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Emission modeling at toll plaza under mixed traffic condition using simulation. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:803. [PMID: 37266734 DOI: 10.1007/s10661-023-11409-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
Mixed traffic conditions, i.e., the presence of different vehicle classes in a toll lane, causes congestion, leading to extra delay and emissions. The determination of the emission levels in the field is tedious process and thus there is need to look over it. Further, the dynamic toll pricing schemes are well established in developed countries to mitigate the congestion, but its application in developing countries is not observed so far. Hence, an attempt is made in the present study to establish the dynamic toll rates based on emission at toll plazas operating under mixed traffic conditions. The sensitivity analysis is carried out by changing the traffic composition and the approach volume in simulation. After that, the traffic composition and approach volume-based emission estimation equations are developed that can be used to predict the emissions easily in the field. The methodology finally moves towards the development of emission-based toll rates (EBTR).
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Thrombophilic risk factors and ABO blood group profile for arteriovenous access failure in end stage kidney disease patients: a single-center experience. Ren Fail 2022; 44:34-42. [PMID: 35094650 PMCID: PMC8812770 DOI: 10.1080/0886022x.2021.2011746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
INTRODUCTION Thrombosis of fistula occurs most frequently in end-stage kidney disease (ESKD) patients receiving hemodialysis. However, the role of thrombophilia in arteriovenous fistula (AVF) failure has not been well established. Hence, this study was aimed at assessing the roles of hereditary and acquired thrombophilic factors in association with AVF failure among patients with ESKD undergoing hemodialysis. METHODS A cross-sectional study was conducted on 100 ESKD patients, of whom 50 patients with well-functioning AVFs with no fistula failures earlier were enrolled as Group 1, and 50 patients who have had AVF failure were enrolled as Group 2. The hereditary factors as factor V Leiden, factor XIII, prothrombin, and methylene tetrahydrofolate reductase and the acquired factors as lipoprotein (a), fibrinogen, homocysteine, and anticardiolipin antibodies IgG and IgM were studied. RESULTS Among the hereditary factors, no statistically significant difference was observed in relation to factor V Leiden and Prothrombin (p > 0.05). However, for factor XIII and methylene tetrahydrofolate reductase, a statistically significant difference was observed between patients with well-functioning AVFs and patients who have had AVF failure (p < 0.05). We found a statistically significant increase in all the acquired factors in patients who have had AVF failure in comparison with patients with well-functioning AVFs (p < 0.001). Association between ABO blood groups and thrombophilic factors showed significant association between factor V Leiden, anticardiolipin antibody IgG and IgM and ABO blood groups (p < 0.05), whereas none of the other thrombophilic factors showed significant association (p > 0.05). CONCLUSION Thus, our study suggests significant role of acquired factors in causing AVF failure.
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Andrographolide binds to spike glycoprotein and RNA-dependent RNA polymerase (NSP12) of SARS-CoV-2 by in silico approach: a probable molecule in the development of anti-coronaviral drug. J Genet Eng Biotechnol 2021; 19:101. [PMID: 34255214 PMCID: PMC8276218 DOI: 10.1186/s43141-021-00201-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 06/19/2021] [Indexed: 01/03/2023]
Abstract
The SARS-CoV-2 belongs to Coronaviridae family infects host cells by the interaction of its spike glycoprotein and angiotensin-converting enzyme 2 (ACE 2) of host cells. Upon entry, the virus uses its RNA dependent RNA polymerase (NSP12) for transcribing its genome to survive in the cell and spread its infection. The protein sequences of receptor-binding domain (RBD) of spike glycoprotein, and NSP12 exhibits high homology in the family of Coronoviridae and are ideal candidates for the development of anti-coronaviral drugs. In the quest to identify inhibitory molecules against these proteins, we searched several molecules that are present in naturally occurring medicinal plants database. Andrographolide which is largely present in the leaf extracts of Andrographis paniculata (AP) and is known to exhibit antiviral, antibacterial, and stabilizes Th1/Th2/Th17 responses; taking this clue, we used in silico approaches to see the binding of andrographolide to RBD and NSP12 molecules. Our docking results showed very strong affinity of andrographolide to RBD and NSP12 of the SARS-CoV-2 virus with dock scores of -10.3460 for RBD and -10.7313 for NSP12 indicating andrographolide acts as an inhibitor of RBD and NSP12. These unique properties of andrographolide, AP extract, can be tested as anti-coronaviral drug.
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Down-regulation of SOX17, GATA4 and FoxA2 promotes differentiation potential of hepatocytes from human hematopoietic stem cells. Tissue Cell 2020; 62:101312. [PMID: 32433020 DOI: 10.1016/j.tice.2019.101312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 01/30/2023]
Abstract
The failure of regeneration of damaged liver in various end-stage liver diseases results in high morbidity and mortality. In this context, we have demonstrated the differentiation ability of human hematopoietic stem cells (HSCs) into hepatocytes. In this study, HSCs were isolated from a donor and cultured which exhibited the presence of CD34 and CD133 and absence of CD90 and CD73 markers. These CD34+ HSCs were induced for 21 days in hepatocyte differentiation medium (HDM). The obtained cells were characterized by immunocytochemical, immunofluorescence, western blot, qRT-PCR and flow cytometry analysis. Further, functional assays were done to accentuate the differentiated cells are hepatocytes. In HDM at day 6 differentiated cells showed the expression of definitive endodermal (DE) markers, SOX17, GATA4 and FoxA2 indicating the beginning of differentiation process. At day 21 the flow cytometry analysis showed 84.2 % positive to ALB-PE, 75.4 % positive to HNF4α-PE, and 77.3% positive to AFP-PE. Further, the qRT-PCR and western blot analysis presented prominent expression of hepatocyte-specific genes AAT, ALB, AFP, CK18, CK19, HNF4α, TFR2, and Hepcidin confirms the generation of hepatocytes in HDM. The ability of albumin secretion, urea production, glycogen storage, uptake of LDL, high ALDH enzyme activity describes the functionality of differentiated hepatocytes. Distinct expression of UGT1A1, CYP2B6, CYP2C9, CYP3A4, and CYP7A1 genes explains the ability to clear toxins and bilirubin as observed in normal hepatocytes. All these results indicate HSCs were differentiated into hepatocytes thus, autologous transplantation of HSCs could be a better option in the regeneration of the damaged liver.
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Chronic persistent surgical pain is strongly associated with COMT alleles in patients undergoing cardiac surgery with median sternotomy. Gen Thorac Cardiovasc Surg 2020; 68:1101-1112. [PMID: 32100171 DOI: 10.1007/s11748-020-01321-6] [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: 12/30/2019] [Accepted: 02/16/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Catechol-O-methyl transferase (COMT), a catechol-dependent enzyme, plays pivotal role in the development of pain. In different ethnic populations, it is associated with chronic persistent surgical pain (CPSP). In this context, the present study is aimed to assess involvement of COMT allele (Val158Met) in the development of CPSP. METHODOLOGY The patients (n = 216) underwent cardiac surgery with median sternotomy were selected to assess the magnitude of the CPSP evaluated with pain questionnaires' after 3 months from surgery. The exon 4 of COMT gene was PCR amplified and sequenced. The quantitative gene expression of COMT using RT-PCR corroborated the COMT enzyme activity. RESULTS Among 216 patients who underwent sternotomy procedure, 54 patients showed CPSP even after 3 months from surgery. The sequence analysis revealed that, in 25% (54/216) patients having following one or more alleles: c.472G>A (Val158Met) (reported), and novel c.382C>G;c.383G>C (Arg128Ala), c.373C>G (Arg125Gly), c.370G>A (Val124Met), c.359G>C (Gly120Ala), c.349G>A, c.350G>A(Ala117Ser), c.349G>C, c.351C>A (Ala117Pro), c.349G>A (Ala117Thr), c.350G>C (Ala117Gly), and c.405G>C (Ala135Ser) were observed for the first time in Indian population. Distinct CPSP (≥ 4 NRS pain score) was observed in these patients correlating with COMT enzyme activity (7.80 ± 0.92 units/mg) which is 14 times lowered when compared with non-CPSP patient's (n = 162) 110.15 ± 6.41 units/mg. The findings of COMT gene expression using quantitative RT-PCR corroborated the COMT enzyme activity. CONCLUSION The dominant effect of mutant COMT alleles connecting with low enzyme activity resulted in CPSP, warrants COMT genetic analysis prior to surgery was useful to predict the occurrence of CPSP.
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Novel mutations in the RING-finger domain of BRCA1 gene in clinically diagnosed breast cancer patients. 3 Biotech 2020; 10:47. [PMID: 31988841 DOI: 10.1007/s13205-019-2037-5] [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: 03/23/2018] [Accepted: 12/23/2019] [Indexed: 11/24/2022] Open
Abstract
In the present study, we investigated the frequency of BRCA1 gene mutations in 30 breast cancer (BC) patients of independent family history and 30 healthy control subjects. The immunohistochemistry (IHC) of BC patients showed duct cell carcinoma and distinct expression of the human epidermal growth factor receptor 2 (HER2). The genomic DNA was extracted from the BC patients and control subjects, the BRCA1 gene was PCR amplified and sequenced. The sequence analysis revealed that BRCA1 gene mutations were detected in 5/30 (16.6%) unrelated patients. One novel deleterious c.53delT mutation was detected in 3/30 (10%) unrelated patients leading to p.Met18Serfs*5 frame shift mutation in exon 2. Two patients 2/30 (6%) had novel c.297_301delinsCTCAA mutation in exon 5 leading to p.Leu99_Tyr101delinsPheSerAsn. Interestingly, the qRT-PCR analysis showed high expression of BRCA1 gene in all these patients having mutations compared with control subjects. Further, in silico analysis revealed loss of zinc-binding region of the RING-finger domain in BRCA1 structure due to these mutations, variable number of helices, helix-helix interactions, β-turns, and γ-turns were identified in the secondary structure, resulted in the formation of non-functional protein which is unable to activate BRCA1-associated genome surveillance complex (BASC) leading to uncontrolled cell proliferation. Moreover, the molecular dynamics (MD) simulations of mutated BRCA1 protein demonstrated extensive variations in the domain and non-domain regions compared with the wild-type structure as indicated by RMSD values. All these results conclusively explain that the c.53delT mutation may be the probable founder of deleterious mutation in this ethnic group.
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Novel Arg128Ala variant in Catechol-O-methyltransferase gene influence persistent pain. Clin Genet 2019; 97:378-380. [PMID: 31646620 DOI: 10.1111/cge.13650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/04/2019] [Accepted: 09/26/2019] [Indexed: 11/30/2022]
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In vitro large scale production of megakaryocytes to functional platelets from human hematopoietic stem cells. Biochem Biophys Res Commun 2018; 505:168-175. [PMID: 30243726 DOI: 10.1016/j.bbrc.2018.09.090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 09/14/2018] [Indexed: 12/18/2022]
Abstract
Megakaryocytopoiesis results in the formation of platelets, which are essential for hemostasis. Decreased production or increased destruction of platelets can cause thrombocytopenia, in which platelet transfusion is the mode of treatment. The present study is aimed in generation of megakaryocytes (MKs) and platelet from human hematopoietic stem cells (HSCs). The purity of HSCs was assessed through Flow cytometry and immunocytochemistry (ICC) studies. These pure HSCs were induced with thrombopoietin (TPO), similarly with Andrographis paniculata extract (APE) for 21 days to generate MKs. The APE is mainly composed of andrographolide which stimulates TPO from the liver, and this binds to CD110 present on the surface of HSCs and triggers the proliferation of HSCs and initiate higher MKs population subsequently, a large number of platelets. The results of the present study showed increased proliferation of HSCs grown in the presence of APE and revealed a high population of CD41a and CD42b positive MKs as enumerated by Flow cytometry compared with TPO induced MKs. These results also concurred with qRT-PCR and western blot analysis. The scanning electron microscopy (SEM) revealed the morphology of differentiated MKs and platelets were similar to human blood platelets. The differentiated MKs in APE exhibited polyploidy up to 32 N while TPO induced MKs showed polyploidy of 8 N, these results corroborated with colony forming unit assay. On thrombin stimulation, high expression of P-selectin (CD62p) and fibrinogen binding were detected in APE induced platelets. Autologous transplantation of platelets generated from APE may be a useful option in thrombocytopenia condition.
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Down-regulation of PAX2 promotes in vitro differentiation of podocytes from human CD34+ cells. Cell Tissue Res 2017; 370:477-488. [DOI: 10.1007/s00441-017-2680-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 08/07/2017] [Indexed: 12/16/2022]
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Phosphorylation of Staphylococcus aureus Protein-Tyrosine Kinase Affects the Function of Glucokinase and Biofilm Formation. IRANIAN BIOMEDICAL JOURNAL 2016; 21:94-105. [PMID: 27695030 PMCID: PMC5274716 DOI: 10.18869/acadpub.ibj.21.2.94] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background: When Staphylococcus aureus is grown in the presence of high concentration of external glucose, this sugar is phosphorylated by glucokinase (glkA) to form glucose-6-phosphate. This product subsequently enters into anabolic phase, which favors biofilm formation. The presence of ROK (repressor protein, open reading frame, sugar kinase) motif, phosphate-1 and -2 sites, and tyrosine kinase sites in glkA of S. aureus indicates that phosphorylation must regulate the glkA activity. The aim of the present study was to identify the effect of phosphorylation on the function of S. aureusglkA and biofilm formation. Methods: Pure glkA and protein-tyrosine kinase (BYK) of S. aureus ATCC 12600 were obtained by fractionating the cytosolic fractions of glkA1 and BYK-1 expressing recombinant clones through nickel metal chelate column. The pure glkA was used as a substrate for BYK, and the phosphorylation of glkA was confirmed by treating with reagent A and resolving in SDS-PAGE, as well as staining with reagent A. The kinetic parameters of glkA and phosphorylated glkA were determined spectrophotometrically, and in silico tools were used for validation. S. aureus was grown in brain heart infusion broth, which was supplemented with glucose, and then biofilm units were calculated. Results: Fourfold elevated glkA activity was observed upon the phosphorylation by BYK. Protein-protein docking analysis revealed that glkA structure docked close to the adenosine triphosphate-binding site of BYK structure corroborating the kinetic results. Further, S. aureus grown in the presence of elevated glucose concentration exhibited an increase in the rate of biofilm formation. Conclusion: The elevated function of glkA is an essential requirement for increased biofilm units in S. aureus, a key pathogenic factor that helps its survival and the progress of infection.
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In vitro differentiation potential of human haematopoietic CD34(+) cells towards pancreatic β-cells. Cell Biol Int 2016; 40:1084-93. [PMID: 27514733 DOI: 10.1002/cbin.10654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/17/2016] [Indexed: 11/06/2022]
Abstract
Haematopoietic stem cells (HSCs) possess multipotent ability to differentiate into various types of cells on providing appropriate niche. In the present study, the differentiating potential of human HSCs into β-cells of islets of langerhans was explored. Human HSCs were apheretically isolated from a donor and cultured. Phenotypic characterization of CD34 glycoprotein in the growing monolayer HSCs was confirmed by immunocytochemistry and flow cytometry techniques. HSCs were induced by selection with beta cell differentiating medium (BDM), which consists of epidermal growth factor (EGF), fibroblast growth factor (FGF), transferrin, Triiodo-l-Tyronine, nicotinamide and activin A. Distinct morphological changes of differentiated cells were observed on staining with dithizone (DTZ) and expression of PDX1, insulin and synaptophysin was confirmed by immunocytochemistry. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed distinct expression of specific β-cell markers, pancreatic and duodenal homeobox-1 (PDX1), glucose transporter-2 (GLUT-2), synaptophysin (SYP) and insulin (INS) in these differentiated cells compared to HSCs. Further, these cells exhibited elevated expression of INS gene at 10 mM glucose upon inducing with different glucose concentrations. The prominent feature of the obtained β-cells was the presence of glucose sensors, which was determined by glucokinase activity and high glucokinase activity compared with CD34(+) stem cells. These findings illustrate the differentiation of CD34(+) HSCs into β-cells of islets of langerhans.
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Role of STPK in Maintaining the Quiescent Nature of Human CD34 + Stem Cells. JOURNAL OF STEM CELLS 2016; 11:125-133. [PMID: 28296877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Haematopoietic stem cell normally exists in the hypoxic niche of bone marrow and in this high anaerobic condition phosphorylation is vital in understanding the stemness of these stem cells in bone marrow. Analysis of human aldehyde dehydrogenase (ALDH) and isocitrate dehydrogenase (IDH) we have observed the presence of serine threonine protein kinase (STPK) sites in the protein sequence of these enzymes conferring that functioning of ALDH and IDH is regulated largely by STPK through phosphorylation. Human CD34+ stem cells and mononuclear cells as a control isolated from peripheral blood and were propagated in DMEM media at 5% CO2, 95% humidity and at 37°C. Thus obtained cells showed high enzyme activity for STPK, ALDH and low enzyme activity for IDH in CD34+ cells compare to control cells. These results were concurred with qRT-PCR studies with high gene expression levels of hypoxia inducing factor-1-alpha (HIF1α), STPK, ALDH and low IDH expression in CD34+ cells while normalized with β-actin. In addition the phosphorylating sites on ALDH and IDH proteins were identified and their importance in maintaining the anaerobic conditions in HSCs was demonstrated. In view of the importance of STPK signalling in the present study mechanism in cell division was addressed with phosphorylation of key regulating enzymes in the metabolic pathway of cell cycle was explored.
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In Staphylococcus aureus the regulation of pyruvate kinase activity by serine/threonine protein kinase favors biofilm formation. 3 Biotech 2015; 5:505-512. [PMID: 28324552 PMCID: PMC4522715 DOI: 10.1007/s13205-014-0248-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 08/26/2014] [Indexed: 11/30/2022] Open
Abstract
Staphylococcus aureus, a natural
inhabitant of nasopharyngeal tract, survives mainly as biofilms. Previously we have observed that S. aureus ATCC 12600 grown under anaerobic conditions exhibited high rate of biofilm formation and l-lactate dehydrogenase activity. Thus, the concentration of pyruvate plays a critical role in S. aureus, which is primarily catalyzed by pyruvate kinase (PK). Analyses of the PK gene sequence (JN645815) revealed presence of PknB site in PK gene indicating that phosphorylation may be influencing the functioning of PK. To establish this hypothesis the pure enzymes of S. aureus ATCC 12600 were obtained by expressing these genes in PK 1 and PV 1 (JN695616) clones and passing the cytosolic fractions through nickel metal chelate column. The molecular weights of pure recombinant PK and PknB are 63 and 73 kDa, respectively. The enzyme kinetics of pure PK showed KM of 0.69 ± 0.02 µM, while the KM of PknB for stpks (stpks = NLCNIPCSALLSSDITASVNCAK) substrate was 0.720 ± 0.08 mM and 0.380 ± 0.07 mM for autophosphorylation. The phosphorylated PK exhibited 40 % reduced activity (PK = 0.2 ± 0.015 μM NADH/min/ml to P-PK = 0.12 ± 0.01 μM NADH/min/ml). Elevated synthesis of pyruvate kinase was observed in S. aureus ATCC 12600 grown in anaerobic conditions suggesting that the formed pyruvate is more utilized in the synthesis phase, supporting increased rate of biofilm formation.
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Mutations in exons 3 and 7 resulting in truncated expression of human ATP6V1B1 gene showing structural variations contributing to poor substrate binding-causative reason for distal renal tubular acidosis with sensorineural deafness. J Biomol Struct Dyn 2015; 33:2094-103. [PMID: 25517796 DOI: 10.1080/07391102.2014.999704] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Distal renal tubular acidosis (dRTA) is an autosomal recessive syndrome results defect in either proximal tubule bicarbonate reabsorption or in distal tubule H(+) secretion and is characterized by severe hyperchloraemic metabolic acidosis in childhood. dRTA is associated with functional variations in the ATP6V1B1 gene encoding β1 subunit of H(+)-ATPase, key membrane transporters for net acid excretion of α-intercalated cells of medullary collecting ducts. In the present study, a 13-year-old male patient suffering with nephropathy and sensorineural deafness was reported in the Department of Nephrology. We predicted improper functioning of ATP6V1B1 gene could be the reason for diseased condition. Therefore, exons 3, 4, and 7 contributing active site of ATP6V1B1 gene was amplified and sequenced (Accession numbers: KF571726, KM222653). The obtained sequences were BLAST searched against the wild type ATP6V1B1 gene which showed novel mutations c.307 A > G, c.308 C > A, c.310 C > G, c.704 T > C, c.705 G > T, c.709 A > G, c.710 A > G, c.714 G > A, c.716 C > A, c.717delC, c.722 C > G, c.728insG, c.741insT, c.753G > C. These mutations resulted in the expression of truncated protein terminating at Lys 209. The mutated ATP6V1B1structure superimposed with wild type showed extensive variations with RMSD 1.336 Å and could not bind to substrate ADP leading to non-functional ATPase. These results conclusively explain these mutations in ATP6V1B1 gene resulted in structural changes causing accumulation of H(+) ions contributing to dRTA with sensorineural deafness.
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Anaerobic Glycolysis and HIF1α Expression in Haematopoietic Stem Cells Explains Its Quiescence Nature. JOURNAL OF STEM CELLS 2015; 10:97-106. [PMID: 27125138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Metabolic alteration that a stem cell undergoes during proliferation and quiescence are decisive. These cells survive in extreme hypoxic environment that prevails in bone marrow. The present study is aimed to understand this nature in hematopoietic stem cells. These stem cells were mobilized from bone marrow into peripheral blood by giving G-CSF at a concentration of 5 μg/Kg/d and the cells were isolated by apheresis technique. The morphological analysis of these cells using Giemsa stain and SEM showed presence of only single type of cells with conspicuous nuclei, the hematopoietic nature was assessed by the presence of CD34, a glycoprotein using anti-CD34 monoclonal antibodies. The ICC results revealed presence of CD34 marker further; pure population of CD34+ stem cells was described by FACS. These cells were cultured separately in DMEM having 5.5mM, 11.1mM and 25mM glucose respectively. In these cells GK, PK and L-LDH enzyme activities were estimated which showed increased activities at 5.5mM glucose concentration and further elevation of glucose concentration the activities were fallen considerably. Similarly, qPCR analysis of HIF1α and GAPDH genes showed very high expression of HIF1α at 5.5mM glucose concentration which reduced with increased glucose concentration. While GAPDH gene expression enhanced on elevation of glucose concentration. Thus, these results indicate high HIF1α expression in low glucose condition with improved anaerobic glycolysis seems to be one of the key factors in maintaining the quiescent state of CD34+ stem cells.
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Comparative Structural and Functional Analysis of Staphylococcus aureus Glucokinase with other Bacterial Glucokinases. Indian J Pharm Sci 2014; 76:430-6. [PMID: 25425757 PMCID: PMC4243260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 08/18/2014] [Accepted: 08/24/2014] [Indexed: 11/16/2022] Open
Abstract
Glucokinase is classified in bacteria based upon having ATP binding site and 'repressor/open reading frames of unknown function/sugar kinases' motif, the sequence of glucokinase gene (JN645812) of Staphylococcus aureus ATCC12600 showed presence of ATP binding site and 'repressor/open reading frames of unknown function/sugar kinases' motif. We have earlier observed glucokinase of S. aureus has higher affinity towards the substrate compared to other bacterial glucokinase and under anaerobic condition with increased glucose concentration S. aureus exhibited higher rate of biofilm formation. To establish this, 3D structure of glucokinase was built using homology modeling method, the PROCHECK and ProSA-Web analysis indicated this built glucokinase structure was close to the crystal structure. This structure was superimposed with different bacterial glucokinase structures and from the root-mean-square deviation values, it is concluded that S. aureus glucokinase exhibited very close homology with Enterococcus faecalis and Clostridium difficle while with other bacteria it showed high degree of variations both in domain and nondomain regions. Glucose docking results indicated -12.3697 kcal/mol for S. aureus glucokinase compared with other bacterial glucokinase suggesting higher affinity of glucose which correlates with enzyme kinetics and higher rate of biofilm formation.
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In silico designing and molecular docking of a potent analog against Staphylococcus aureus porphobilinogen synthase. J Pharm Bioallied Sci 2014; 6:158-66. [PMID: 25035635 PMCID: PMC4097929 DOI: 10.4103/0975-7406.135246] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 12/31/2013] [Accepted: 02/20/2014] [Indexed: 12/01/2022] Open
Abstract
Background: The emergence of multidrug-resistant strains of Staphylococcus aureus, there is an urgent need for the development of new antimicrobials which are narrow and pathogen specific. Aim: In this context, the present study is aimed to have a control on the staphylococcal infections by targeting the unique and essential enzyme; porphobilinogen synthase (PBGS) catalyzes the condensation of two molecules of δ-aminolevulinic acid, an essential step in the tetrapyrrole biosynthesis. Hence developing therapeutics targeting PBGS will be the promising choice to control and manage the staphylococcal infections. 4,5-dioxovalerate (DV) is known to inhibit PBGS. Materials and Methods: In view of this, in this study, novel dioxovalerate derivatives (DVDs) molecules were designed so as to inhibit PBGS, a potential target of S. aureus and their inhibitory activity was predicted using molecular docking studies by molecular operating environment. The 3D model of PBGS was constructed using Chlorobium vibrioform (Protein Data Bank 1W1Z) as a template by homology modeling method. Results: The built structure was close to the crystal structure with Z score − 8.97. Molecular docking of DVDs into the S. aureus PBGS active site revealed that they are showing strong interaction forming H-bonds with the active sites of K248 and R217. The ligand–receptor complex of DVD13 showed a best docking score of − 14.4555 kcal/mol among DV and all its analogs while the substrate showed docking score of − 13.0392 kcal/mol showing interactions with S199, K217 indicating that DVD13 can influence structural variations on the enzyme and thereby inhibiting the enzyme. Conclusion: The substrate analog DVD13 is showing significant interactions with active site of PBGS and it may be used as a potent inhibitor to control S. aureus infections.
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Novel three missense mutations observed in Von Hippel-Lindau gene in a patient reported with renal cell carcinoma. INDIAN JOURNAL OF HUMAN GENETICS 2013; 19:373-6. [PMID: 24339559 PMCID: PMC3841571 DOI: 10.4103/0971-6866.120809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Von Hippel-Lindau (VHL) disease is an autosomal dominant hereditary cancer syndrome that predisposes to the development of a variety of benign and malignant tumors, especially cerebellar hemangioblastomas, retinal angiomas and clear-cell renal cell carcinomas (RCC). We have identified of VHL gene using immunohistochemistry in a patient who was diagnosed for RCC. In order to understand the involvement of mutation in the VHL gene exon 1 was amplified and sequenced (accession number: JX 401534). The sequence analysis revealed the presence of novel missense mutations c.194 C>T, c.239 G>A, c.278 G>A, c.319 C>G, c. 337 C > G leading to the following variations p.Ala 65 Val, p.Gly 80 Asp, p.Gly 93 Glu, p.Gln 107 Glu, p.Gln 113 Glu in the protein.
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Isolation, purification and characterization of Cardiolipin synthase from Mycobacterium phlei {PRIVATE}. Bioinformation 2013; 9:690-5. [PMID: 23930021 PMCID: PMC3732442 DOI: 10.6026/97320630009690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 07/08/2013] [Indexed: 11/23/2022] Open
Abstract
It has been observed that mycobacterial species has high content of cardiolipin (CL) in their cell membranes more so pathogenic
mycobacteria and in bacteria CL activates polymerases, gyrases by removing the bound ADP. Therefore, in the present study
cardiolipin synthase (cls) which catalyses the formation of CL was isolated purified and characterized from the cell membrane of
Mycobacterium phlei. The purified cls obtained from C-18 RP-HPLC column had a molecular weight of 58 kDa with an isoelectric
point of 4.5. The enzyme activity (11.5+0.15 µM of CL phosphorous. ml-1 minute-1 for PG as substrate and 14+0.35µM of CL
phosphorous. ml-1 minute-1 for CDP-DG as substrate) was optimal at pH 4.8 and showed KM values of 55+0.05µM and 2.56+0.04µM
for phosphatidyl glycerol and CDP-diacylglycerol, respectively, with an absolute requirement of Mg2+ and Mn2+ ions for its activity
however, Ca2+ ions inhibited the activity of the cls. The partial amino acid sequence of cls showed significant homology with pgsA3
gene of M. tuberculosis and in this organism the CL biosynthesis is very high having three genes coding for PLs biosynthesis
therefore, enzymes involved in CL biosynthesis may be an attractive drug target in the development of new antimycobacterial
drugs.
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Characterization of inosine monophosphate dehydrogenase from Staphylococcus aureus ATCC12600 and its involvement in biofilm formation. JOURNAL OF CLINICAL AND SCIENTIFIC RESEARCH 2013; 2:203. [DOI: 10.4103/2277-5706.241526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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