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Biomedical subjects

R Majumdar

Publications and source records attributed to R Majumdar.

At least 19 recordsLinked to original sources
PubMed2005

Spinal muscular atrophy carrier screening by multiplex polymerase chain reaction using dried blood spot on filter paper.

Spinal muscular atrophy (SMA) is a common, often fetal, autosomal recessively inherited disease leading to progressive muscle wasting and paralysis as a result of degeneration of anterior horn cells of the spinal cord. The SMA-determining gene, called the survival of motor neuron gene (SMN), is present on 5q13 in two nearly identical copies, telomeric SMN (SMN1) and centromeric SMN (SMN2). It has been established that SMA is caused by mutations in SMN1 whereas homozygous deletion of SMN2 has apparently no pathological consequences. The aim of this study is to develop an easy and inexpensive method for the isolation of high-quality template DNA from blood samples for SMA carrier screening by multiplex polymerase chain reaction. We have developed a protocol that optimizes detection of the SMN1 copy number in the human genome, producing a specific and sensitive assay using DNA extracted from a dried blood spot on IsoCode paper.

Chromosomes, Human, Pair 5↗
PubMed2004

A clinical and genetic study of 56 Saudi Wilson disease patients: identification of Saudi-specific mutations.

Wilson disease (WD) is a hereditary disorder, with recessive transmission and genetic heterogeneity. Several mutations of ATP7B, the gene underlying WD, were reported in many ethnic groups. In this study, mutation screening in ATP7B of 56 Saudi Arabian WD patients was undertaken. The clinical data of all patients were recorded. The entire ATP7B coding sequence, including intron-exon boundaries were screened for mutation by the polymerase chain reaction (PCR)-based mutation detection technique and DNA sequencing. Thirty-nine patients were symptomatic at presentation and 17 subjects were pre-symptomatic siblings of affected patients. Fourteen patients had neurological, 11 patients had mixed (hepatic and neurological), and 14 patients had hepatic presentations. Family history suggestive of WD was present in 72% of cases and 68% had consanguineous parents. Genetic analysis showed disease-causing mutations in three exons (exons 8, 19 and 21) of the ATP7B gene in 28 patients (50%). Mutations in exons 21 (18 cases) and 19 (one case) were unique for Saudis. This large series of Saudi patients with WD has shown wide variability in the genomic substrate of WD. There is no correlation between genotype and clinical presentation.

Adenosine Triphosphatases↗
PubMed2003

4193delC, a common mutation causing Wilson's disease in Saudi Arabia: rapid molecular screening of patients and carriers.

BACKGROUND: In patients with Wilson's disease (WD), an autosomal recessive disorder, toxic accumulation of copper results in fatal liver disease and irreversible neuronal degeneration. ATP7B, the gene mutated in WD, contains 21 exons and encodes a copper transporting ATPase. A novel disease causing mutation (4193delC) in exon 21 of the ATP7B gene has previously been detected by heteroduplex analysis and DNA sequencing. AIMS: To screen for the above mutation in patients with WD and carriers using an amplification refractory mutation system (ARMS). METHODS: ARMS was used to screen for the 4193delC mutation in 30 patients with WD and their relatives. RESULTS: A homozygous mutation was detected in 16 of 30 patients with WD. CONCLUSIONS: This polymerase chain reaction based method, which has been known for years, is a simple, inexpensive, and rapid method for screening common and specific mutations in patients with WD and carriers.

Adenosine Triphosphatases↗
PubMed2001

Nucleosomal positioning and genetic divergence study based on DNA flexibility map.

Based on worm like chain model, DNA structural parameters--tilt, roll and rise, derived from crystallographic database have been used to determine the flexibility of DNA that regulates the nucleosomal translational positioning. Theoretically derived data has been compared to the experimental values available in loshikhes and Trifonov's database. The methodology has been extended to determine the flexibility of 18S rRNA genome in eukarya, where yeast shows a distinct difference when compared with mammals like human, mouse and rabbit.

Animals↗
PubMed2000

A novel deletion mutation within the carboxyl terminus of the copper-transporting ATPase gene causes Wilson disease.

In patients with Wilson disease (WD), an autosomal recessive disorder, toxic accumulation of copper results in fatal liver disease and irreversible neuronal degeneration. ATP7B, the gene mutated in WD, contains 21 exons and encodes a copper-transporting ATPase. In this study, all exons of the ATP7B gene of nine WD patients were screened for alterations by conventional mutation detection enhancement (MDE) heteroduplex analysis, followed by direct sequencing of the regions that showed heteroduplex formation. For the first time, a novel deletion mutation (4193delC) in exon 21, causing a frameshift leading to premature truncation of the protein was detected in four of nine patients. The 4193delC removes several signals within the carboxyl terminal domain that may disrupt trafficking of ATP7B protein through trans-Golgi network at the cellular level.

Adenosine Triphosphatases↗
PubMed2000

An investigation into the quantity of secretions removed by inflated and deflated laryngeal mask airways.

It has been suggested that removal of a laryngeal mask airway with the cuff inflated may remove more secretions than with the cuff deflated. We performed a study to determine whether this suggestion is correct. Patients were randomly allocated to removal of the laryngeal mask airway with the cuff deflated (n = 75) or inflated (n = 74). The laryngeal mask airways were weighed before insertion and after removal, the difference in these two weights being taken to be the mass of secretions adherent to the airways on removal. The mean (SD) increase in laryngeal mask airway weight was 2.45 (1.47) g with the cuff deflated and 3.03 (1.76) g with the cuff inflated (p = 0.03). We conclude that removal of the laryngeal mask airway with the cuff inflated removes approximately 0.5 g more secretions than with the cuff deflated.

Adolescent↗
PubMed1999

Sequence directed flexibility of DNA and the role of cross-strand hydrogen bonds.

Persistence length and torsional rigidity for different B-DNA sequences have been calculated by analysing crystal structure database. The values of these parameters for mixed sequence DNA are in good agreement with those estimated by others. Persistence lengths for the homopolymeric sequences, namely poly(dA).poly(dT) and poly(dG).poly(dC), are significantly large compared to those of others as expected from the inability of these sequences to form nucleosome under normal conditions. The heteropolymeric sequences poly(dA-dC).poly(dG-dT) and poly(dG-dC).poly(dG-dC), on the other hand, have smaller persistence lengths. This implies larger flexibility of the d(AC).d(GT), d(CA).d(TG), d(GC).d(GC) and d(CG).d(CG) doublets, some of which constitute the genetic disease forming triplet repeats d(CTG).d(CAG) and d(CGG).d(CCG). Thus it is expected that these triplet repeat sequences are also flexible and wrap around the histone octamer efficiently. Persistence length calculations also indicate larger flexibility for these triplet repeat sequences. Furthermore, our computations reveal that the rigidity of a given DNA sequence is controlled by its ability to form cross-strand bifurcated hydrogen bonds between the successive base pairs. Molecular orbital calculations suggest that these hydrogen bonds are generally extended with bond lengths around 3A.

Base Sequence↗
PubMed1999

Application of DNA-based tests for diagnosis of spinal muscular atrophy in Saudi Arabia.

We examined the deletion of the survival motor neuron (SMN) and neuronal apoptosis inhibitory protein (NAIP) genes in patients with spinal muscular atrophy (SMA) using polymerase chain reaction followed by restriction site assay methods. The study included 16 Saudi patients (9 SMA type I and 7 SMA type II) and 6 healthy Saudi volunteers. The homozygous deletions of exons 7 and 8 of the telomeric SMN gene, and exon 5 of the NAIP gene were found in all SMA type I patients. Exons 7 and 8 of telomeric SMN were deleted in all SMA type II patients. However, exon 5 of NAIP was deleted in three of the seven cases. All control volunteers and all family members of the patients had normal SMN and NAIP. The incidence of NAIP deletion was higher in the more severe SMA cases and the dual deletion of the SMN and NAIP genes was more common in Saudi SMA type I patients compared with patients of other ethnic groups.

Case-Control Studies↗
PubMed1998

Molecular analysis of the SMN and NAIP genes in Saudi spinal muscular atrophy patients.

In this study we examined the deletion of the SMN and NAIP genes in 14 Saudi families (16 patients and 38 relatives of the patients, including parents and siblings) and six healthy Saudi volunteers. The homozygous deletions of exons 7 and 8 of the telomeric SMN gene and exon 5 of the NAIP gene were found in seven out of eight spinal muscular atrophy (SMA) type-I patients. In seven SMA type-II patients, exons 7 and 8 of telomeric SMN were deleted in six cases and exon 5 of NAIP was deleted in three cases. Three patients with SMA diagnosis did not show either of the above deletions. All control Saudi volunteers and all but two family members of the patients had both normal SMN and NAIP genes. Our results show that the incidence of NAIP deletion is higher in the more severe SMA cases and the dual deletions of the SMN and NAIP genes are more common in Saudi SMA type-I patients compared to patients of other ethnic groups.

Arabs↗
PubMed1998

Myosin light chain phosphatase and kinase abnormalities in fetal sheep pulmonary hypertension.

Inasmuch as smooth muscle contractile protein abnormalities may account for the maintenance of a high pulmonary vascular resistance, we evaluated the pulmonary arterial myosin light chain kinase (MLCK) and phosphatase (MLCP) in normal and pulmonary hypertensive (PH) fetal sheep. In addition, aorta and vena cava MLCP and MLCK activities were also measured. The MLCK activity (nanomoles/min/mg) was determined by the incorporation of [32P]PO4(-3) to the 20-kD smooth muscle myosin light chains and the MLCP activity by assaying for the dephosphorylation of the 20-kD myosin light chain (MLCP-light chain) and heavy meromyosin (MLCP-HMM). The MLCP content was determined by Western blot analysis. PH was characterized by a significant increase in the right-to-left ventricular wall weight ratio from 0.99 +/- 0.04 in the control to 1.52 +/- 0.12 in the experimental group (p < 0.01). The pulmonary MLCP-light chain and MLCP-HMM activities in the experimental group were 2.0 +/- 0.2 and 1.3 +/- 0.2 and significantly lower than in the control group values (3.8 +/- 0.5 and 2.5 +/- 0.3; p < 0.01). The MLCK activity was 9.6 +/- 1.2 in the control and 7.8 +/- 0.7 in the experimental fetal pulmonary artery (p = NS). The activities of both enzymes in the aorta and vena cava samples were not altered by PH. The MLCP content in experimental animals (0.50 +/- 0.09 OD x mm2) was significantly lower than that for the control pulmonary tissue (1.72 +/- 0.42; p < 0.01), suggesting that PH down-regulates pulmonary vascular MLCP expression. In conclusion, the maintenance of a high pulmonary vascular resistance in PH may be secondary to abnormalities in tissue content and/or activity of MLCP.

Animals↗
PubMed1997

Identification of membrane spanning beta strands in bacterial porins.

The membrane assembly of outer membrane proteins is more complex than that of transmembrane helical proteins owing to the intervention of many charged and polar residues in the membrane. Accordingly, the predictive accuracy of transmembrane beta strands is considerably lower than that of transmembrane alpha helices. In this paper we develop a set of conformational parameters for membrane spanning beta strands. We formulate an algorithm to predict the transmembrane beta strands in the family of bacterial porins based on the conformational parameters and surrounding hydrophobicities of amino acid residues. A Fortran program has been developed which takes the amino acid sequence as the input file and gives the predicted transmembrane beta strand as output. The present method predicts at an accuracy level of 82% for all the bacterial porins considered.

Amino Acid Sequence↗
PubMed1996

Ligand binding isotherm for DNA in the presence of supercoil-induced non-B form: a theoretical analysis.

A binding isotherm in the form of a modified McGhee-Von Hippel equation is proposed, on the basis of thermodynamical considerations, to include the non-cooperative binding of extended ligands to supercoiled DNA, where a stretch of non-B form may be present under superhelical stress. It is then studied, on the basis of a non-linear Scatchard plot, how the presence of an intercalating ligand can relax the supercoiled molecule and thus destabilise the non-B stretch, which may be recognised by the existence of a significant kink in the Scatchard plot.

Journal Article↗
PubMed1995

Evidence of a temperature-sensitive step in the release of prostaglandin E2 in calcium ionophore-stimulated rat muscle.

Recent studies have shown that mild hypothermia (32-35 degrees C) confers striking protection against ischemic muscle and neuronal injuries, although the mechanisms are unknown. We previously demonstrated that the release of prostaglandin E2 (PGE2) from metabolically stressed muscles was dependent on calcium and was abolished at or below 35 degrees C. In this study, we examined the temperature response of the release of arachidonic acid (AA) and its cyclooxygenase metabolites, PGE2 and prostaglandin F2 alpha (PGF2 alpha) from rat skeletal muscle in the presence of calcium ionophore A23187, an agent that directly elevates intracellular calcium. Calcium ionophore markedly stimulated the release of AA, PGE2 and PGF2 alpha at 37 degrees C, as expected. Reducing the temperature to 35 degrees C and below sharply decreased PGE2 and PGF2 alpha release but not AA release. The activity of phospholipase A2 stimulated by calcium ionophore was unaffected when temperature of incubation was lowered from 37 to 32 degrees C. The results suggest that reducing temperature from 37 degrees C to 35 degrees C or below inhibits the conversion from free arachidonate to PGs in calcium ionophore-stimulated muscle.

Animals↗
PubMed1994

Effects of calcium channel antagonists on the release of prostaglandin E2 from metabolically stressed muscle.

Calcium influx plays a critical role in the activation of the arachidonic cascade in muscle damage. We examined the effects of L-type calcium channel antagonists on the release of prostaglandin E2 (PGE2), a bioactive metabolite of arachidonic acid metabolism, from skeletal muscle. The basal release of PGE2 was not affected by calcium channel inhibitors, such as nifedipine and verapamil. The release of PGE2 induced by dinitrophenol, an uncoupler of oxidative phosphorylation, was abolished by nifedipine and verapamil at 50 and 150 microM, respectively. It was not necessary to include the calcium channel blockers in the medium before or at the time of dinitrophenol stimulation to produce the effect on PGE2 release. The release of PGE2 was prevented for as long as calcium channel blockers were present in the medium after the dinitrophenol stress.

2,4-Dinitrophenol↗
PubMed1994

Mild hypothermia preserves contractile function and inhibits prostaglandin E2 release from metabolically stressed skeletal muscle.

An in vitro model of muscle damage was used to investigate the protective effect of mild hypothermia in muscle injury. Rat epitrochlearis muscles were dissected in their entirety and suspended in Krebs-Ringer solution and DNP, a mitochondrial uncoupler, was added. PGE2 and lactate release and the contractile response to stimulation were measured and compared to untreated controls. Experiments were done at 37, 35, 33 and 27 degrees C. At 37 degrees C, DNP stimulated muscle releases large amounts of PGE2 and lactate and is unable to contract. As the temperature is reduced, there is progressive preservation of contractile force, although high lactate levels at the lowest temperatures indicate that the metabolic stress is still present. In contrast, DNP stimulated PGE2 release is completely inhibited at or below 35 degrees C and may be related to a similar protective phenomenon seen in experimental ischemic neuronal death.

Animals↗
PubMed1993

Relationship of oxypurine release to contractile failure in dinitrophenol-treated rat skeletal muscle.

The efflux of hypoxanthine and uric acid from skeletal muscle has been noted to follow exercise and metabolic stress both in vivo and in vitro. Since the action of xanthine oxidase and hypoxanthine generates free radicals with potential damaging effect on the muscle membranes, an in vitro model was used to study the relationship of metabolic stress, oxypurine release and muscle contraction. When rat epitrochlearis muscle was exposed to the mitochondrial uncoupler dinitrophenol at 37 degrees C, lactate release was pronounced and hypoxanthine and uric acid appeared in the incubating medium. The twitch tension, in response to supramaximal stimulation, was reduced to less than 5% of the initial value. When the same experiment was repeated at 27 degrees C, hypoxanthine and uric acid formation was inhibited, although lactate release indicated that metabolic stress was still present. Twitch tension was relatively preserved (57% of the initial value). The lower temperature did not alter the decrease in ATP and phosphocreatine levels in the muscle which is produced by dinitrophenol. There was an inverse relationship between oxypurine release and twitch tension in individual muscles (r = 0.80, P < 0.01 for hypoxanthine and r = 0.95, P < 0.0002 for uric acid). Xanthine dehydrogenase/xanthine oxidase was detected in muscle and between 16 and 22% of the activity was in the oxidase form.

2,4-Dinitrophenol↗