The respiratory diseases in humans, such as aspergilloma, allergic bronchopulmonary aspergillosis... more The respiratory diseases in humans, such as aspergilloma, allergic bronchopulmonary aspergillosis and invasive aspergillosis are caused by the fungal pathogen Aspergillus fumigatus (A. fumigatus) The enzyme catalase of A. fumigatus provides a putative virulence to this fungal pathogen against the toxic effects of human hydrogen peroxide, which they cleave into water and molecular oxygen. The 3-D structure of this protein in A. fumigatus is not known, while it is very important for understanding the molecular mechanism of action of this enzyme and development of new drugs for various respiratory diseases. This article proposes the 3-D structure of catalase enzyme from A. fumigatus which has been predicted and validated using different computational programs. Based on the percentage of residue occurrence in helical, strand and loop regions, four structural domains have been identifi ed in the modeled structure. The structure and function relationship for all identifi ed structural domains have been also described. This study will be helpful for in silico drug discovery against the virulence nature of Aspergillus fumigatus.
Environmental factors are implicated in aging as well as genetic predisposition-induced Parkinson... more Environmental factors are implicated in aging as well as genetic predisposition-induced Parkinson's disease (PD) pathogenesis. Wrongdoers increase oxidative stress and nitrosative burden, which eventually degenerate the nigrostriatal dopaminergic neurons. Inhibition of the expression of nitric oxide synthase (NOS), an enzyme responsible for nitric oxide (NO) biosynthesis, prevents the demise of the nigrostriatal dopaminergic neurons. Polymorphism of NOS is thus expected to alter PD susceptibility. The study therefore aimed to examine an association of neuronal NOS (nNOS) gene polymorphism with nitrite, an indicator of nitrosative load; lipid peroxidation, an index of oxidative stress and PD susceptibility. An age-matched case-control study was performed in the north Indian residents enrolled at the Neurology Department of the King George's Medical University, Lucknow, India. While nNOS exon 29 TT variant genotype [odds ratio (OR) = 2.20, 95 % CI = 1.08-5.34, P = 0.040], combined TT and CT variants [OR = 1.68, 95 % CI = 1.05-2.69, P = 0.031] and T allele [OR = 1.58, 95 % CI = 1.10-2.28, P = 0.014] were found to be significantly associated with PD susceptibility, no association between nNOS exon 18 [OR for TT carriers = 1.97, 95 % CI = 0.89-4.20, P = 0.09 and OR for T allele = 1.35, 95 % CI = 0.94-1.93, P = 0.098] and PD risk was observed. Lipid peroxidation was augmented in all patients irrespective of their genotype. While genotype independent increase in nitrite content was observed in PD patients of exon 29 polymorphic groups, only heterozygous variant genotype of exon 18 was associated with augmentation in nitrite level as compared with respective control. The results obtained thus demonstrate that selected nNOS polymorphisms do not significantly contribute to PD risk in north Indian population.
Environmental factors are implicated in aging as well as genetic predisposition-induced Parkinson... more Environmental factors are implicated in aging as well as genetic predisposition-induced Parkinson's disease (PD) pathogenesis. Wrongdoers increase oxidative stress and nitrosative burden, which eventually degenerate the nigrostriatal dopaminergic neurons. Inhibition of the expression of nitric oxide synthase (NOS), an enzyme responsible for nitric oxide (NO) biosynthesis, prevents the demise of the nigrostriatal dopaminergic neurons. Polymorphism of NOS is thus expected to alter PD susceptibility. The study therefore aimed to examine an association of neuronal NOS (nNOS) gene polymorphism with nitrite, an indicator of nitrosative load; lipid peroxidation, an index of oxidative stress and PD susceptibility. An age-matched case-control study was performed in the north Indian residents enrolled at the Neurology Department of the King George's Medical University, Lucknow, India. While nNOS exon 29 TT variant genotype [odds ratio (OR) = 2.20, 95 % CI = 1.08-5.34, P = 0.040], combined TT and CT variants [OR = 1.68, 95 % CI = 1.05-2.69, P = 0.031] and T allele [OR = 1.58, 95 % CI = 1.10-2.28, P = 0.014] were found to be significantly associated with PD susceptibility, no association between nNOS exon 18 [OR for TT carriers = 1.97, 95 % CI = 0.89-4.20, P = 0.09 and OR for T allele = 1.35, 95 % CI = 0.94-1.93, P = 0.098] and PD risk was observed. Lipid peroxidation was augmented in all patients irrespective of their genotype. While genotype independent increase in nitrite content was observed in PD patients of exon 29 polymorphic groups, only heterozygous variant genotype of exon 18 was associated with augmentation in nitrite level as compared with respective control. The results obtained thus demonstrate that selected nNOS polymorphisms do not significantly contribute to PD risk in north Indian population.
A soluble and thermostable peroxidase enzyme (POD) was extracted from the leaf of Citrus medica. ... more A soluble and thermostable peroxidase enzyme (POD) was extracted from the leaf of Citrus medica. The enzyme was purified 15.10-fold with a total yield of 28.6% by ammonium sulfate precipitation followed by Sephadex G-100 gel filtration chromatography. The purified enzyme came as a single band on native polyacrylamide gel electrophoresis (PAGE) as well as sodium dodecyl sulfate (SDS) PAGE. The molecular mass of the enzyme was about 32 kD as determined by SDS-PAGE. The enzyme was optimally active at pH 6.0 and 50°C temperature. The enzyme was active in wide range of pH (5.0-8.0) and temperature (30-80°C). From the thermal inactivation studies in the range of 60-75°C, the half-life (t(1/2)) values of the enzyme ranged from 8 to 173 min. The inactivation energy (Ea) value of POD was estimated to be 21.7 kcal mol(-1). The Km values for guaiacol and H(2)O(2) were 8 mM and 1.8 mM, respectively. This enzyme was activated by some metals and reagents such as Ca(2+), Cu(2+), Mg(2+), Co(2+), fe...
A soluble and thermostable peroxidase enzyme (POD) was extracted from the leaf of Citrus medica. ... more A soluble and thermostable peroxidase enzyme (POD) was extracted from the leaf of Citrus medica. The enzyme was purified 15.10-fold with a total yield of 28.6% by ammonium sulfate precipitation followed by Sephadex G-100 gel filtration chromatography. The purified enzyme came as a single band on native polyacrylamide gel electrophoresis (PAGE) as well as sodium dodecyl sulfate (SDS) PAGE. The molecular mass of the enzyme was about 32 kD as determined by SDS-PAGE. The enzyme was optimally active at pH 6.0 and 50°C temperature. The enzyme was active in wide range of pH (5.0-8.0) and temperature (30-80°C). From the thermal inactivation studies in the range of 60-75°C, the half-life (t(1/2)) values of the enzyme ranged from 8 to 173 min. The inactivation energy (Ea) value of POD was estimated to be 21.7 kcal mol(-1). The Km values for guaiacol and H(2)O(2) were 8 mM and 1.8 mM, respectively. This enzyme was activated by some metals and reagents such as Ca(2+), Cu(2+), Mg(2+), Co(2+), fe...
In the present study the complete genome sequence of Human Immunodeficiency Virus-1 was searched ... more In the present study the complete genome sequence of Human Immunodeficiency Virus-1 was searched and retrieved from Genbank database with accession number NC_001802.1. The sequence of HIV-1 applied for gene Identification by ORFs prediction method. ORF Finder revealed that total 39 ORFs were identified in all six possible reading frames (RF). Three ORFs were identified in +1 RF, four in +2RF, six in +3RF, six in -1RF, thirteen in -2RF, and seven in -3RF. The translated sequences of all identified ORFs were searched in NCBI nonredundant database using Protein BLAST. All ORFs found in +1, +2, +3RF, and ORF 4 in -1RF, ORF 10 in -2RF, ORF 2 and ORF 3 in -3RF were already identified by previous workers but the remaining ORFs in -1,-2, and -3 RFs, eleven different ORFs translations showed similarity with different protein sequences of different organisms in nonredundant protein sequence database.
Response surface methodology was used to evaluate the effect of main variables such as concentrat... more Response surface methodology was used to evaluate the effect of main variables such as concentration of galactose, yeast extract and wheat bran on alpha-galactosidase production from Aspergillus parasiticus MTCC-2796 under submerged fermentation conditions. A full factorial Central Composite Design was applied to study these main factors that affected alpha-galactosidase production. The experimental results showed that the optimum concentration of galactose, yeast extract and wheat bran were 1.5 %, 0.06 % and 1.5 %, respectively. This method was efficient as only 20 experiments were necessary to asses these conditions, and model adequacy was very satisfactory as the coefficient of determination was 0.9921.
Interdisciplinary Sciences: Computational Life Sciences, 2014
L-asparaginases are widely distributed enzymes among plants, fungi and bacteria. This enzyme cata... more L-asparaginases are widely distributed enzymes among plants, fungi and bacteria. This enzyme catalyzes the conversion of l-asparagine to l-aspartate and ammonia and to a lesser extent the formation of l-glutamate from l-glutamine. In the present study, forty-five full-length amino acid sequences of L-asparaginases from bacteria, fungi and plants were collected and subjected to multiple sequence alignment (MSA), domain identification, discovering individual amino acid composition, and phylogenetic tree construction. MSA revealed that two glycine residues were identically found in all analyzed species, two glycine residues were also identically found in all the fungal and bacterial sources and three glycine residues were identically found in all plant and bacterial sources while no residue was identically found in plant and fungal L-asparaginases. Two major sequence clusters were constructed by phylogenetic analysis. One cluster contains eleven species of fungi, twelve species of bacteria, and one species of plant, whereas the other one contains fourteen species of plant, four species of fungi and three species bacteria. The amino acid composition result revealed that the average frequency of amino acid alanine is 10.77 percent that is very high in comparison to other amino acids in all analyzed species.
Nitric oxide (NO) is an important inorganic molecule of the biological system owing to diverse ph... more Nitric oxide (NO) is an important inorganic molecule of the biological system owing to diverse physiological implications. NO is synthesised from a semi-essential amino acid L-arginine. NO biosynthesis is catalysed by a family of enzymes referred to as nitric oxide synthases (NOSs). NO is accused in many acute and chronic illnesses, which include central nervous system disorders, inflammatory diseases, reproductive impairments, cancer and cardiovascular anomalies. Owing to very unstable nature, NO gets converted into nitrite, peroxynitrite and other reactive nitrogen species that could lead to nitrosative stress in the nigrostriatal system. Nitrosative stress is widely implicated in Parkinson's disease (PD), and its beneficial and harmful effects are demonstrated in in vitro, rodent and primate models of toxins-induced parkinsonism and in the blood, cerebrospinal fluid and nigrostriatal tissues of sporadic PD patients. The current article updates the roles of NO and NOSs in sporadic PD and toxins-induced parkinsonism in rodents along with the scrutiny of how inhibitors of NOSs could open a new line of approach to moderately rescue from PD pathogenesis based on the existing literature. The article also provides a perspective concerning the lack of ample admiration to such an approach and how to minimise the underlying lacunae.
The respiratory diseases in humans, such as aspergilloma, allergic bronchopulmonary aspergillosis... more The respiratory diseases in humans, such as aspergilloma, allergic bronchopulmonary aspergillosis and invasive aspergillosis are caused by the fungal pathogen Aspergillus fumigatus (A. fumigatus) The enzyme catalase of A. fumigatus provides a putative virulence to this fungal pathogen against the toxic effects of human hydrogen peroxide, which they cleave into water and molecular oxygen. The 3-D structure of this protein in A. fumigatus is not known, while it is very important for understanding the molecular mechanism of action of this enzyme and development of new drugs for various respiratory diseases. This article proposes the 3-D structure of catalase enzyme from A. fumigatus which has been predicted and validated using different computational programs. Based on the percentage of residue occurrence in helical, strand and loop regions, four structural domains have been identifi ed in the modeled structure. The structure and function relationship for all identifi ed structural domains have been also described. This study will be helpful for in silico drug discovery against the virulence nature of Aspergillus fumigatus.
Environmental factors are implicated in aging as well as genetic predisposition-induced Parkinson... more Environmental factors are implicated in aging as well as genetic predisposition-induced Parkinson's disease (PD) pathogenesis. Wrongdoers increase oxidative stress and nitrosative burden, which eventually degenerate the nigrostriatal dopaminergic neurons. Inhibition of the expression of nitric oxide synthase (NOS), an enzyme responsible for nitric oxide (NO) biosynthesis, prevents the demise of the nigrostriatal dopaminergic neurons. Polymorphism of NOS is thus expected to alter PD susceptibility. The study therefore aimed to examine an association of neuronal NOS (nNOS) gene polymorphism with nitrite, an indicator of nitrosative load; lipid peroxidation, an index of oxidative stress and PD susceptibility. An age-matched case-control study was performed in the north Indian residents enrolled at the Neurology Department of the King George's Medical University, Lucknow, India. While nNOS exon 29 TT variant genotype [odds ratio (OR) = 2.20, 95 % CI = 1.08-5.34, P = 0.040], combined TT and CT variants [OR = 1.68, 95 % CI = 1.05-2.69, P = 0.031] and T allele [OR = 1.58, 95 % CI = 1.10-2.28, P = 0.014] were found to be significantly associated with PD susceptibility, no association between nNOS exon 18 [OR for TT carriers = 1.97, 95 % CI = 0.89-4.20, P = 0.09 and OR for T allele = 1.35, 95 % CI = 0.94-1.93, P = 0.098] and PD risk was observed. Lipid peroxidation was augmented in all patients irrespective of their genotype. While genotype independent increase in nitrite content was observed in PD patients of exon 29 polymorphic groups, only heterozygous variant genotype of exon 18 was associated with augmentation in nitrite level as compared with respective control. The results obtained thus demonstrate that selected nNOS polymorphisms do not significantly contribute to PD risk in north Indian population.
Environmental factors are implicated in aging as well as genetic predisposition-induced Parkinson... more Environmental factors are implicated in aging as well as genetic predisposition-induced Parkinson's disease (PD) pathogenesis. Wrongdoers increase oxidative stress and nitrosative burden, which eventually degenerate the nigrostriatal dopaminergic neurons. Inhibition of the expression of nitric oxide synthase (NOS), an enzyme responsible for nitric oxide (NO) biosynthesis, prevents the demise of the nigrostriatal dopaminergic neurons. Polymorphism of NOS is thus expected to alter PD susceptibility. The study therefore aimed to examine an association of neuronal NOS (nNOS) gene polymorphism with nitrite, an indicator of nitrosative load; lipid peroxidation, an index of oxidative stress and PD susceptibility. An age-matched case-control study was performed in the north Indian residents enrolled at the Neurology Department of the King George's Medical University, Lucknow, India. While nNOS exon 29 TT variant genotype [odds ratio (OR) = 2.20, 95 % CI = 1.08-5.34, P = 0.040], combined TT and CT variants [OR = 1.68, 95 % CI = 1.05-2.69, P = 0.031] and T allele [OR = 1.58, 95 % CI = 1.10-2.28, P = 0.014] were found to be significantly associated with PD susceptibility, no association between nNOS exon 18 [OR for TT carriers = 1.97, 95 % CI = 0.89-4.20, P = 0.09 and OR for T allele = 1.35, 95 % CI = 0.94-1.93, P = 0.098] and PD risk was observed. Lipid peroxidation was augmented in all patients irrespective of their genotype. While genotype independent increase in nitrite content was observed in PD patients of exon 29 polymorphic groups, only heterozygous variant genotype of exon 18 was associated with augmentation in nitrite level as compared with respective control. The results obtained thus demonstrate that selected nNOS polymorphisms do not significantly contribute to PD risk in north Indian population.
A soluble and thermostable peroxidase enzyme (POD) was extracted from the leaf of Citrus medica. ... more A soluble and thermostable peroxidase enzyme (POD) was extracted from the leaf of Citrus medica. The enzyme was purified 15.10-fold with a total yield of 28.6% by ammonium sulfate precipitation followed by Sephadex G-100 gel filtration chromatography. The purified enzyme came as a single band on native polyacrylamide gel electrophoresis (PAGE) as well as sodium dodecyl sulfate (SDS) PAGE. The molecular mass of the enzyme was about 32 kD as determined by SDS-PAGE. The enzyme was optimally active at pH 6.0 and 50°C temperature. The enzyme was active in wide range of pH (5.0-8.0) and temperature (30-80°C). From the thermal inactivation studies in the range of 60-75°C, the half-life (t(1/2)) values of the enzyme ranged from 8 to 173 min. The inactivation energy (Ea) value of POD was estimated to be 21.7 kcal mol(-1). The Km values for guaiacol and H(2)O(2) were 8 mM and 1.8 mM, respectively. This enzyme was activated by some metals and reagents such as Ca(2+), Cu(2+), Mg(2+), Co(2+), fe...
A soluble and thermostable peroxidase enzyme (POD) was extracted from the leaf of Citrus medica. ... more A soluble and thermostable peroxidase enzyme (POD) was extracted from the leaf of Citrus medica. The enzyme was purified 15.10-fold with a total yield of 28.6% by ammonium sulfate precipitation followed by Sephadex G-100 gel filtration chromatography. The purified enzyme came as a single band on native polyacrylamide gel electrophoresis (PAGE) as well as sodium dodecyl sulfate (SDS) PAGE. The molecular mass of the enzyme was about 32 kD as determined by SDS-PAGE. The enzyme was optimally active at pH 6.0 and 50°C temperature. The enzyme was active in wide range of pH (5.0-8.0) and temperature (30-80°C). From the thermal inactivation studies in the range of 60-75°C, the half-life (t(1/2)) values of the enzyme ranged from 8 to 173 min. The inactivation energy (Ea) value of POD was estimated to be 21.7 kcal mol(-1). The Km values for guaiacol and H(2)O(2) were 8 mM and 1.8 mM, respectively. This enzyme was activated by some metals and reagents such as Ca(2+), Cu(2+), Mg(2+), Co(2+), fe...
In the present study the complete genome sequence of Human Immunodeficiency Virus-1 was searched ... more In the present study the complete genome sequence of Human Immunodeficiency Virus-1 was searched and retrieved from Genbank database with accession number NC_001802.1. The sequence of HIV-1 applied for gene Identification by ORFs prediction method. ORF Finder revealed that total 39 ORFs were identified in all six possible reading frames (RF). Three ORFs were identified in +1 RF, four in +2RF, six in +3RF, six in -1RF, thirteen in -2RF, and seven in -3RF. The translated sequences of all identified ORFs were searched in NCBI nonredundant database using Protein BLAST. All ORFs found in +1, +2, +3RF, and ORF 4 in -1RF, ORF 10 in -2RF, ORF 2 and ORF 3 in -3RF were already identified by previous workers but the remaining ORFs in -1,-2, and -3 RFs, eleven different ORFs translations showed similarity with different protein sequences of different organisms in nonredundant protein sequence database.
Response surface methodology was used to evaluate the effect of main variables such as concentrat... more Response surface methodology was used to evaluate the effect of main variables such as concentration of galactose, yeast extract and wheat bran on alpha-galactosidase production from Aspergillus parasiticus MTCC-2796 under submerged fermentation conditions. A full factorial Central Composite Design was applied to study these main factors that affected alpha-galactosidase production. The experimental results showed that the optimum concentration of galactose, yeast extract and wheat bran were 1.5 %, 0.06 % and 1.5 %, respectively. This method was efficient as only 20 experiments were necessary to asses these conditions, and model adequacy was very satisfactory as the coefficient of determination was 0.9921.
Interdisciplinary Sciences: Computational Life Sciences, 2014
L-asparaginases are widely distributed enzymes among plants, fungi and bacteria. This enzyme cata... more L-asparaginases are widely distributed enzymes among plants, fungi and bacteria. This enzyme catalyzes the conversion of l-asparagine to l-aspartate and ammonia and to a lesser extent the formation of l-glutamate from l-glutamine. In the present study, forty-five full-length amino acid sequences of L-asparaginases from bacteria, fungi and plants were collected and subjected to multiple sequence alignment (MSA), domain identification, discovering individual amino acid composition, and phylogenetic tree construction. MSA revealed that two glycine residues were identically found in all analyzed species, two glycine residues were also identically found in all the fungal and bacterial sources and three glycine residues were identically found in all plant and bacterial sources while no residue was identically found in plant and fungal L-asparaginases. Two major sequence clusters were constructed by phylogenetic analysis. One cluster contains eleven species of fungi, twelve species of bacteria, and one species of plant, whereas the other one contains fourteen species of plant, four species of fungi and three species bacteria. The amino acid composition result revealed that the average frequency of amino acid alanine is 10.77 percent that is very high in comparison to other amino acids in all analyzed species.
Nitric oxide (NO) is an important inorganic molecule of the biological system owing to diverse ph... more Nitric oxide (NO) is an important inorganic molecule of the biological system owing to diverse physiological implications. NO is synthesised from a semi-essential amino acid L-arginine. NO biosynthesis is catalysed by a family of enzymes referred to as nitric oxide synthases (NOSs). NO is accused in many acute and chronic illnesses, which include central nervous system disorders, inflammatory diseases, reproductive impairments, cancer and cardiovascular anomalies. Owing to very unstable nature, NO gets converted into nitrite, peroxynitrite and other reactive nitrogen species that could lead to nitrosative stress in the nigrostriatal system. Nitrosative stress is widely implicated in Parkinson's disease (PD), and its beneficial and harmful effects are demonstrated in in vitro, rodent and primate models of toxins-induced parkinsonism and in the blood, cerebrospinal fluid and nigrostriatal tissues of sporadic PD patients. The current article updates the roles of NO and NOSs in sporadic PD and toxins-induced parkinsonism in rodents along with the scrutiny of how inhibitors of NOSs could open a new line of approach to moderately rescue from PD pathogenesis based on the existing literature. The article also provides a perspective concerning the lack of ample admiration to such an approach and how to minimise the underlying lacunae.
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