the purpose of this study was to evaluate the effect of diclofenac sodium gel phonophoresis in grade -l ankle sprain. Materials & Methods: 54 patients were randomly included in this study and allocated equally into two groups. Group-1 was ... ...

Abstract	Purpose: the purpose of this study was to evaluate the effect of diclofenac sodium gel phonophoresis in grade -l ankle sprain. Materials & Methods: 54 patients were randomly included in this study and allocated equally into two groups. Group-1 was managed with therapeutic ultrasound (digital ultrasound machine, a product of HMS marketed in India with frequency of 1 MHz and 3MHz) with diclofenac sodium gel and group-2 was managed with therapeutic ultrasound with aquasonic gel. Therapeutic ultrasound with diclofenac sodium gel, marketed under the name of Voltaren, was administered at a frequency of 1MHz, an intensity of 0.8 W/cm2 with continuous mode (1:1) for five times a week for 2 weeks. The patients were examined by using Numeric Pain Rating Scale (NPRS) and Foot and Ankle Disability Index (FADI). They were assessed on the baseline, after 1st week, and after 2nd week of treatment. Results: one way ANOVA test was used to determine the significant difference at the 0.05 level of significance. There was reduction in NPRS and FADI p-value 0.000 after 2nd week of treatment in group-1 and group-2. But on the basis of mean difference score of NPRS and FADI, group-1 was better effective in terms of reduction of pain and improvement of function periodical manner (Table 3). Conclusion: significant dose-dependently relief was observed in NPRS and FADI for pain in disability for each group treated with diclofenac sodium gel compared with aquasonic gel using ultrasound. Acoustic streaming increased these benefits significantly when used after topical application of diclofenac sodium gel, and the dose-dependent effects of diclofenac sodium gel using therapeutic ultrasound.
Keywords	diclofenac sodium gel ; therapeutic ultrasound ; sports activities ; ankle sprain ; Medicine ; R
Subject code	796
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Kharkiv State Academy of Physical Culture
Document type	Article ; Online
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