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S Pradhan

Publications and source records attributed to S Pradhan.

At least 37 records · Page 2Linked to original sources
PubMed2001

SMN2-deletion in childhood-onset spinal muscular atrophy.

The human genome has two homologous survival motor neuron genes, SMN1 and SMN2. Although deletions of SMN1 are frequently reported in childhood-onset spinal muscular atrophy (SMA), SMN2 have been found to be intact in patients with the disorder. We report on a 5-year-old boy with childhood-onset SMA who has a homozygous deletion of SMN2. He had wasting, weakness, and hyporeflexia, predominantly in the distal muscles. The muscles involved showed chronic neurogenic changes on electromyogram. There was no sensory involvement. A nerve conduction study showed near normal conduction velocity with reduction in the amplitude of the compound muscle action potential. Analysis of polymerase chain reaction-restriction fragment length polymorphism as well as single-strand conformation polymorphism on exons 7 and 8 of the SMN genes revealed the SMN2-deletion. Base sequencing and densitometric analysis of the critical region (exon 7) did not show any microdeletion or duplication of SMN1, but confirmed the deletion of SMN2. We conclude that a deletion of SMN2 may also result in the SMA phenotype.

Child↗
PubMed2001

The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA.

The mammalian DNA methyltransferase Dnmt1 is responsible for the maintenance of the pattern of DNA methylation in vivo. It is a large multidomain enzyme comprising 1620 amino acid residues. We have purified and characterized individual domains of Dnmt1 (NLS-containing domain, NlsD, amino acid residues: 1-343; replication foci-directing domain, 350-609; Zn-binding domain (ZnD), 613-748; polybromo domain, 746-1110; and the catalytic domain (CatD), 1124-1620). CatD, ZnD and NlsD bind to DNA, demonstrating the existence of three independent DNA-binding sites in Dnmt1. CatD shows a preference for binding to hemimethylated CpG-sites; ZnD prefers methylated CpGs; and NlsD specifically binds to CpG-sites, but does not discriminate between unmethylated and methylated DNA. These results are not compatible with the suggestion that the target recognition domain of Dnmt1 resides in the N terminus of the enzyme. We show by protein-protein interaction assays that ZnD and CatD interact with each other. The isolated catalytic domain does not methylate DNA, neither alone nor in combination with other domains. Full-length Dnmt1 was purified from baculovirus-infected insect cells. Under the experimental conditions, Dnmt1 has a strong (50-fold) preference for hemimethylated DNA. Dnmt1 is stimulated to methylate unmodified CpG sites by the addition of fully methylated DNA. This effect is dependent on Zn, suggesting that binding of methylated DNA to ZnD triggers the allosteric activation of the catalytic center of Dnmt1. The allosteric activation model can explain kinetic data obtained by others. It suggests that Dnmt1 might be responsible for spreading of methylation, a process that is observed during aging and carcenogenesis but may be important for de novo methylation of DNA.

5-Methylcytosine↗
PubMed2001

Recombinant human DNA (cytosine-5) methyltransferase. III. Allosteric control, reaction order, and influence of plasmid topology and triplet repeat length on methylation of the fragile X CGG.CCG sequence.

Steady-state kinetic analyses revealed that the methylation reaction of the human DNA (cytosine-5) methyltransferase 1 (DNMT1) is repressed by the N-terminal domain comprising the first 501 amino acids, and that repression is relieved when methylated DNA binds to this region. DNMT1 lacking the first 501 amino acids retains its preference for hemimethylated DNA. The methylation reaction proceeds by a sequential mechanism, and either substrate (S-adenosyl-l-methionine and unmethylated DNA) may be the first to bind to the active site. However, initial binding of S-adenosyl-l-methionine is preferred. The binding affinities of DNA for both the regulatory and the catalytic sites increase in the presence of methylated CpG dinucleotides and vary considerably (more than one hundred times) according to DNA sequence. DNA topology strongly influences the reaction rates, which increased with increasing negative superhelical tension. These kinetic data are consistent with the role of DNMT1 in maintaining the methylation patterns throughout development and suggest that the enzyme may be involved in the etiology of fragile X, a syndrome characterized by de novo methylation of a greatly expanded CGG.CCG triplet repeat sequence.

Allosteric Regulation↗
PubMed2001

Herbicide resistance from a divided EPSPS protein: the split Synechocystis DnaE intein as an in vivo affinity domain.

We report that the N- and C-terminal splicing domains of the intein found in the dnaE gene of Synechocystis sp. PCC6803 (Ssp DnaE intein) are capable of association in vivo and in vitro, even with key splicing residues changed to alanine (Cys(1), Asn(159), and Cys(+1) to Ala). These studies utilized the herbicide resistant form of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Salmonella typhimurium and an Escherichia coli strain with the EPSPS gene deleted from its genome (E. coli strain ER2799). EPSPS was mapped to identify potential split sites using a facile Tn7 linker scanning procedure. Forty positions were found to tolerate a five amino acid insertion while 21 sites did not, as assayed by the rescue of growth of E. coli strain ER2799. Further characterization of these sites by inserting a full length Ssp DnaE intein identified residue 235 of EPSPS as the optimal position. The EPSPS gene was then divided into amino acids 1-235 and 236-427 which were fused to residues 1-123 and 124-159 of a splicing defective Ssp DnaE intein, respectively. Expression of the EPSPS-intein fusions from separate DNA molecules conferred resistance to the herbicide glyphosate, indicating that the intein splicing domains were bringing the EPSPS fragments together to generate activity. As a control the split EPSPS without the intein-affinity domain did not allow cell growth. The use of an intein as an in vivo affinity domain was termed intein-mediated protein complementation (IPC). Intein fragment assembly was verified in vitro by immobilizing the C-terminal splicing domain of the Ssp DnaE intein on a resin and demonstrating that the N-terminal 235 amino acids of EPSPS only bound to the resin when fused to the N-terminal splicing domain of the Ssp DnaE intein. As chloroplast DNA is not transmitted by pollen in plants such as corn and soybean, transgene spread via pollen may be controlled in the future by expressing inactive gene fragments from separate DNA locations, such as the nuclear and chloroplast genome, and using the split intein to generate protein activity.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗
PubMed2001

Biphasic illness pattern due to early relapse in Japanese-B virus encephalitis.

Japanese-B virus encephalitis (JE) is considered a uniphasic illness with a variable outcome. Biphasic illness patterns have never been reported previously. From an endemic zone in India we observed six patients of JE (from 62 patients treated in 7 years) who had an early relapse resulting in the biphasic clinical course. Five had poor socio-economic status and three had laboratory evidence of nutritional deficiency. Two patients were adults and the other four were children. Fever, rigors, headaches, body aches, altered consciousness, rigidity and tremors predominated the first phase of illness. During the second phase, behavioural changes, dystonia, pen-oral dyskinesia, drooling, mutism and muscle wasting due to anterior horn cell involvement were the important features. Though the serial antibody titres against the JE virus showed a four-fold rise in the initial or late convalescent phases, there was no increase during the second phase of the illness as compared to the first phase. On MRI, fresh lesions appeared during the second phase at the sites known for their involvement in JE, suggesting recrudescence of the virus. One patient survived with major sequelae, two with minor sequelae and the other three had complete recovery. We conclude that some patients with JE may have an early relapse after partial recovery, giving rise to the biphasic illness pattern. A locally prevalent genetic variant of the virus or host factors may be responsible for the altered clinical course of the disease. Biphasic illness does not necessarily mean a bad prognosis.

Adolescent↗
PubMed2001

Pulmonary thromboendarterectomy combined with other cardiac operations: indications, surgical approach, and outcome.

BACKGROUND: Patients with pulmonary hypertension due to chronic thromboembolic disease benefit from pulmonary thromboendarterectomy. A subset of these patients present with concomitant coronary or valvular disease. METHODS: From July 1990 to July 2000, 90 patients (68 males, 22 females, mean age 68 years) with pulmonary vascular resistance (PVR) ranging from 297 to 2261 dynes x sec x cm(-5) underwent pulmonary thromboendarterectomy in conjunction with coronary bypass grafting (59 patients), coronary artery bypass grafting/foramen ovale closure (24 patients), tricuspid annuloplasty (3 patients), mitral valve repair (2 patients), and aortic valve replacement (2 patients). The perioperative and hemodynamic outcomes of these patients were compared with the cohort of 1,100 isolated pulmonary thromboendarterectomies performed at our institution during this time. RESULTS: Overall perioperative survival (93.3%; 84 of 90 patients) and mean diminution in PVR (521 dynes x sec x cm(-5)) for patients undergoing combined operations were similar to those undergoing pulmonary thromboendarterectomy alone (94.2% survival; 1034 of 1100 patients; 547 dynes x sec x cm(-5) mean PVR reduction). Although patients undergoing combined operations were older (mean age 68 vs 50 years, p < 0.0001), had longer hospital stays (median 14 vs 9 days), and had worse left ventricular function (mean preoperative cardiac output 3.1 vs 4.4, p < 0.0001), there was no difference in cross-clamp time, resolution of tricuspid regurgitation, or postoperative systolic function between these two groups. CONCLUSIONS: Pulmonary thromboendarterectomy for chronic thromboembolic pulmonary hypertension may be performed safely in conjunction with other cardiac operations. Older patients evaluated for pulmonary thromboendarterectomy should be screened for concomitant coronary and valvular disease.

Adult↗
PubMed2001

Biotechnological potential of Microcystis sp. in Cu, Zn and Cd biosorption from single and multimetallic systems.

This paper provides information on biosorption of Cu, Zn and Cd by Microcystis sp. in single, bi and trimetallic combination. Highest biosorption of Cu followed by Zn and Cd in single as well as in mixtures containing two or three metals was noticed. The order of inhibition of Cu, Zn and Cd biosorption in bi and trimetallic combinations was suggestive of screening or competition for the binding sites on the cell surface. This observation was reconfirmed by Freundlich adsorption isotherm. Kf values were maximum for Cu (Kf = 45.18), followed by Zn (Kf = 16.71), and Cd (Kf = 15.63) in single metallic system. The Kf values for each test metal was reduced in solution containing more than one metal. Further, the reduction in biosorption of each metal ion due to presence of other metal ion was of greater magnitude at relatively higher concentrations of interfering metal ion. The biosorption of Cu at saturation was less affected when secondary metal (Cd or Zn) was added in the medium. Above results suggest that Microcystis holds great potential for metal biosorption from mixture.

Adsorption↗
PubMed2001

Human angiopoietin gene expression is a marker for severity of pulmonary hypertension in patients undergoing pulmonary thromboendarterectomy.

OBJECTIVE: A consistent pathologic feature seen in lungs of patients with pulmonary hypertension from thromboembolic disease is hyperplasia of the media of pulmonary arterioles. The molecular factors responsible for these vessel wall changes are unknown. Angiopoietin-1 is a gene responsible for the formation of the media of blood vessels in utero. We hypothesized that aberrant expression of the angiopoietin-1 gene in the adult lung would be a major contributing factor in the development of pulmonary hypertension. METHODS: From April 1999 to March 2000, a total of 35 patients (18 men, 17 women, mean age 52 years) with pulmonary hypertension and pulmonary vascular resistance ranging from 407 to 2006 dynes x sec x cm(-5) underwent pulmonary endarterectomy at our institution. Before cardiopulmonary bypass, lung biopsy specimens were taken from each patient. Biopsy specimens were also obtained from 10 patients (5 women, 5 men, mean age 55 years) undergoing lung resection for causes other than pulmonary hypertension. All specimens were blindly scored by a pathologist for degree of medial hyperplasia. Quantitative reverse transcriptase-polymerase chain reaction, Western blot, and immunohistochemistry were used to quantitate angiopoietin-1 messenger RNA and protein in each sample. RESULTS: Lung specimens from all patients with pulmonary hypertension demonstrated up-regulation of angiopoietin-1 at the messenger RNA level. The degree of angiopoietin-1 transcription was directly proportional to the preoperative pulmonary vascular resistance and medial wall hyperplasia/hypertrophy in each patient. By immunohistochemistry, angiopoietin-1 protein was confined to the media of pulmonary arterioles. Lung biopsy specimens from patients without pulmonary hypertension had no detectable expression of angiopoietin-1 at the messenger RNA or protein level. CONCLUSION: Angiopoietin-1, a gene responsible for vessel development in the embryonic lung, is up-regulated in the lung parenchyma of patients with pulmonary hypertension. The level of expression of angiopoietin-1 at messenger RNA and protein levels correlates to the severity of pulmonary hypertension in patients with thromboembolic disease and serves as a target for strategies to treat this disease.

Adult↗
PubMed2001

Carrier detection in non-deletional Duchenne/Becker muscular dystrophy families using polymorphic dinucleotide (CA) repeat loci of dystrophin gene.

BACKGROUND & OBJECTIVES: Carrier detection and prenatal diagnosis is of great importance for families with one or more sons affected with Duchenne/Becker muscular dystrophy (D/BMD). In about 35-40 per cent of these patients, the causative mutation does not involve gross rearrangement in the structure of dystrophin gene. In these non-deletional families, genetic counselling can be provided only by linkage analysis. The aim of the present study was to determine the carrier status of female relatives in north Indian families with non-deletional D/BMD using highly polymorphic intragenic dinucleotide (CA) repeat markers. METHODS: Six short tandem repeats (STRs) spanning 5' (1), central (4) and 3' regions of the dystrophin gene were used to analyse 14 unrelated families comprising 68 individuals with 12 female siblings at risk of being carriers. RESULTS: Five female siblings inherited at risk STR haplotype, six inherited normal haplotype and one had meiotic recombination. The intragenic recombinations were observed in three families at the central region STR loci and in one family between the proximal and central regions of the gene. INTERPRETATION & CONCLUSIONS: Our study suggested that at least 6 STR markers spanning 5', central and 3' regions of the dystrophin gene are essential to ascertain one or more informative loci and to rule out recombinations in non-deletional D/BMD families for carrier analysis.

Dinucleotide Repeats↗
PubMed2001

Guillain-Barre syndrome and Campylobacter infection.

Campylobacter infection of the gastrointestinal tract has been observed as an antecedent illness in some patients with Guillain-Barre syndrome (GBS); these patients have been reported to have poor prognosis. We investigated 29 patients with GBS, admitted to our hospital from January 1996 to December 1999 for recent Campylobacter enteritis by culture of their stool specimens. Campylobacter upsaliensis and C. jejuni were isolated from stools of one patient each with acute motor axonal neuropathy (AMAN) and acute inflammatory demyelinating polyradiculoneuropathy (AIDP) respectively. The patient with C. upsaliensis infection was a 7 year-old male child who developed features of AMAN, 7 days after onset of diarrhea. He recovered gradually within 24 days with residual deficit in the form of foot drop. This deficit has persisted for last three and half years. The other patient with C. jejuni infection was a 9 year-old boy, who developed AIDP after 9 days of acute diarrhea. This patient recovered completely within 28 days of illness without any deficit. None of the patients had relapse of GBS. The present findings indicate the need of planned systematic studies to explore the role of C. upsaliensis and other campylobacters as agents of antecedent diarrhea in patients of GBS with different clinical presentations and prognosis.

Adolescent↗
PubMed2000

Hybrid mouse-prokaryotic DNA (cytosine-5) methyltransferases retain the specificity of the parental C-terminal domain.

The mouse (cytosine-5) DNA methyltransferase (Dnmt1) consists of a regulatory N-terminal and a catalytic C-terminal domain, which are fused by a stretch of Gly-Lys dipeptide repeats. The C-terminal region contains all of the conserved motifs found in other cytosine-5 DNA methyltransferases including the relative position of the catalytic Pro-Cys dipeptide. In prokaryotes, the methyltransferases are simpler and lack the regulatory N-terminal domain. We constructed three hybrid methyltransferases, containing the intact N-terminus of the murine Dnmt1 and most of the coding sequences from M.HhaI (GCGC), M.HpaII (CCGG) or M.SssI (CG). These hybrids are biologically active when expressed in a baculovirus system and show the specificity of the parental C-terminal domain. Expression of these recombinant constructs leads to de novo methylation of both host and viral genomes in a sequence-specific manner. Steady-state kinetic analyses were performed on the murine Dnmt1-HhaI hybrid using poly(dG-dC).poly (dG-dC), unmethylated and hemimethylated oligonucleotides as substrates. The enzyme has a slow catalytic turnover number of 4.38 h(-1) for poly(dG-dC). poly(dG-dC), and exhibits 3-fold higher catalytic efficiency for hemimethylated substrates.

Amino Acid Motifs↗
PubMed2000

Structure and function of the mouse DNA methyltransferase gene: Dnmt1 shows a tripartite structure.

Dnmt1 is the predominant DNA methyltransferase (MTase) in mammals. The C-terminal domain of Dnmt1 clearly shares sequence similarity with many prokaryotic 5mC methyltransferases, and had been proposed to be sufficient for catalytic activity. We show here by deletion analysis that the C-terminal domain alone is not sufficient for methylating activity, but that a large part of the N-terminal domain is required in addition. Since this complex structure of Dnmt1 raises issues about its evolutionary origin, we have compared several eukaryotic MTases and have determined the genomic organization of the mouse Dnmt1 gene. The 5' most part of the N-terminal domain is dispensible for enzyme activity, includes the major nuclear import signal and comprises tissue-specific exons. Interestingly, the functional subdivision of Dnmt1 correlates well with the structure of the Dnmt1 gene in terms of intron/exon size distribution as well as sequence conservation. Our results, based on functional, structural and sequence comparison data, suggest that the gene has evolved from the fusion of at least three genes.

Amino Acid Motifs↗
PubMed2000

Vascularization of developing human olfactory neuroepithelium - a morphometric study.

The present study reveals intraepithelial capillaries in the olfactory neuroepithelium of human fetuses aged between 12 and 24 weeks of gestation, which disappear at birth. The area occupied by the intraepithelial capillaries increases significantly with fetal age (0.047 +/- 0.014 microm(2)/microm(2) at 12 weeks and 0.101 +/- 0. 025 microm(2)/microm(2) at 24 weeks) and with the thickness of the epithelium (45.00 +/- 6.74 microm at 8 weeks and 64.10 +/- 8.51 microm at 24 weeks). The vascularization of the developing neuroepithelium may suggest increased metabolic demand during development and maturation of the olfactory neuroepithelium, and postnatal retreat of capillaries to the underlying lamina propria may suggest diffusion of nutrients and gases from blood vessels into the lamina propria and direct gaseous exchange from the atmosphere.

Blood Cells↗
PubMed2000

Perilesional gliosis and seizure outcome: a study based on magnetization transfer magnetic resonance imaging in patients with neurocysticercosis.

We studied the effect of perilesional gliosis on seizure recurrence after stopping antiepileptic drug (AED) therapy in 108 patients with a solitary cysticercal brain cyst. All patients received albendazole therapy in the beginning, and magnetic resonance imaging (MRI) done after 2 seizure-free years showed complete disappearance of the lesion in 67, partial degeneration in 12, and healing by calcification in 29. The gliosis, which was not visible on initial MRI, was observed near the lesion in 22 (20%) patients on T1-weighted magnetization transfer spin-echo (MTSE) MRI. Initial seizure control was difficult with single AED therapy in 16 of 22 patients with gliosis but only in 8 of 86 patients without gliosis. On stopping AED therapy, patients with perilesional gliosis had a higher incidence of seizure recurrence (19 of 22 patients) compared with those who did not demonstrate gliosis (9 of 86 patients). The presumption that gliosis visible on MTSE MRI correlates with seizure recurrence had a high specificity (96%) but only moderate sensitivity (68%). Our findings suggest that there is a group of patients with neurocysticercosis in whom the risk of seizure recurrence is actually high. Several such patients have perilesional gliosis that can be identified on T1-weighted MTSE MRI. These patients probably need long-term AED administration.

Adult↗
PubMed1999

Recombinant human DNA (cytosine-5) methyltransferase. I. Expression, purification, and comparison of de novo and maintenance methylation.

A method is described to express and purify human DNA (cytosine-5) methyltransferase (human DNMT1) using a protein splicing (intein) fusion partner in a baculovirus expression vector. The system produces approximately 1 mg of intact recombinant enzyme >95% pure per 1.5 x 10(9) insect cells. The protein lacks any affinity tag and is identical to the native enzyme except for the two C-terminal amino acids, proline and glycine, that were substituted for lysine and aspartic acid for optimal cleavage from the intein affinity tag. Human DNMT1 was used for steady-state kinetic analysis with poly(dI-dC).poly(dI-dC) and unmethylated and hemimethylated 36- and 75-mer oligonucleotides. The turnover number (k(cat)) was 131-237 h(-1) on poly(dI-dC).poly(dI-dC), 1.2-2.3 h(-1) on unmethylated DNA, and 8.3-49 h(-1) on hemimethylated DNA. The Michaelis constants for DNA (K(m)(CG)) and S-adenosyl-L-methionine (AdoMet) (K(m)(AdoMet)) ranged from 0.33-1.32 and 2.6-7.2 microM, respectively, whereas the ratio of k(cat)/K(m)(CG) ranged from 3.9 to 44 (237-336 for poly(dI-dC).poly(dI-dC)) x 10(6) M(-1) h(-1). The preference of the enzyme for hemimethylated, over unmethylated, DNA was 7-21-fold. The values of k(cat) on hemimethylated DNAs showed a 2-3-fold difference, depending upon which strand was pre-methylated. Furthermore, human DNMT1 formed covalent complexes with substrates containing 5-fluoro-CNG, indicating that substrate specificity extended beyond the canonical CG dinucleotide. These results show that, in addition to maintenance methylation, human DNMT1 may also carry out de novo and non-CG methyltransferase activities in vivo.

Animals↗
PubMed1999

Recombinant human DNA (cytosine-5) methyltransferase. II. Steady-state kinetics reveal allosteric activation by methylated dna.

Initial velocity determinations were conducted with human DNA (cytosine-5) methyltransferase (DNMT1) on unmethylated and hemimethylated DNA templates in order to assess the mechanism of the reaction. Initial velocity data with DNA and S-adenosylmethionine (AdoMet) as variable substrates and product inhibition studies with methylated DNA and S-adenosylhomocysteine (AdoHcy) were obtained and evaluated as double-reciprocal plots. These relationships were linear for plasmid DNA, exon-1 from the imprinted small nuclear ribonucleoprotein-associated polypeptide N, (CGG.CCG)(12), (m(5)CGG. CCG)(12), and (CGG.CCG)(73) but were not linear for (CGG. Cm(5)CG)(12). Inhibition by AdoHcy was apparently competitive versus AdoMet and uncompetitive/noncompetitive versus DNA at </=20 microM AdoMet. Addition of the product (methylated DNA) to unmethylated plasmid DNA increased V(max(app)) resulting in mixed stimulation and inhibition. Velocity equations indicated a two-step mechanism as follows: first, activation of DNMT1 by methylated DNA that bound to an allosteric site, and second, the addition of AdoMet and DNA to the catalytic site. The preference of DNMT1 for hemimethylated DNA may be the result of positive cooperativity of AdoMet binding mediated by allosteric activation by the methylated CG steps. We propose that this activation plays a role in vivo in the regulation of maintenance methylation.

Allosteric Regulation↗