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R Sengupta

Publications and source records attributed to R Sengupta.

At least 19 recordsLinked to original sources
PubMed2006

The role of histone modifications in epigenetic transitions during normal and perturbed development.

Epigenetic mechanisms control eukaryotic development beyond DNA-stored information. DNA methylation, histone modifications and variants, nucleosome remodeling and noncoding RNAs all contribute to the dynamic make-up of chromatin under distinct developmental options. In particular, the great diversity of covalent histone tail modifications has been proposed to be ideally suited for imparting epigenetic information. While most of the histone tail modifications represent transient marks at transcriptionally permissive chromatin, some modifications appear more robust at silent chromatin regions, where they index repressive epigenetic states with functions also outside transcriptional regulation. Under-representation of repressive histone marks could be indicative of epigenetic plasticity in stem, young and tumor cells, while committed and senescent (old) cells often display increased levels of these more stable modifications. Here, we discuss profiles of normal and aberrant histone lysine methylation patterns, as they occur during the transition of an embryonic to a differentiated cell or in controlled self-renewal vs pro-neoplastic or metastatic conditions. Elucidating these histone modification patterns promises to have important implications for novel advances in stem cell research, nuclear reprogramming and cancer, and may offer novel targets for the combat of tumor cells, potentially leading to new diagnostic and therapeutic avenues in human biology and disease.

Animals↗
PubMed2004

Accuracy of absence of fetal breathing movements in predicting preterm birth: a systematic review.

OBJECTIVE: To determine the accuracy with which the absence of fetal breathing movements on ultrasound examination predicts spontaneous preterm birth in women with threatened preterm labor. METHODS: Data sources included Medline, Embase, Pascal, Biosis, Cochrane Library, Medion, National Research Register, SciSearch, conference papers, and manual searching of bibliographies of known primary and review articles. A study was selected if it used absence of fetal breathing movements on ultrasound to predict spontaneous preterm birth in women with threatened preterm labor but before advanced cervical dilatation. Two reviewers independently selected studies and extracted data on their characteristics, quality and accuracy. Accuracy data were used to form 2 x 2 contingency tables with birth within 48 h and within 7 days of testing as the reference standards. Likelihood ratios for a positive test (LR+) and negative test (LR-) were calculated as a measure of accuracy. RESULTS: There were eight studies, which included a total of 328 women, evaluating the accuracy of absence of fetal breathing movements in predicting spontaneous preterm birth in women with threatened preterm labor. There were differences in the methodological quality among the included studies. All were lacking in one or more item that make up an ideal test accuracy study. For women presenting with threatened preterm labor, meta-analysis showed a summary LR+ of 14.80 (95% CI, 6.30-34.79) with a corresponding summary LR- of 0.46 (95% CI, 0.36-0.58) for predicting preterm birth within 7 days, and summary LR+ of 7.84 (95% CI, 1.12-54.99) and summary LR- of 0.25 (95% CI, 0.13-0.48) for predicting preterm birth within 48 h of testing. CONCLUSION: Absence of fetal breathing movements has the potential to be a useful test in predicting preterm birth both within 7 days and within 48 h of testing. However, the available studies were deficient in their sample size and quality of methodology. Future research should be undertaken to evaluate this technology and to address the methodological deficiencies.

Female↗
PubMed2003

P elements are found in the genomes of nematoceran insects of the genus Anopheles.

We report the identification of genomic sequences in various anopheline mosquitoes (family Culicidae: suborder Nematocera: order Diptera) showing homology to the class II, short inverted-terminal-repeat (ITR) transposable element P from Drosophila melanogaster (family Drosophilidae; suborder Brachycera: order Diptera). Anopheles gambiae appears to have at least six distinct P elements. Other anopheline species, including four additional members of the An. gambiae species complex (An. arabiensis, An. merus, An. melas and An. quadriannulatus), Anopheles stephensi (all subgenus Cellia), An. quadrimaculatus (subgenus Anopheles) and Anopheles albimanus (subgenus Nyssorhynchus) also possess P elements similar to those found in An. gambiae. Ten distinct P element types were identified in the genus Anopheles. At least two of the An. gambiae elements appears to be intact and potentially functional. Phylogenetic analysis of the anopheline P elements reveals them to belong to a distinctly different clade from the brachyceran P elements.

Amino Acid Sequence↗
PubMed2003

Improved gene selection for classification of microarrays.

In this paper we derive a method for evaluating and improving techniques for selecting informative genes from microarray data. Genes of interest are typically selected by ranking genes according to a test-statistic and then choosing the top k genes. A problem with this approach is that many of these genes are highly correlated. For classification purposes it would be ideal to have distinct but still highly informative genes. We propose three different pre-filter methods--two based on clustering and one based on correlation--to retrieve groups of similar genes. For these groups we apply a test-statistic to finally select genes of interest. We show that this filtered set of genes can be used to significantly improve existing classifiers.

Algorithms↗
PubMed2001

Traumatic fracture of the clivus and vermian contusion in a child.

The case of a fracture of the clivus in a 10-year-old boy following a road traffic accident is reported. He also suffered a contusion of the cerebellar vermis and the management dilemma in this case is highlighted. Fracture of the clivus in a child is extremely rare; this is the second reported case and the first reported with survival.

Brain Diseases↗
PubMed2001

Quality control in manufacturing oligo arrays: a combinatorial design approach.

The advent of the DNA microarray technology has brought with it the exciting possibility of simultaneously observing the expression levels of all genes in an organism. One such microarray technology, called "oligo arrays", manufactures short single strands of DNA (called probes) onto a glass surface using photolithography. An altered or missed step in such a manufacturing protocol can adversely affect all probes using this failed step, and is in general impossible to disentangle from experimental variation when using such a defective array. The idea of designing special quality control probes to detect a failed step was first formulated by Hubbell and Pevzner. We consider an alternative formulation of this problem and use a combinatorial design approach to solve it. Our results improve over prior work in guaranteeing coverage of all protocol steps and in being able to tolerate a greater number of unreliable probe intensities.

Combinatorial Chemistry Techniques↗
PubMed2001

Prevention of adrenocortical hyperactivity by dietary casein in rats exposed to forced swimming stress.

Adrenal weight, adrenal hydroxysteroid dehydrogenase activity and serum corticosterone level were significantly higher in rats fed with 5% casein diet after 7 days of swimming stress (45 min/day) as compared to their controls. All the parameters were similar to their control levels in rats receiving 20% casein diet and exposed to swimming stress. The results suggest that casein can play an important role in preventing adrenocortical hyperactivity in swimming stressed rats.

3-Hydroxysteroid Dehydrogenases↗
PubMed2000

Modified constructs of the tRNA TPsiC domain to probe substrate conformational requirements of m(1)A(58) and m(5)U(54) tRNA methyltransferases.

The TPsiC stem and loop (TSL) of tRNA contains highly conserved nucleoside modifications, m(5)C(49), T(54), Psi(55)and m(1)A(58). U(54)is methylated to m(5)U (T) by m(5)U(54)methyltransferase (RUMT); A(58)is methylated to m(1)A by m(1)A(58)tRNA methyltransferase (RAMT). RUMT recognizes and methylates a minimal TSL heptadecamer and RAMT has previously been reported to recognize and methylate the 3'-half of the tRNA molecule. We report that RAMT can recognize and methylate a TSL heptadecamer. To better understand the sensitivity of RAMT and RUMT to TSL conformation, we have designed and synthesized variously modified TSL constructs with altered local conformations and stabilities. TSLs were synthesized with natural modifications (T(54)and Psi(55)), naturally occurring modifications at unnatural positions (m(5)C(60)), altered sugar puckers (dU(54)and/or dU(55)) or with disrupted U-turn interactions (m(1)Psi(55)or m(1)m(3)Psi(55)). The unmodified heptadecamer TSL was a substrate of both RAMT and RUMT. The presence of T(54)increased thermal stability of the TSL and dramatically reduced RAMT activity toward the substrate. Local conformation around U(54)was found to be an important determinant for the activities of both RAMT and RUMT.

Animals↗
PubMed2000

Influence of adrenal cortex on testicular activity in the toad during the breeding season.

The aim of the present study was to determine the role of adrenals in gonadal activity in the male toad during the breeding season. Exogenous administration of corticosterone or metapyrone for 6 days inhibited adrenal delta5-3beta(delta 5-3 beta) hydroxysteroid (delta5-3beta-HSD) and testicular 17beta (17 beta) hydroxysteroid dehydrogenase (17beta-HSD) activities, decreased the serum levels of testosterone and inhibited spermatogenesis. When toads were treated with corticosterone a significant rise of serum corticosterone was noted while metapyrone treatment appeared to decrease serum corticosterone levels. It is concluded that adrenocortical hormone plays an indirect role in testicular activity in toads during the breeding season.

3-Hydroxysteroid Dehydrogenases↗
PubMed2000

Practicalities of nutrition support in chronic liver disease.

The underlying causative agent in the majority of patients with chronic liver disease is ethanol; the rest of the cases are largely viral in aetiology (hepatitis B or C viruses). Nutrition supplementation improves the quality of life and decreases morbidity in chronic liver disease, but evidence that it prolongs long-term survival is lacking. The situation is very different in chronic liver disease patients who receive a liver transplant, however, with better pretransplantation nutrition status predicting a distinctly improved survival after transplantation.

Chronic Disease↗
PubMed2000

Thermal endometrial ablation: a simple technique.

BACKGROUND: To evaluate the effectiveness and safety of a technique for thermal endometrial ablation. METHOD: The study was carried out in three steps; step I on 10 fresh uterine specimens, step II on 14 intact uteri during hysterectomy and step III in five patients, two weeks prior to hysterectomy. A simple device comprising a Foley catheter No. 14F, a three way cannula and a 20 cc syringe was used for the procedure. The balloon of the catheter was inflated within the uterine cavity with boiling normal saline for 9 minutes. Uterine cavity and serosal temperature was recorded during the procedure. Thermal injury was assessed by gross and histological examination of the specimens. RESULTS: The mean maximum endometrial cavity temperature was 91 degrees C whereas serosal temperatures in steps I and II were 34 degrees C and 35.9 degrees C respectively. None of the balloons ruptured in any of the steps and there were no complications. In 13 of 14 specimens in step II, there was a zone of hyperemia with a depth of 3 to 7 mm. The corresponding histological picture was extensive hemorrhage and fragmentation of glands throughout the endometrium including the cornual regions. Consistent findings were noted in step III in which all but one showed extensive coagulative necrosis of the whole of endometrium with edema of the underlying myometrium. There was a statistically significant positive correlation between the volume of fluid injected and depth of hyperemia. CONCLUSION: This technique could be a simple, effective, inexpensive and safe alternative to hysteroscopic endometrial ablation.

Catheter Ablation↗
PubMed1999

Antitesticular effect of copper chloride in albino rats.

Copper chloride treatment adversely affects testicular activity in albino rats. To investigate its antitesticular effects mature (120 days) Wistar strain albino rats were treated intraperitoneally (i.p.) with copper chloride at doses of 1000, 2000 and 3000 micrograms/kg body weight/day for 26 days. Significant reduction of testicular and accessory sex organs (seminal vesicle, ventral prostate) weight, along with inhibition of testicular delta 5-3 beta-hydroxysteroid dehydrogenase (delta 5-3 beta-HSD) and 17 beta-hydroxysteroid dehydrogenase (17 beta-HSD) activity and reduction in plasma testosterone level, were observed at the doses of 2000 and 3000 micrograms/kg body weight/day. The degree of inhibition in all the parameters were increased with the increase of dosage. But no significant change was observed in the above parameters when the animals were treated with 1000 micrograms/kg body weight/day dose. This suggests that copper produces a suppressive influence on male reproductive activity, mainly on testicular weight and steroidogenesis and accessory sex organ weight in a dose-dependent manner.

Animals↗
PubMed1998

Mephentermine hemisulfate monohydrate: an adrenergic agent.

The title molecule, a hydrated hemisulfate salt of ethyl(2-methyl-1-phenyl-2-propyl)ammonium, C11H18N+.0.5SO4(2-).H2O, consists of a phenethylamine skeleton in which the N atom is protonated. There are two molecules in the asymmetric unit, with the S atom of the SO4(2-) ion lying on a pseudo-twofold axis. The ethylamine side chain is in an extended conformation in both the symmetry-independent molecules. The distance of the N atom from the centre of the benzene ring is 5.1 A for molecule 1 and 5.3 A for molecule 2. The packing is stabilized by N-H...O and O-H...O hydrogen bonds.

Adrenergic Agents↗
PubMed1997

[Measurement of intracranial pressure as a factor in the prognosis of the course of serious cranio-encephalic injuries].

We have analyzed the course and outcome in 100 consecutive cases with severe head injuries, all were treated in a uniform manner. Surgery was performed immediately in patients with extracerebral or intracerebral hematomas. Intracranial pressure (ICP) was monitored in all. Forty-five patients recovered with no or minimal neurological deficit, fifteen patients are moderately disabled, four are severely disabled and eight remain in a persistent vegetative state. The mortality was 28%. The favourable outcome in this series suggests that control of intracranial hypertension with careful attention to medical complication can improve the outcome in patients with severe head injuries.

Adult↗
PubMed1995

Importance of modified nucleosides to the structure and function of tRNAs.

Although a few modifications are found in DNA, 93 modified nucleosides have been found in the various RNAs. For the most part, the chemistry and structure that modified nucleosides, individually and in combination, uniquely contribute to DNA or RNA function have yet to be explained. However, there are ten physicochemical contributions that can be attributed to modified nucleosides. Of particular interest is the increasingly documented relationship between the presence of modified nucleosides in tRNAs, and the site and affinity of Mg2+ binding to RNA and its effect on function.

Binding Sites↗
PubMed1994

Aminoacyl-tRNA synthetase and U54 methyltransferase recognize conformations of the yeast tRNA(Phe) anticodon and T stem/loop domain.

The enzyme-catalyzed posttranscriptional modification of tRNA and the contributions of modified nucleosides to tRNA structure and function can be investigated with chemically synthesized domains of the tRNA molecule. Heptadecamer RNAs with and without modified nucleosides and DNAs designed as analogs to the anticodon and T stem/loop domains of yeast tRNA(Phe) were produced by automated chemical synthesis. The unmodified T stem/loop domain of yeast tRNA(Phe) was a substrate for the E coli m5U54-tRNA methyltransferase activity, RUMT. Surprisingly, the DNA analog of the T stem/loop domain composed of d(A,U,G,C) was also a substrate. In addition, the DNA analog inhibited the methylation of unfractionated, undermodified E coli tRNA lacking the U54 methylation. RNA anticodon domains and DNA analogs differentially and specifically affected aminoacylation of the wild type yeast tRNA(Phe). Three differentially modified tRNA(Phe) anticodon domains with psi 39 alone, m1G37 and m5C40, or psi 39 with m1G37 and m5C40,stimulated phenylalanyl-tRNA synthetase (FRS) activity. However, one anticodon domain, with m5C40 as the only modified nucleoside and a closed loop conformation, inhibited FRS activity. Modified and unmodified DNA analogs of the anticodon, tDNA(PheAC), inhibited FRS activity. Analysis of the enzyme activity in the presence of the DNA analog characterized the DNA/enzyme interaction as either partial or allosteric inhibition. The disparity of action between the DNA and RNA hairpins provides new insight into the potential allosteric relationship of anticodon binding and open loop conformational requirements for active site function of FRS and other aaRSs. The comparison of the stimulatory and inhibitory properties of variously modified RNA domains and DNA analogs demonstrates that conformation, in addition to primary sequence, is important for tRNA-protein interaction. The enzyme recognition of various DNA analogs as substrate and/or inhibitors of activity demonstrates that conformational determinants are not restricted to ribose and the standard A-form RNA structure.

Amino Acyl-tRNA Synthetases↗