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Singh D, Tripathi A, Mitra R, Bhati J, Rani V, Taunk J, Singh D, Yadav RK, Siddiqui MH, Pal M. Genome-wide identification of MATE and ALMT genes and their expression profiling in mungbean (Vigna radiata L.) under aluminium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116558. [PMID: 38850702 DOI: 10.1016/j.ecoenv.2024.116558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/10/2024]
Abstract
The Multidrug and toxic compound extrusion (MATE) and aluminium activated malate transporter (ALMT) gene families are involved in response to aluminium (Al) stress. In this study, we identified 48 MATE and 14 ALMT gene families in Vigna radiata genome and classified into 5 (MATE) and 3 (ALMT) clades by phylogenetic analysis. All the VrMATE and VrALMT genes were distributed across mungbean chromosomes. Tandem duplication was the main driving force for evolution and expansion of MATE gene family. Collinearity of mungbean with soybean indicated that MATE gene family is closely linked to Glycine max. Eight MATE transporters in clade 2 were found to be associated with previously characterized Al tolerance related MATEs in various plant species. Citrate exuding motif (CEM) was present in seven VrMATEs of clade 2. Promoter analysis revealed abundant plant hormone and stress responsive cis-elements. Results from quantitative real time-polymerase chain reaction (qRT-PCR) revealed that VrMATE19, VrMATE30 and VrALMT13 genes were markedly up-regulated at different time points under Al stress. Overall, this study offers a new direction for further molecular characterization of the MATE and ALMT genes in mungbean for Al tolerance.
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Singh D, Tripathi A, Bhati J, Taunk J, Singh D, Siddiqui MH, Singh MP. Genome wide identification and expression profiling of ATP binding cassette (ABC) transporters gene family in lentil (Lens culinaris Medikus) under aluminium stress condition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108710. [PMID: 38735154 DOI: 10.1016/j.plaphy.2024.108710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 05/14/2024]
Abstract
Adenosine triphosphate-binding cassette transporters (ABC transporters) are involved in regulating plant growth, development and tolerance to environmental stresses. In this study, a total of 138 ABC transporter genes were identified in the lentil genome that were classified into eight subfamilies. Four lentil ABC transporters from subfamily B and I were clustered together with the previously characterized ABC transporter proteins related to aluminium (Al) detoxification. Lentil ABC transporter genes were distributed across the chromosomes. Tandem duplication was the main driving force for expansion of the ABC gene family. Collinearity of lentil with soybean indicated that ABC gene family is closely linked to Glycine max. ABC genes in the same subfamily showed similar gene structure and conserved motifs. The ABC promoter regions harboured a large number of plant hormones and multiple stress responsive cis-regulatory elements. The qRT-PCR showed that ABC genes had varied expression in roots of lentil at different time points under Al stress. This is the first report on genome wide identification and expression analyses of genes encoding ABC transporter genes in lentil which has provided in-depth insight for future research on evolution and elucidation of molecular mechanisms for aluminium tolerance.
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Haefner J, Navarro KE, Guenette R, Jones BJP, Tripathi A, Adams C, Almazán H, Álvarez V, Aparicio B, Aranburu AI, Arazi L, Arnquist IJ, Auria-Luna F, Ayet S, Azevedo CDR, Bailey K, Ballester F, Barrio-Torregrosa MD, Bayo A, Benlloch-Rodríguez JM, Borges FIGM, Brodolin A, Byrnes N, Cárcel S, Carrión JV, Cebrián S, Church E, Cid L, Conde CAN, Contreras T, Cossío FP, Dey E, Díaz G, Dickel T, Elorza M, Escada J, Esteve R, Felkai R, Fernandes LMP, Ferrario P, Ferreira AL, Foss FW, Freitas EDC, Freixa Z, Generowicz J, Goldschmidt A, Gómez-Cadenas JJ, González R, Grocott J, Hafidi K, Hauptman J, Henriques CAO, Morata JAH, Herrero-Gómez P, Herrero V, Hervés Carrete C, Ifergan Y, Labarga L, Larizgoitia L, Larumbe A, Lebrun P, Lopez F, López-March N, Madigan R, Mano RDP, Marques AP, Martín-Albo J, Martínez-Lema G, Martínez-Vara M, Meziani ZE, Miller RL, Mistry K, Molina-Canteras J, Monrabal F, Monteiro CMB, Mora FJ, Muñoz Vidal J, Novella P, Nuñez A, Nygren DR, Oblak E, Palacio J, Palmeiro B, Para A, Parmaksiz I, Pelegrin J, Pérez Maneiro M, Querol M, Redwine AB, Renner J, Rivilla I, Rodríguez J, Rogero C, Rogers L, Romeo B, Romo-Luque C, Santos FP, dos Santos JMF, Shomroni I, Simón A, Soleti SR, Sorel M, Soto-Oton J, Teixeira JMR, Toledo JF, Torrent J, Trettin A, Usón A, Veloso JFCA, Waiton J, White JT. Demonstration of event position reconstruction based on diffusion in the NEXT-white detector. THE EUROPEAN PHYSICAL JOURNAL. C, PARTICLES AND FIELDS 2024; 84:518. [PMID: 38784120 PMCID: PMC11108901 DOI: 10.1140/epjc/s10052-024-12865-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
Noble element time projection chambers are a leading technology for rare event detection in physics, such as for dark matter and neutrinoless double beta decay searches. Time projection chambers typically assign event position in the drift direction using the relative timing of prompt scintillation and delayed charge collection signals, allowing for reconstruction of an absolute position in the drift direction. In this paper, alternate methods for assigning event drift distance via quantification of electron diffusion in a pure high pressure xenon gas time projection chamber are explored. Data from the NEXT-White detector demonstrate the ability to achieve good position assignment accuracy for both high- and low-energy events. Using point-like energy deposits from 83mKr calibration electron captures (E ∼ 45 keV), the position of origin of low-energy events is determined to 2 cm precision with bias < 1 mm. A convolutional neural network approach is then used to quantify diffusion for longer tracks (E ≥ 1.5 MeV), from radiogenic electrons, yielding a precision of 3 cm on the event barycenter. The precision achieved with these methods indicates the feasibility energy calibrations of better than 1% FWHM at Qββ in pure xenon, as well as the potential for event fiducialization in large future detectors using an alternate method that does not rely on primary scintillation.
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Patel M, Jaiswal A, Naseer A, Tripathi A, Joshi A, Minocha T, Kautu A, Gupta S, Joshi KB, Pandey MK, Kumar R, Dubey KD, Nazir A, Verma S, Gour N. Amyloidogenic Propensity of Metabolites in the Uric Acid Pathway and Urea Cycle Critically Impacts the Etiology of Metabolic Disorders. ACS Chem Neurosci 2024; 15:916-931. [PMID: 38369717 DOI: 10.1021/acschemneuro.3c00563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024] Open
Abstract
Novel insights into the etiology of metabolic disorders have recently been uncovered through the study of metabolite amyloids. In particular, inborn errors of metabolism (IEMs), including gout, Lesch-Nyhan syndrome (LNS), xanthinuria, citrullinemia, and hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome, are attributed to the dysfunction of the urea cycle and uric acid pathway. In this study, we endeavored to understand and mechanistically characterize the aggregative property exhibited by the principal metabolites of the urea cycle and uric acid pathway, specifically hypoxanthine, xanthine, citrulline, and ornithine. Employing scanning electron microscopy (SEM), transmission electron microscopy (TEM), and atomic force microscopy (AFM), we studied the aggregation profiles of the metabolites. Insights obtained through molecular dynamics (MD) simulation underscore the vital roles of π-π stacking and hydrogen bonding interactions in the self-assembly process, and thioflavin T (ThT) assays further corroborate the amyloid nature of these metabolites. The in vitro MTT assay revealed the cytotoxic trait of these assemblies, a finding that was substantiated by in vivo assays employing the Caenorhabditis elegans (C. elegans) model, which revealed that the toxic effects were more pronounced and dose-specific in the case of metabolites that had aged via longer preincubation. We hence report a compelling phenomenon wherein these metabolites not only aggregate but transform into a soft, ordered assembly over time, eventually crystallizing upon extended incubation, leading to pathological implications. Our study suggests that the amyloidogenic nature of the involved metabolites could be a common etiological link in IEMs, potentially providing a unified perspective to study their pathophysiology, thus offering exciting insights into the development of targeted interventions for these metabolic disorders.
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Tripathi A, Santos D, Daniel D, Dhamoon MS. Patterns and outcomes of weekend admission for acute ischemic stroke. J Stroke Cerebrovasc Dis 2023; 32:107250. [PMID: 37441891 DOI: 10.1016/j.jstrokecerebrovasdis.2023.107250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND AND OBJECTIVES The "weekend effect" describes worse care delivery during off-hours or weekends and has been demonstrated in multiple sub-specialties. Off-hours care for acute ischemic stroke (AIS) has been associated with poorer outcomes. However, there is less data about the "weekend effect" on endovascular thrombectomy (ET) outcomes. METHODS We used Medicare 100% sample datasets and included all AIS admissions from 2018-2019, using validated International Classification of Diseases, 10th Revision, Clinical Modification codes to identify AIS and comorbidities. Medicare provides the date of admission for all hospitalizations, and the day of the week was determined and assigned to weekend (Saturday or Sunday) or weekday (Monday through Friday). We defined 3 major outcomes: inpatient mortality, discharge home (vs. other destination), and 30-day mortality. RESULTS Among 471427 AIS admissions,13.0% and 12.9% of all AIS admissions occurred on a Saturday and Sunday, respectively, less than the expected 14.3% occurring on any given day (p-value <0.0001). AIS admissions on a weekend were less likely to receive IV thrombolysis (13.6% on Saturday and 12.9% on Sunday) and ET (13.1% on Saturday and 13.2% on Sunday), p-value <0.0001. Among all AIS admissions, weekend admission was associated with worse outcomes, including higher odds of inpatient mortality (adjusted OR 1.04 [95% CI 1.01-1.08, p<0.0001]), lower odds of discharge home (0.94 [0.93-0.96, p<0.0001]), and higher odds of 30-day mortality (1.06 [1.04-1.08, p<0.0001]). However, among AIS patients treated with ET, there was no association of weekend admission with outcomes. CONCLUSIONS In this national and contemporary dataset, we observed that the proportion of thrombolysis and ET cases was less over the weekend, and outcomes (inpatient mortality, 30-day mortality and odds of discharge home) were worse overall. We did not observe this association among AIS patients undergoing ET on a weekend vs. weekday.
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Tripathi A, Dubey KD. A single site mutation can induce functional promiscuity in homoserine kinase. Org Biomol Chem 2023. [PMID: 37212194 DOI: 10.1039/d3ob00459g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
L-Homoserine kinase is crucial in the biosynthesis of L-threonine, L-isoleucine, and L-methionine, where it catalyzes ATP-dependent phosphorylation of L-homoserine (Hse) to yield L-homoserine phosphate as its native activity. However, a single site mutation of H138 → L shows the emergence of ATPase activity as a secondary function. However, a previous mechanistic study proposes direct involvement of ATP and the substrate without any catalytic base; therefore, how the mutation of H138 → L causes the secondary function remains an enigma. Using computational tools herein, we provide new insight into the catalytic mechanism of L-homoserine kinase, showing direct involvement of H138 as a catalytic base. We show that mutation of H138 → L opens a new water channel connecting ATP, which facilitates the ATPase activity and reduces the native activity. The proposed mechanism agrees with the experimental finding that an H138 → L mutation reduces the kinase activity but enhances a promiscuous function, i.e. ATPase activity. Since homoserine kinase catalyzes the biosynthesis of amino acids, we believe that an accurate mechanism could be significant for enzyme engineering to synthesize amino acid analogs.
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Tripathi A, Stein LK, Dhamoon MS. Patterns in the number of interventionalists for endovascular treatment of acute ischemic stroke in the US. J Stroke Cerebrovasc Dis 2023; 32:106943. [PMID: 36521372 DOI: 10.1016/j.jstrokecerebrovasdis.2022.106943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/10/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Endovascular thrombectomy (ET) has become the standard of stroke care for large vessel occlusion acute ischemic stroke (AIS) involving the anterior circulation. With continued eligibility expansion, the demand for neuro-intervention is growing. Current estimates indicate inadequate supply of interventionalists. However, there is limited data describing the number of interventionalists per hospital in the US, and correlations with outcomes. METHODS We used Medicare 100% sample datasets and included all AIS admissions from 2018 to 2019, using validated International Classification of Diseases, 10th Revision, Clinical Modification codes to identify AIS and comorbidities. We utilized National Provider Identifier codes to identify distinct interventionalists at the hospital. We examined outcomes at the hospital level, including percent of AIS treated with thrombolysis, percent of AIS with inpatient mortality, percent of AIS with discharge home, and percent of AIS with death within 30 days. RESULTS Among 471,427 AIS admissions, 16,253 received ET over the 2-year period of the study. Only 683 of 4576 AIS-treating institutions provided ET (14.9%). These ET centers most frequently only had one interventionalist performing ET and were clustered in large metropolitan areas with high AIS volumes. As AIS volumes, ET volumes, and mean NIHSS scores increased, so did the number of interventionalists. With each additional interventionalist, there was an increased likelihood of poor outcomes including inpatient mortality, discharge home, and 30-day mortality. CONCLUSIONS We confirmed a relative lack of neuro-interventionalists among US hospitals, with a concentration of interventionalists in urban, high-volume centers. The greater likelihood of poor outcomes associated with increasing number of interventionalists is likely due to increasing complexity and severity of cases at high-volume ET centers, but further study is needed.
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Yadav S, Kardam V, Tripathi A, T G S, Dubey KD. The Performance of Different Water Models on the Structure and Function of Cytochrome P450 Enzymes. J Chem Inf Model 2022; 62:6679-6690. [PMID: 36073971 DOI: 10.1021/acs.jcim.2c00505] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Modeling approaches and modern simulations to investigate the biomolecular structure and function rely on various methods. Since water molecules play a crucial role in all sorts of chemistry, the accurate modeling of water molecules is vital for such simulations. In cytochrome P450 (CYP450), in particular, water molecules play a key role in forming active oxidant that ultimately performs oxidation and metabolism. In the present study, we have highlighted the behavior of the three most widely used water models─TIP3P, SPC/E, and OPC─for three different CYP450 enzymes─CYP450BM3, CYP450OleT, and CYP450BSβ─during MD simulations and QM/MM calculations. We studied the various properties, such as RMSD, RMSF, H-bond, water occupancy, and hydrogen atom transfer (HAT), using QM/MM calculations and compared them for all three water models. Our study shows that the stabilities of the enzyme complexes are well maintained in all three water models. However, the OPC water model performs well for the polar active sites, that is, in CYP450OleT and CYP450BSβ, while the TIP3P water model is superior for the hydrophobic site, such as CYP450BM3.
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Tripathi DK, Chadha S, Tripathi A. Metaheuristic enabled intelligent model for stock market prediction via integrating volatility spillover: India and its Asian and European counterparts. DATA KNOWL ENG 2022. [DOI: 10.1016/j.datak.2022.102127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Singh P, Efstathiou J, Plets M, Jhavar S, Delacroix S, Tripathi A, Gupta A, Sachdev S, Jani A, Kirschner A, Tangen C, Bangs R, Joshi M, Costello B, Thompson I, Feng F, Lerner S. INTACT (S/N1806): Phase III Randomized Trial of Concurrent Chemoradiotherapy with or without Atezolizumab in Localized Muscle Invasive Bladder Cancer—Toxicity Update on First 213 Patients. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gupta S, Das N, Amaranath-Bj J, Gupta I, Tripathi A, Singh D. Knowledge and Awareness about Systemic Effects of Periodontal Disease among Medical, Dental and Alternate Medical Practitioners and Their Referral Practice to Periodontists. Mymensingh Med J 2022; 31:1153-1161. [PMID: 36189566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the past few decades, many medical professionals and dentists have paid close notice to their own fields, specializing in medicine pertaining to body and oral cavity respectively. Currently, this void is rapidly closing between all medical specialties, in presence of significant findings that supports association between periodontal disease and systemic conditions. Till now, some practitioners are not aware about the specialties of dentistry that results in improper referral practices. There are few studies on referral practice pertaining to periodontist, not with standing the fact that clear and effective communication between all health practitioners is essential for good practice. A cross-sectional study was carried out to assess the knowledge and awareness about systemic effects of periodontal disease among medical, dental and alternate medical practitioners and their referral practice to periodontist in Kanpur city. This cross-sectional study was carried out using self-reported questionnaire, distributed to 560 practitioners of various medical fields from January 2020 to August 2021. A total of 206(36.8%) Medical, 194(34.6%) Dentists and 160(28.6%) alternative practitioners participated in study. More than half participants agreed about relationship between periodontal diseases and Diabetes Mellitus, Cardio-VascularDisease and Adverse Pregnancy Outcomes. Among all 31.3% showed good knowledge level while 2.7% showed perfect level of practitioner's referral practice to periodontist. Dentists had statistically higher level of awareness compared to physicians. Referral practice to periodontist was deficit by medical and alternate medical practitioners despite of fact; they have good knowledge of relationship between periodontal disease and systemic health. Hence, interdisciplinary dental and medical training of practitioners is recommended.
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Tripathi A, Ranjan MR, Verma DK, Singh Y, Shukla SK, Rajput VD, Minkina T, Mishra PK, Garg MC. Author Correction: ANN-GA based biosorption of As(III) from water through chemo-tailored and iron impregnated fungal biofilter system. Sci Rep 2022; 12:13228. [PMID: 35918382 PMCID: PMC9345897 DOI: 10.1038/s41598-022-17593-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Tripathi A, Dutta Dubey K. Combined MD and QM/MM Calculations Reveal Allostery‐Driven Promiscuity in Dipeptide Epimerases of Enolase Family. Chem Asian J 2022. [DOI: 10.1002/asia.202200690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Tripathi A, Ranjan MR, Verma DK, Singh Y, Shukla SK, Rajput VD, Minkina T, Mishra PK, Garg MC. ANN-GA based biosorption of As(III) from water through chemo-tailored and iron impregnated fungal biofilter system. Sci Rep 2022; 12:12414. [PMID: 35858932 PMCID: PMC9300712 DOI: 10.1038/s41598-022-14802-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/13/2022] [Indexed: 11/22/2022] Open
Abstract
The iron impregnated fungal bio-filter (IIFB) discs of luffa sponge containing Phanerochaete chrysosporium mycelia have been used for the removal of As(III) from water. Two different forms of same biomass viz. free fungal biomass (FFB) and modified free fungal biomass (chemically modified and iron impregnated; CFB and IIFB) have been simultaneously investigated to compare the performance of immobilization, chemo-tailoring and iron impregnation for remediation of As(III). IIFB showed highest uptake capacity and percentage removal of As(III), 1.32 mg/g and 92.4% respectively among FFB, CFB and IIFB. Further, the application of RSM and ANN-GA based mathematical model showed a substantial increase in removal i.e. 99.2% of As(III) was filtered out from water at optimised conditions i.e. biomass dose 0.72 g/L, pH 7.31, temperature 42 °C, and initial As(III) concentration 1.1 mg/L. Isotherm, kinetic and thermodynamic studies proved that the process followed monolayer sorption pattern in spontaneous and endothermic way through pseudo-second order kinetic pathway. Continuous mode of As(III) removal in IIFB packed bed bioreactor, revealed increased removal of As(III) from 76.40 to 88.23% with increased column height from 5 to 25 cm whereas the removal decreased from 88.23 to 69.45% while increasing flow rate from 1.66 to 8.30 mL/min. Moreover, the IIFB discs was regenerated by using 10% NaOH as eluting agent and evaluated for As(III) removal for four sorption–desorption cycles, showing slight decrease of their efficiency by 1–2%. SEM–EDX, pHzpc, and FTIR analysis, revealed the involvement of hydroxyl and amino surface groups following a non-electrostatic legend exchange sorption mechanism during removal of As(III).
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Tripathi A, Dutta Dubey K. Combined MD and QM/MM Calculations Reveal Allostery-Driven Promiscuity in Dipeptide Epimerases of Enolase Family. Chem Asian J 2022; 17:e202200528. [PMID: 35722826 DOI: 10.1002/asia.202200528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/19/2022] [Indexed: 11/10/2022]
Abstract
The adaptability of the active site to amplify the secondary function is supposed to be the fundamental cause of the promiscuity and the evolution of new functions in enzymes. In most cases, mutations occur close to the active site and/or in the catalytic site to change the active site plasticity to accommodate the non-native substrate. In the present study, using MD simulations and hybrid QM/MM calculations, we have shown a way to enhance the promiscuity, i. e., the allostery-driven promiscuity. Using a case study of the AEE enzyme where the capping loop recognizes the substrate, herein, we show that a single site mutation (D321G) far from the capping loop can induce a large conformational change in the capping loop to recognize different substrates for different functions. The QM/MM calculations for the WT and mutated enzyme provide a first validation of the mechanism of 1,1-proton transfer and dehydration by the AEE enzyme. Since AEE epimerase possesses a highly conserved TIM-barrel fold, we believe that our study provides a crucial lead to understanding the mechanism of emergence of secondary function which can be useful to repurpose ancient enzymes for modern usage.
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Shrestha R, Khadka SK, Basi A, Malla M, Thapa S, Tripathi A, Shrestha R. Meniscal Tear at Knee: Repair or Resect? An Early Experience from a University Hospital in Nepal. Kathmandu Univ Med J (KUMJ) 2022; 20:47-50. [PMID: 36273290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background The meniscus plays an important role in maintaining healthy articular cartilage. Meniscus tear, one of the common intra-articular knee lesions, is treated by either debridement or repair. Objective This study aims at identifying the early outcome of meniscus tears treated by debridement or repair. This study also elaborates on the spectrum of meniscal injuries presented in a tertiary care hospital in Nepal. Method A retrospective descriptive cross-sectional study was conducted at Orthopedic Department of Dhulikhel Hospital from February 2018 until January 2020 among patients who underwent knee arthroscopies for meniscal tears treated either by debridement or repair. Patients having intra articular fractures, osteochondral injuries and multi-ligament injuries were excluded. The meniscal tears were classified according to location and type of tear. Those patients who had at least one-year of follow up were evaluated with Lysholm score for functional outcome. Data were compiled and analyzed with Microsoft Excel 2011. Result One hundred and ten cases of meniscal tears were managed over the study period. Ninty-three cases could be traced for outcome evaluation, which included 50 cases of meniscal debridement and 43 cases of meniscal repair. The mean Lysholm score of the patients who received debridement was 81.5 (SD 10.4) and those who received meniscal repair was 84.9 (SD 9.1) (p=0.105). The population distribution was found to be similar in both the groups according to age and sex distribution and associated ligamentous injuries. Conclusion Good functional outcome was seen for meniscal tears managed with debridement or repair in at least one year follow up and could not establish one modality of management better than the other.
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Sandra N, Tripathi A, Lal SK, Mandal B, Jain RK. Molecular and biological characterization of soybean yellow mottle mosaic virus severe strain infecting soybean in India. 3 Biotech 2021; 11:381. [PMID: 34458057 DOI: 10.1007/s13205-021-02925-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 07/13/2021] [Indexed: 11/26/2022] Open
Abstract
The complete nucleotide sequence and genome organization of soybean yellow mottle mosaic virus severe strain causing bright yellow mosaic, mottling and puckering symptoms in soybean (Glycine max) from India was determined. The monopartite single stranded genomic RNA is 3974 nuclotides long and has the potential to encode six viral proteins viz., p25, p83, p8, p10, p39 and p25. The SYMMV-Sb isolate differed from mungbean strain with 69 nucleotides and nine aminoacids dispersed over the various ORFs. Comparative sequence analysis revealed that SYMMV-Sb shared 98% nt sequence identity at complete genome level and 96-100% at all ORFs level with SYMMV mungbean strain from India and 71-92% identity with SYMMV Korean soybean isolate, whereas it showed very low sequence identity with other tombusviridae members (2-53%). The phylogenetic analysis showed the clustering of SYMMV-Sb along with other members of genus Gammacarmovirus. The SYMMV-Sb isolate produced chlorotic blotches, mild and veinal mottling, necrosis and puckering symptoms in various leguminous host plants. The symptomatalogy of the soybean isolate was differed from mungbean strain as earlier induced severe symptoms on soybean and mild symptoms on mungbean. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02925-2.
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Misra UK, Kalita J, Kumar M, Tripathi A, Mishra P. Complications of tuberculous meningitis and their effect on outcome in a tertiary care cohort. Int J Tuberc Lung Dis 2021; 24:1194-1199. [PMID: 33172527 DOI: 10.5588/ijtld.20.0036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND: To report the frequency and severity of complications, and their effect on the outcome of tuberculous meningitis (TBM).METHODS: In this retrospective cohort study, the following TBM complications were observed: status epilepticus (SE), hydrocephalus, paradoxical clinical worsening (PCW), hyponatremia, drug-induced hepatitis (DIH), infarction and mechanical ventilation (MV). These were recorded and correlated with stage of meningitis and outcome.RESULTS: A total of 144 patients with TBM (median age 26 years, range 12-75) were included. There were 76 (52.8%) females. The patients were in Stage I (n = 33), Stage II (n = 82) and Stage III (n = 29); 58 had definite TBM. Complications occurred in 128 (88.9%); complications included hydrocephalus (n = 58, 40.3%), hyponatremia (n = 70, 48.6%), infarction (n = 48, 33.3%), DIH (n = 42, 29.2%), SE (n = 16, 18.0%), MV (n = 43, 29.9%) and PCW (n = 24, 16.7%), with variable overlap. By 6 months, 33 patients had died. Death was related to PCW (P = 0.016), hyponatremia (P = 0.03), MV (P = 0.02), infarction (P = 0.03) and the number of complications. Except PCW, most complications occurred during the first month.CONCLUSIONS: In TBM, complications occurred in 128 (88.9%) patients, mainly in the early stages, with variable overlap. Infarction, PCW, hyponatremia and MV were predictive of poor outcome.
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Sharma M, Prajapati S, Kumar A, Tripathi A, Godlaveti VNK, Gupta P. Effect of Acute Exposure of Belladonna Mother Tincture on Zebrafish Embryonic Development. Indian J Pharm Sci 2021. [DOI: 10.36468/pharmaceutical-sciences.847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Shevtsov DS, Shikhaliev KS, Komarova ES, Kruzhilin AA, Kipriyanova GO, Potapov AY, Zartsyn ID, Kozaderov OA, Prabhakar C, Tripathi A. Inhibition of Copper Corrosion with N-Arylaminotriazoles in Aqueous Chloride Solutions and in Air. RUSS J APPL CHEM+ 2020. [DOI: 10.1134/s1070427220080078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Dhara L, Tripathi A. The use of eugenol in combination with cefotaxime and ciprofloxacin to combat ESBL-producing quinolone-resistant pathogenic Enterobacteriaceae. J Appl Microbiol 2020; 129:1566-1576. [PMID: 32502298 DOI: 10.1111/jam.14737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 05/05/2020] [Accepted: 05/19/2020] [Indexed: 11/29/2022]
Abstract
AIM Emergence of extended-spectrum beta-lactamase (ESBL) producing with quinolone-resistant (QR) pathogenic Enterobacteriaceae augmented the need to establish therapeutic options against them. Present study aimed towards determination of synergistic combination of eugenol (EG) with cefotaxime (CTX) and ciprofloxacin (CIP) to combat against this resistance and potentiation of antibacterial drugs by EG against these bacteria. METHODS AND RESULTS Synergistic interaction between EG and CTX/CIP (FICI: 0·08-0·5) were observed among ESBL-QR bacteria using checkerboard assay. Approximately, 2- to 1024-fold minimum inhibitory concentration value reduction and 17- to 165 030-fold dose reduction index strongly suggested synergistic interaction between EG and antibiotics. Cell viability assay showed reduction in log10 CFU per ml from 16·6 to 3·1 at synergistic concentration. Scanning electron microscopy further proved disruptive effect of EG on cell architecture. Eugenol and/or its combination also altered genes' expressions that imparted antibiotic resistance by ~1·6 to ~1226 folds. CONCLUSIONS Reduced doses of antibiotics, bacterial morphological alterations, efflux pump down regulation, porin over expression and beta-lactamase gene inhibition of ESBL-QR bacteria by EG alone or in combination with CTX/CIP might have reversed antibiotic resistance profile of ESBL-QR bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY This study provided a molecular insight into action of EG and/with CTX and CIP, which might have potentiated antibiotic's activity against ESBL-QR bacteria.
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Sar S, Tripathi A, Dubey KD, Sen S. Iodine-Catalyzed Aerobic Diazenylation-Amination of Indole Derivatives. J Org Chem 2020; 85:3748-3756. [PMID: 32019297 DOI: 10.1021/acs.joc.9b03392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A mild strategy for consecutive diazenylation and amination of indole moieties has been demonstrated. The functionalization occurs at C3 and C2 carbon atoms, respectively, at the indole scaffold in the presence of catalytic iodine and air at 40 °C in the 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) solvent. It is noteworthy that the aromatic amines are generated in situ by the reaction of aryl hydrazine with iodine. In general, bright red products are obtained in moderate to good yield. Control reactions are conducted to establish the reaction mechanism.
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Sandra N, Tripathi A, Dikshit HK, Mandal B, Jain RK. Seed transmission of a distinct soybean yellow mottle mosaic virus strain identified from India in natural and experimental hosts. Virus Res 2020; 280:197903. [PMID: 32105764 DOI: 10.1016/j.virusres.2020.197903] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/20/2020] [Accepted: 02/23/2020] [Indexed: 10/24/2022]
Abstract
Soybean yellow mottle mosaic virus (SYMMV) is a newly identified member of the genus Gammacarmovirus from grain legumes in India. As the modes of transmission of this virus have not been described, we assessed the possibility of SYMMV to be transmitted through seed collected from field infected mungbean plants and mechanically sap inoculated French bean plants using serological and molecular techniques followed by progeny assays. Direct antigen coated enzyme linked immunosorbent assay (DAC-ELISA) and reverse transcription polymerase chain reaction (RT-PCR) results are inconsistent with field infected mungbean seed tissues to ensure seed transmissibility irrespective of seed number used. Seed from mechanical sap inoculated French bean showed higher absorbance values in DAC-ELISA and amplification corresponding to replicase, movement and coat protein regions of SYMMV genome. The relative accumulation of SYMMV was higher in pod walls, immature seed and stamens and stigma of mechanical sap inoculated French bean. Progeny assays with infected seed revealed the seed transmissibility of SYMMV at the rate of 63.33% in mungbeanand 73.33% in French bean. Mechanical sap inoculation of mungbean progeny seedlings on French bean cv. Pusa Parvati produced characteristic symptoms of SYMMV. The results obtained from this study demonstrate that SYMMV is seed borne in nature and can be transmitted to next generation seedlings. This is the first report of seed transmission of SYMMV in mungbean and French bean.
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Sudha MR, Ahire J, Jayanthi N, Tripathi A, Nanal S. Effect of multi-strain probiotic (UB0316) in weight management in overweight/obese adults: a 12-week double blind, randomised, placebo-controlled study. Benef Microbes 2019; 10:855-866. [DOI: 10.3920/bm2019.0052] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
This clinical trial was carried out to assess the effects of multi-strain probiotic capsule (UB0316: Lactobacillus salivarius UBLS-22, Lactobacillus casei UBLC-42, Lactobacillus plantarum, UBLP-40, Lactobacillus acidophilus UBLA-34, Bifidobacterium breve UBBr-01, Bacillus coagulans Unique IS2 5×109 cfu each and fructo-oligosaccharide, 100 mg) on overweight/obesity-related parameters. Ninety subjects (age, 30-65 years; body mass index (BMI), 25-32 kg/m2) were randomised into two groups, i.e. UB0316 (probiotic) and placebo (excipient maltodextrin). They were instructed to take 2 capsules (UB0316 or placebo) per day after meals for 12 weeks. Primary (BMI), and secondary (waist-to-hip ratio: WHR; body weight, body fat; sugar and lipid profile) endpoint measures were evaluated at scheduled visits. Vital signs, physical investigations, quality of life, physician/subjects global assessment and adverse events were also recorded. A total of 71 subjects completed the scheduled study visits and analysis thereof showed that a 12-week UB0316 supplementation significantly reduced BMI (95% CI: -0.64, -0.27; P=0.0001), body weight (95% CI: -1.16, -0.50; P<0.0001), and WHR (95% CI: -0.06, -0.01; P=0.007) from the baseline, compared to placebo. Fat, blood lipid and sugar profile changes were non-significant. UB0316 significantly improved quality of life of overweight/obese individuals. Furthermore, no severe adverse events or abnormal findings were noted during vital, blood and physical examinations. In conclusion, this 12-week trial demonstrates that UB0316 is effective in reducing BMI, body weight and WHR in overweight/obese adults.
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Schneider L, Cui F, Brodsky A, Fraser M, Toloue M, Tripathi A. 14. A FULLY AUTOMATED INSTRUMENT FOR PREIMPLANTATION GENETIC TESTING (PGT-A) LIBRARY PREPARATION. Reprod Biomed Online 2019. [DOI: 10.1016/j.rbmo.2019.04.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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