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R Biswas

Publications and source records attributed to R Biswas.

At least 19 recordsLinked to original sources
PubMed2000

The crystal structure of the octamer [r(guauaca)dC]2 with six Watson-Crick base-pairs and two 3' overhang residues.

The crystal structure of an alternating RNA octamer, r(guauaca)dC (RNA bases are in lower case while the only DNA base is in upper case), with two 3' overhang residues one of them a terminal deoxycytosine and the other a ribose adenine, has been determined at 2.2 A resolution. The refined structure has an Rwork 18.6% and Rfree 26.8%. There are two independent duplexes (molecules I and II) in the asymmetric unit cell, a = 24.95, b = 45.25 and c = 73.67 A, with space group P2(1)2(1)2(1). Instead of forming a blunt end duplex with two a+.c mispairs and six Watson-Crick base-pairs, the strands in the duplex slide towards the 3' direction forming a two-base overhang (radC) and a six Watson-Crick base-paired duplex. The duplexes are bent (molecule I, 20 degrees; molecule II, 25 degrees) and stack head-to-head to form a right-handed superhelix. The overhang residues are looped out and the penultimate adenines of the two residues at the top end (A15) are anti and at the bottom (A7) end are syn. The syn adenine bases form minor groove A*(G.C) base triples with C8-H...N2 hydrogen bonds. The anti adenine in molecule II also forms a triple and a different C2-H...N3 hydrogen bond, while the other anti adenine in molecule I does not, it stacks on the looped out overhang base dC. The 3' terminal deoxycytosines form two stacked hemiprotonated trans d(C.C)+ base-pairs and the pseudo dyad related molecules form four consecutive deoxyribose and ribose zipper hydrogen bonds in the minor groove.

Adenine↗
PubMed2000

Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe.

The protein subunit of Escherichia coli ribonuclease P (which has a cysteine residue at position 113) and its single cysteine-substituted mutant derivatives (S16C/C113S, K54C/C113S and K66C/C113S) have been modified using a sulfhydryl-specific iron complex of EDTA-2- aminoethyl 2-pyridyl disulfide (EPD-Fe). This reaction converts C5 protein, or its single cysteine-substituted mutant derivatives, into chemical nucleases which are capable of cleaving the cognate RNA ligand, M1 RNA, the catalytic RNA subunit of E. coli RNase P, in the presence of ascorbate and hydrogen peroxide. Cleavages in M1 RNA are expected to occur at positions proximal to the site of contact between the modified residue (in C5 protein) and the ribose units in M1 RNA. When EPD-Fe was used to modify residue Cys16 in C5 protein, hydroxyl radical-mediated cleavages occurred predominantly in the P3 helix of M1 RNA present in the reconstituted holoenzyme. C5 Cys54-EDTA-Fe produced cleavages on the 5' strand of the P4 pseudoknot of M1 RNA, while the cleavages promoted by C5 Cys66-EDTA-Fe were in the loop connecting helices P18 and P2 (J18/2) and the loop (J2/4) preceding the 3' strand of the P4 pseudoknot. However, hydroxyl radical-mediated cleavages in M1 RNA were not evident with Cys113-EDTA-Fe, perhaps indicative of Cys113 being distal from the RNA-protein interface in the RNase P holoenzyme. Our directed hydroxyl radical-mediated footprinting experiments indicate that conserved residues in the RNA and protein subunit of the RNase-P holoenzyme are adjacent to each other and provide structural information essential for understanding the assembly of RNase P.

Amino Acid Sequence↗
PubMed2000

Maternal mortality associated with eclampsia and severe preeclampsia of pregnancy.

OBJECTIVE: To analyse factors associated with maternal mortality in eclampsia and preeclampsia. METHOD: Retrospective analysis of 69 maternal deaths due to (eclampsia-61; severe preeclampsia-8) was carried out during a period of 17 years (1982-1998). Maternal condition on admission, associated complications and principal cause of death was analysed in each case. RESULTS: Mean time interval between hospitalization and maternal death was 49.56 +/- 62.01 hrs (1-240 hrs). Twenty (28.9%) women died undelivered. Twenty-three (37.7%) women were in grade IV coma and 52.4% of eclampsia patients had recurrent convulsions (> 10) prior to admission. Associated complications in form of hemorrhage, cerebrovascular accidents, acute renal failure, jaundice, aspiration pneumonia and pulmonary oedema were 30.4, 31.8, 34.8, 18.8, 17.8, and 5.8%, respectively. Maternal mortality in eclampsia was significantly low in time period B (4.1%) when magnesium sulphate was used as an anticonvulsant. CONCLUSIONS: Maternal condition on admission and associated complications are the major determinant of maternal outcome. Use of magnesium sulphate is associated with significant reduction of maternal mortality.

Adult↗
PubMed2000

Vibrio cholerae O139 Bengal: a descriptive study.

A prospective study was conducted to determine the clinical and laboratory characteristics and the clinical course of cholera due to Vibrio cholerae O139 Bengal. The study subjects included 22 adult males with stool culture-proven V. cholerae O139. On enrollment, mean +/- SD concentrations (mmol/L) of serum sodium, potassium, chloride, and bicarbonate were 134 +/- 3, 4 +/- 1, 102 +/- 4, and 13 +/- 4 respectively, and stool sodium, potassium, chloride, and bicarbonate concentrations were 120 +/- 24, 18 +/- 6, 93 +/- 16, and 37 +/- 9 respectively. Seventeen patients (7.8%) had faecal leukocytes ranging from 11 to 50 per high-power field. All V. cholerae O139 isolates (100%) were susceptible to tetracycline, erythromycin, and ciprofloxacin, 92% to furazolidine, and only 5% to trimethoprim-sulphamethaxazole. The median (interquartile) volume of liquid stool during the first 24 hours was 9 (5-12) litre. The median (interquartile) volume of liquid stool and the amounts of intravenous and oral rehydration fluids required during the entire study period were 16 (9-24) litre, 9 (6-18) litre, and 14 (9-20) litre respectively. The median (interquartile) duration of diarrhoea was 80 (48-104) hours. The median (interquartile) duration of excretion of V. cholerae O139 in stool was 5 (3-6) days. Clinical and laboratory features, and case management of cholera due to V. cholerae O139 are very similar to conventional cholera due to V. cholerae O1.

Adolescent↗
PubMed1999

Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using electron paramagnetic resonance spectroscopy.

Ribonuclease P (RNase P) is a catalytic ribonucleoprotein (RNP) essential for tRNA biosynthesis. In Escherichia coli, this RNP complex is composed of a catalytic RNA subunit, M1 RNA, and a protein cofactor, C5 protein. Using the sulfhydryl-specific reagent (1-oxyl-2,2,5, 5-tetramethyl-Delta3-pyrroline-3-methyl)methanethiosulfonate (MTSL), we have introduced a nitroxide spin label individually at six genetically engineered cysteine residues (i.e., positions 16, 21, 44, 54, 66, and 106) and the native cysteine residue (i.e., position 113) in C5 protein. The spin label covalently attached to any protein is sensitive to structural changes in its microenvironment. Therefore, we expected that if the spin label introduced at a particular position in C5 protein was present at the RNA-protein interface, the electron paramagnetic resonance (EPR) spectrum of the spin label would be altered upon binding of the spin-labeled C5 protein to M1 RNA. The EPR spectra observed with the various MTSL-modified mutant derivatives of C5 protein indicate that the spin label attached to the protein at positions 16, 44, 54, 66, and 113 is immobilized to varying degrees upon addition of M1 RNA but not in the presence of a catalytically inactive, deletion derivative of M1 RNA. In contrast, the spin label attached to position 21 displays an increased mobility upon binding to M1 RNA. The results from this EPR spectroscopy-based approach together with those from earlier studies identify residues in C5 protein which are proximal to M1 RNA in the RNase P holoenzyme complex.

Amino Acid Sequence↗
PubMed1999

Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A2.

Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A2 have been determined at around 1.9 A resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P212121. The H48Q and the calcium-loop mutant D49E are isomorphous to the trigonal recombinant enzyme, space group P3121. The two active-site mutants show no major structural perturbations. The structural water is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the second water found in native His48 is absent. In the calcium-loop mutant D49E, the two water molecules forming the pentagonal bipyramid around calcium are absent and only one O atom of the Glu49 carboxylate group is coordinated to calcium, resulting in only four ligands.

Animals↗
PubMed1999

Histopathological study of placental bed biopsy in placenta previa.

BACKGROUND: To study placental bed biopsy changes in placenta previa and normally implanted placenta. SUBJECT AND METHOD: Fifty placental bed biopsies from 50 patients with placenta previa and 50 placental bed biopsies from normally implanted placenta were taken at cesarean section. Placental bed biopsy was stained with hematoxyline and eosin for histological examination. Both the groups were compared for trophoblastic invasion and vascular changes of placental bed spiral arteries. Statistical analysis was done by Chi-square test. RESULTS: Placenta bed biopsy was representative in 42/50 (84%) biopsy samples of the study group (placenta previa) and 35/50 (70%) of the control group (normally located placenta). Trophoblastic giant cell migration into decidua was present in 100% of representative samples of both the groups while migration into myometrium was seen in 66.67% and 51.14% of samples of study and control group. Average number of trophoblastic giant cells per sample was significantly higher in placenta previa (decidua 41.3%, myometrium 52%) than the control group (decidua 17.4%; myometrium 14.5%). Trophoblastic giant cell infiltration into myometrial spiral arterioles was higher in placenta previa (81.83 cells per vessel). Percentage of myometrial spiral arterioles showing physiological changes was significantly higher in the study group (50.39%) compared to the control group (21.14%). Incidence of inflammatory cell infiltration was higher in the study group (42.86%). Hemorrhage into decidua and myometrium were seen in biopsy samples of the placenta previa. CONCLUSION: Placenta previa is associated with significantly higher trophoblastic giant cell infiltration and physiological changes of the myometrial spiral arterioles.

Adult↗
PubMed1998

1.76 A structure of a pyrimidine start alternating A-RNA hexamer r(CGUAC)dG.

The crystal structure of the alternating RNA r(CGUAC)dG with a 3'-terminal deoxy G residue has been determined at 1.76 A resolution. The crystal belongs to the orthorhombic space group C2221, unit-cell dimensions a = 29.53, b = 44.61 and c = 94.18 A, with two independent duplexes (I and II) per asymmetric unit. The structure was solved by the molecular-replacement method. The final R factor was 18.8% using 4757 reflections in the resolution range 8.0-1.76 A. The model contains a total of 496 atoms and 85 solvent molecules. The two duplexes form the repeating unit and stack in the usual head-to-tail (5',3'/5',3') fashion into a pseudocontinuous helical column. Almost all of the 2'-hydroxyl groups are engaged in the three modes of water-mediated interactions to the base N3/O2 atoms, the sugar O4' atoms and the backbone phosphates. Thus, the 2'-hydroxyl group of RNA is probably contributing to the stability of the duplexes.

Biopolymers↗
PubMed1998

Single dose vitamin A treatment in acute shigellosis in Bangladesh children: randomised double blind controlled trial.

OBJECTIVE: To evaluate the efficacy of a single large oral dose of vitamin A in treating acute shigellosis in children in Bangladesh. DESIGN: Randomised double blind controlled clinical trial. SETTING: Dhaka Hospital, International Centre for Diarrhoeal Disease Research, Bangladesh. SUBJECTS: 83 children aged 1-7 years with bacteriologically proved shigellosis but no clinical signs of vitamin A deficiency; 42 were randomised to treatment with vitamin A and 41 formed a control group. INTERVENTION: Children were given a single oral dose of 200,000 IU of vitamin A plus 25 IU vitamin E or a control preparation of 25 IU vitamin E. MAIN OUTCOME MEASURES: Clinical cure on study day 5 and bacteriological cure. RESULTS: Baseline characteristics of the subjects in the two treatment groups were similar. Significantly more children in the vitamin A group than in the control group achieved clinical cure (19/42 (45%) v 8/14 (20%); chi 2 = 5.14, 1 df, P = 0.02; risk ratio = 0.68 (95% confidence interval; 0.50 to 0.93)). When cure was determined bacteriologically, the groups had similar rates (16/42 (38%) v 16/41 (39%); chi 2 = 0.02, 1 df, P = 0.89; risk ratio = 0.98 (0.70 to 1.39)). CONCLUSIONS: Vitamin A reduces the severity of acute shigellosis in children living in areas where vitamin A deficiency is a major public health problem.

Acute Disease↗
PubMed1997

Crystal structure of r(GUGUGUA)dC with tandem G x U/U x G wobble pairs with strand slippage.

To better understand the frequent occurrence of adjacent wobble pairs in ribosomal RNAs we have determined the crystal structure of the RNA duplex, r(GUGUGUA)dC with the 3'-terminal deoxy C residue. Two different crystal forms of the duplex were obtained and both belong to the rhombohedral space group, R3. Crystal form I has hexagonal unit cell dimensions, a = b = 40.82 A and c = 66.09 A and diffracts to 1.58 A resolution, while crystal form II has a = b = 47.11 A and c = 59.86 A, diffracting only to 2.50 A resolution. Both structures were solved by the molecular replacement method using different starting models. In spite of the large differences in the cell dimensions the overall structures in both crystals are similar. Instead of the expected blunt-end duplex with four consecutive G x U pairs, the slippage of the strands resulted in two different tandem G x U/U x G wobble pairs involving two of the central and two of the 5' overhang bases, still yielding a total of four wobble pairs. These tandem wobble pairs are flanked by two Watson-Crick pairs. The A-type duplexes stack in the familiar head-to-tail fashion forming a pseudocontinuous helix. The wobble pairs of the present motif II (G x U/U x G) structure stack with a low twist angle of 25.3 degrees in contrast to that of motif I (U x G/G x U), 38.1 degrees. The four wobble pairs are characteristically heavily hydrated in both the grooves accounting for their stability.

Crystallography, X-Ray↗
PubMed1997

Crystal structure of an alternating octamer r(GUAUGUA)dC with adjacent G x U wobble pairs.

The crystal structure of the RNA duplex, r(GUAUGUA)dC, with a 3'-terminal deoxy C residue, has been determined at 1.38 A resolution. The r(GUAUGU) hexameric consensus sequence is present at the exon-intron junction in pre-mRNAs of yeast and higher eukaryotic organisms. The crystal belongs to the rhombohedral space group R3. The hexagonal unit cell dimensions are a = b = 39.71 A, c = 68.15 A and gamma = 120 degrees with one duplex in the asymmetric unit. The structure was solved using the molecular replacement method. The final model contains 332 atoms of the duplex and 67 solvent molecules. The R-factor is 17.6% (Rfree of 23.1%) for 4035 reflections with F > or = 1.5sigma(F) in the resolution range 10.0 to 1.38 A. The duplex is of the A-type with a pseudodyad relating the two strands. The RNA helix is slightly distorted, in spite of the presence of two adjacent G x U wobble base-pairs located at the center of the helix. The twist angle between the wobble pairs, 38.1 degrees, is above the average value and those between the wobble base-pairs and the flanking Watson-Crick base-pairs, 26.7 degrees and 26.3 degrees, respectively, are lower than the average values. The twist between the junction base-pairs are about 24 degrees. The G x U wobble pairs are bridged by water molecules and solvated in the grooves. G x U base-pairs are as stable as the Watson-Crick A x U pairs and only slightly less stable than the G x C pairs accounting for their frequent occurrence in RNA.

Crystallography, X-Ray↗
PubMed1997

Sequence characterization of the 5' noncoding region of GB virus C/hepatitis G virus.

The nucleotide sequences of the 5' noncoding region of the GB virus C/hepatitis G virus (GBV-C/HGV) were determined in 18 isolates from the United States. Two genotypes have been classified based on the sequence heterogeneity within the 5' noncoding region of GBV-C/HGV. The most distantly related isolates between the two genotypes were 84.6% identical. Sequence identity of the isolates within a genotype was 95-99%. The 5' noncoding region of this virus contains four highly conserved domains. These conserved elements would facilitate the selection of optimal primers for the sensitive detection of GBV-C/HGV RNA by PCR. In addition, they suggest a crucial role for this region in viral replication and/or gene expression. Detection of genotypic variation among GBV-C/HGV infected individuals may provide further insight into the possible pathogenicity and into the transmission of the virus.

Base Sequence↗
PubMed1997

Prevalence of hepatitis G virus in hepatitis C virus (HCV)-infected patients and in HCV-contaminated intravenous immunoglobulin products.

Hepatitis GB virus C/hepatitis G virus (HGV) is an RNA virus, which appears to be transmitted by parenteral exposure to contaminated blood and blood products, and may be associated with clinical hepatitis in humans. The prevalence of HGV was investigated in hepatitis C virus (HCV)-infected patients, and (HCV)-contaminated immune globulin intravenous products (IGIV), manufactured prior to the introduction of viral inactivation processing, and in recipients of these lots. Nested primers, specific for the 5' non-coding region of HGV, were designed and used to test 100 chronic HCV patients, 10 HCV RNA-positive IGIV lots and 36 of the recipients of these products. Hepatitis G virus specificity of the polymerase chain reaction (PCR) products was confirmed by sequencing a number of the amplified products and comparing the results with the published prototype sequence for HGV RNA. HGV RNA was detected in 23 of the 100 (23%) HCV-infected patients. The level of alanine aminotransferase (ALT) was lower in HCV-HGV coinfected patients than those with HCV infection alone. Hence, the severity of HCV infections is not influenced by HGV. Two of the 10 (20%) IGIV lots tested positive for HGV RNA; however, none of the serum samples from recipients of IGIV contained detectable HGV RNA although many were infected with HCV. This suggests that the transmission of HGV RNA from IGIV to the recipients is less efficient than that seen for HCV.

Adult↗
PubMed1997

Correlation of hydrophobicity and packing in A-DNA oligonucleotides.

A-DNA oligomers pack in a slanted fashion with the terminal base pairs abutting into the minor groove of neighboring molecules unlike the other forms of DNA which pack by vertically stacking one over the other into helical columns. To explain the differences in packing we have advanced a hypothesis that the orientation of the sugar-phosphate backbone is different in A-DNA from that in the other forms of DNA, mainly due to the differences in the sugar puckering.

DNA↗
PubMed1997

Effect of hepatitis B virus X protein on the expression of retinoblastoma gene product.

Hepatitis B virus X protein (HBX) was studied for its capacity to form a specific complex with the retinoblastoma tumour suppressor protein (pRB), and for its effect on the expression of pRB. HBX was synthesized by in vitro transcription and translation in the presence of [35S]methionine. The synthesized HBX was assayed for its binding to a glutathione-S-transferase (GST)-pRB fusion protein bound to Sepharose beads. The in vivo binding was investigated by a co-immunoprecipitation and Western blot analysis of the cell extract from a CMV-HBX-transfected hepatoblastoma cell line, Hep G2 cells. These experiments demonstrated that HBX was unable to form a detectable complex with pRB. However, the level of pRB increased considerably in Hep G2 cells transfected with CMV-HBX clone. The alteration of pRB expression by HBX could be a mechanism, contributing to the development of hepatocellular carcinoma (HCC) in human.

Gene Expression Regulation, Neoplastic↗
PubMed1997

Impact of nutrition education on health of the mother and newborn belonging to the poor urban slum community.

To find the nutritional knowledge among mothers of one child of the poor community and to relate status of education to the nutritional health of them and the newborn and to get a thorough knowledge on the impact of nutritional education, a comprehensive study was undertaken in an urban slum area. Nutritional grading was done through scoring system. There were 47 mothers (24.1%) out of 195 having normal nutritional grade and 37 mothers (19%) having severe nutritional grade. There were 80 mothers having 'no knowledge' on maternal nutrition. 'Adequate knowledge' was found in 31 cases. Mothers (n = 80) of 'no knowledge' delivered babies of average weight 2.3 kg whereas 'adequate knowledge' mothers gave birth to babies of average weight 2.9 kg.

Adult↗