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S Das

Publications and source records attributed to S Das.

At least 235 records · Page 13Linked to original sources
PubMed1999

Gating kinetics of E. coli poly-3-hydroxybutyrate/polyphosphate channels in planar bilayer membranes.

Nonproteinaceous calcium channel complexes from Escherichia coli, composed of poly-(R)-3-hydroxybutyrate (PHB) and inorganic polyphosphate (polyP), exhibit two distinct gating modes (modes 1 and 2) in planar lipid bilayers. Here we report the kinetic characterization of the channel in mode 2, a mode characterized by two well-defined conductance levels, a fully open state (87 +/- 3 pS), and a major subconductance state (56 +/- 2 pS). Other subconductance states and full closures are rare (<0.5% of total time). Several kinetic properties of the channel showed asymmetric voltage-dependence indicating an asymmetry in the channel structure. Accordingly, single channels responded to potential change in one of two mirror-image patterns, postulated to arise from opposite orientations of the asymmetrical channel complex in the bilayer. The fraction of time spent in each conductance level was strongly voltage-sensitive. For channels reported in this study, presumably all oriented in the same direction, residence time in the fully open state increased as clamping potentials became more positive whereas residence time in the major subconductance state increased at more negative potentials. Analysis of open time distributions revealed existence of two kinetically distinct states for each level. The shorter time constants for both conductance states exhibited weak voltage-sensitivity; however, the longer time constants were strongly voltage-sensitive. A kinetic scheme, consistent with the complex voltage dependence of the channel, is proposed.

Animals↗
PubMed1999

Spectroscopic studies on the interaction of aristololactam-beta-D-glucoside with DNA and RNA double and triple helices: A comparative study.

The interaction of aristololactam-beta-D-glucoside (ADG), a DNA intercalating alkaloid, with the DNA triplexes, poly(dT). poly(dA)xpoly(dT) and poly(dC).poly(dG)xpoly(dC+), and the RNA triplex poly(rU).poly(rA)xpoly(rU) was investigated by circular dichroic, UV melting profile, spectrophotometric, and spectrofluorimetric techniques. Comparative interaction with the corresponding Watson-Crick duplexes has also been examined under identical experimental conditions. Triplex formation has been confirmed from biphasic thermal melting profiles and analysis of temperature-dependent circular dichroic measurements. The binding of ADG to triplexes and duplexes is characterized by the typical hypochromic and bathochromic effects in the absorption spectrum, quenching of steady-state fluorescence intensity, a decrease in fluorescence quantum yield, an increase or decrease of thermal melting temperatures, and perturbation in the circular dichroic spectrum. Scatchard analysis indicates that ADG binds both to the triplexes and the duplexes in a noncooperative manner. Binding parameters obtained from spectrophotometric measurements are best fit by the neighbor exclusion model. The binding affinity of ADG to the DNA triplexes is substantially stronger than to the RNA triplex. Thermal melting study further indicates that ADG stabilizes the Hoogsteen base-paired third strand of the DNA triplexes whereas it destabilizes the same strand of RNA triplex but stabilizes its Watson-Crick strands. Comparative data reveal that ADG exhibits a stronger binding to the triple helical structures than to the respective double helical structures.

Alkaloids↗
PubMed1999

Conversions of the left-handed form and the protonated form of DNA back to the bound right-handed form by sanguinarine and ethidium: a comparative study.

The interaction of sanguinarine and ethidium with right-handed (B-form), left-handed (Z-form) and left-handed protonated (designated as H(L)-form) structures of poly(dG-dC).poly(dG-dC) and poly(dG-me5dC).poly(dG-me5dC) was investigated by measuring the circular dichroism and UV absorption spectral analysis. Both sanguinarine and ethidium bind strongly to the B-form DNA and convert the Z-form and the H(L)-form back to the bound right-handed form. Circular dichroic data also show that the conformation at the binding site is right-handed, even though adjacent regions of the polymer have a left-handed conformation either in Z-form or in H(L)-form. Both the rate and extent of B-form to Z-form transition were decreased by sanguinarine and ethidium under ionic conditions that otherwise favour the left-handed conformation of the polynucleotides. The rate of decrease is faster in the case of ethidium as compared to that of sanguinarine. Scatchard analysis of the spectrophotometric data shows that sanguinarine binds strongly to both the polynucleotides in a non-cooperative manner under B-form conditions, in sharp contrast to the highly-cooperative binding under Z-form and H(L)-form conditions. Correlation of binding isotherms with circular dichroism data indicates that the cooperative binding of sanguinarine under the Z-form and the H(L)-form conditions is associated with a sequential conversion of the polymer from a left-handed to a bound right-handed conformation. Determination of bound alkaloid concentration by spectroscopic titration technique and the measurement of circular dichroic spectra have enabled us to calculate the number of base pairs of Z-form and H(L)-form that adopt a right-handed conformation for each bound alkaloid. Analysis reveals that 2-3 base pairs (bp) of Z-form of poly(dG-dC).poly(dG-dC) and poly(dG-me5dC).poly(dG-me5dC) switch to the right-handed form for each bound sanguinarine, while approximately same number of base pairs switch to the bound right-handed form in complexes with H(L)-form of these polynucleotides. Comparative binding analysis shows that ethidium also converts approximately 2 bp of Z-form or H(L)-form to bound right-handed form under same experimental conditions. Since sanguinarine binds preferentially to alternating GC sequences, which are capable of undergoing the B to Z or B to H(L) transition, these effects may be an important part in understanding its extensive biological activities.

Journal Article↗
PubMed1999

Structure and function of a small RNA that selectively inhibits internal ribosome entry site-mediated translation.

A 60 nt long RNA termed IRNA, isolated from the yeast Saccharomyces cerevesiae, was previously shown to selectively block internal ribosome entry site (IRES)-mediated translation without interfering with cap-dependent translation of cellular mRNAs both in vivo and in vitro. IRNA specifically bound cellular proteins believed to be important for IRES-mediated translation. We demonstrate here that a complementary copy of IRNA (cIRNA) is also active in blocking IRES-mediated translation and that it binds many of the same cellular proteins that IRNA does. We have probed the secondary structure of both IRNA and cIRNA using single-strand- and double-strand-specific nucleases as well as using oligonucleotide hybridization followed by RNase H digestion. Both IRNA and cIRNA share secondary structural homology, although distinct differences do exist between the two structures. Mutational analysis of IRNA shows that sequences that form both the main stem and one loop are critical for its translation inhibitory activity. Maintenance of the established secondary structure appears to be required for both IRNA's ability to bind cellular trans -acting proteins believed to be required for IRES-mediated translation and its ability to block IRES-mediated translation.

Computer Simulation↗
PubMed1999

Trisomy 8 in stage I and stage III ovarian cancer detected by fluorescence in situ hybridization.

Ovarian cancer is the leading cause of death from gynecologic maligancy among women in the United States. In 1997, there were nearly 27,000 ovarian cancer cases with over 14,000 deaths. Recent attempts at early detection of ovarian cancer have been aimed at the identification of biomarkers that would indicate an underlining malignant process or reflect the biological behavior of the tumor. Our previous studies revealed that chromosome 8 copy number abnormality, especially trisomy, is common in several cancers. Archival tissues from 24 cases of papillary serous ovarian carcinoma (10 stage I and 14 stage III) were analyzed by fluorescence in situ hybridization (FISH) with a chromosome 8-specific alpha-satellite probe (Oncor, Gaithersburg, MD). The analysis was done according to standard protocols of the Lifespan Academic Medical Center Cytogenetics Laboratory at Rhode Island Hospital. Twenty-one of 24 cases (87.5%) were found to be trisomic for chromosome 8, if a cutoff point of >/=15% cells with three signals is adopted. Overall, 80% of stage I and 93% of stage III tumors had trisomy 8. This study confirms the presence of a high frequency of trisomy 8 in both early and late stages of the disease and suggests that trisomy 8 may be an early event in the multistep process leading to ovarian cancer. It is of interest to note that a higher frequency of trisomy 8 was found in a higher stage of disease, consistent with our previous results on breast cancer. Thus, additional FISH studies of ovarian tumors for chromosome 8 copy number assessment may be warranted.

Adult↗
PubMed1999

Fluorescence in situ hybridization study of HER-2/neu oncogene amplification in prostate cancer.

Prostate cancer is a serious disease affecting men worldwide and treatment compromises the quality of life of prostate cancer patients. We conducted a study of 88 cases of prostate cancer in an attempt to identify prognostic biomarkers that can distinguish aggressive cases that must be treated immediately. HER-2/neu oncogene amplification was initially studied because amplification of this gene has been reported in many other cancers, including those studied in this laboratory. Fluorescence in situ hybridization (FISH) using a HER-2/neu gene probe with a chromosome 17 centromere control probe was performed on formalin-fixed, paraffin-embedded tissues. Of a total of 86 cases successfully analyzed, only 8 (9.3%) were found to be amplified. This frequency was lower than the frequency of amplification found in other cancers studied. Furthermore, no case was found where the level of amplification can be considered high. Only one case was found to have moderate amplification. The rest of the positive cases can all be classified as low amplification. Thus, while we have demonstrated that FISH is a sensitive technique for detecting oncogene amplification, the frequency and level of HER-2/neu amplification detected in prostate cancer seem to be lower than those in most cancers that we studied. In view of the fact that HER-2/neu amplification does not seem to play as significant a role, exploration of other biomarkers in prostate cancer is warranted.

Aged↗
PubMed1999

Assessment of chromosome 8 copy number in cervical cancer by fluorescent in situ hybridization.

Cervical carcinoma is a malignancy which typically occurs at the transformation zone between squamous and glandular epithelium. The vast majority falls into two histologic types, squamous cell and adenocarcinoma. In an effort to identify a subset of cervical cancer characterized by chromosome 8 trisomy, a biomarker extensively explored by this laboratory, we conducted a study of formalin-fixed, paraffin-embedded materials of cervical cancer. A total of 24 cases of cervical cancer were identified from the archives of the Rhode Island Hospital. Fluorescent in situ hybridization (FISH) using a chromosome 8 centromere enumeration probe was conducted to assess the chromosome 8 copy number in these specimens. Hybridization signals were scored among tumor cells in a blinded fashion. Tumors with >/=15% of cells with three signals were scored as trisomic. Of 24 cases studied, 23 were informative. Of the 23 informative cases, 12 (52.2%) were found to be trisomic. Eleven cases (47.8%) were disomic. The frequency of trisomy in a control chromosome 17 probe was 13.0% (3/23). Selected clinicopathologic characteristics of the tumors were also reviewed. The frequency of trisomy 8 among cases of invasive squamous cell carcinoma was 44.4% (8 of 18 tumors) and that of invasive adenocarcinoma was 80% (4 of 5 tumors). The sole tumor which was both trisomic 8 and amplified for the HER-2/neu oncogene was found to be an invasive adenocarcinoma. While the sample size in this pilot study is not large, the data obtained thus far clearly demonstrate that FISH is an appropriate technique for detecting chromosomal trisomies and that a subset of cervical cancer exists that is characterized by chromosome 8 trisomy. Further exploration of this biomarker is warranted.

Adenocarcinoma↗
PubMed1999

Assessment of chromosomal trisomies in prostate cancer using fluorescent in situ hybridization.

In a previous study, we observed a low frequency of HER-2/neu oncogene amplification in prostate cancer using fluorescent in situ hybridization (FISH). In our continued effort to identify prognostic biomarkers in prostate cancer, we analyzed 74 cases of prostate cancer to assess the presence of chromosomal trisomies in this cohort of patients. Previous results from this laboratory have implicated a role of chromosomal trisomies in various cancers. FISH using a chromosome 7 and a chromosome 8 centromere probe was utilized to study abnormal chromosome copy numbers together with data from a chromosome 17 control. The frequency of trisomy 7 was found to be 58.1% (43 of 74 informative cases), while the frequency of trisomy 8 was found to be 9.5% (7 of 74 informative cases). The frequency of cells showing chromosome 17 trisomy was 18.5% (15 of 81 cases successfully studied). While chromosome 8 trisomy did not seem to play as significant a role here as in other cancers that we studied, the results of chromosome 7 trisomy are consistent with those reported in the literature. Further exploration of selected trisomies as biomarkers in prostate cancer using a larger study sample size is warranted to establish their clinical utilities.

Aged↗
PubMed1999

Giardia lamblia: incorporation of free and conjugated fatty acids into glycerol-based phospholipids.

Giardia lamblia trophozoites are flagellated protozoa that inhabit the human small intestine, where they are exposed to various dietary lipids and fatty acids. It is believed that G. lamblia, which colonizes a lipid-rich environment of the human small intestine, is unable to synthesize phospholipids, long-chain fatty acids, and sterols de novo. Therefore, it is possible that this protozoan has developed a special process for acquiring lipids from its host. We have previously shown that G. lamblia can take up saturated fatty acids and incorporate them into phosphatidylglycerol (PG) and other glycerol-based phospholipids (Stevens et al., Experimental Parasitology, 86, 133-143, 1997). In the present study, an attempt has been made to investigate the underlying mechanisms of transesterification and interesterification reactions of giardial phospholipids by free and conjugated fatty acids. Results show that exogenously supplied, unsaturated, fatty acids were taken up by Giardia and incorporated into various phosphoglycerides, including PG. To test whether this intestinal pathogen can utilize conjugated fatty acids, live trophozoites were exposed to either [3]H;cbphosphatidylcholine (PC), where the fatty acid was 3H-labeled at its sn2 position, or to [14C]lyso-PC (fatty acid was 14C-labeled at the sn1 position) for 90 min, followed by phospholipid analysis using thin-layer chromatography. The results suggest that conjugated fatty acids, like free fatty acids, were incorporated into PG. It was also observed that aristolochic acid, an inhibitor of Ca2+-ionophore-stimulated phospholipase A2, decreased the transfer of fatty acids from [3H]PC to PG, indicating that giardial phospholipases were involved in these esterification reactions. Additional experiments, which include culturing trophozoites in serum-supplemented and serum-deprived medium, along with numerous biochemical analyses suggest that (i) PG is a major transesterified and interesterified product, (ii) it is likely that giardial phospholipases are involved in esterification reactions, (iii) in G. lamblia, PG is localized in perinuclear membranes, as well as intracellularly, but not in the plasma membrane, and (iv) various synthetic analogs of PG inhibit the growth of the parasite in vitro. These studies suggest that PG is an important phospholipid of Giardia and a potential target for lipid-based chemotherapy against giardiasis.

Animals↗
PubMed1999

Benign triton tumor of the trigeminal nerve.

Benign triton tumor (neuromuscular hamartoma) is a rare tumor of the peripheral nerves, comprising mature neural and striated muscle elements. We report the third case, according to the literature, of a benign triton tumor affecting the Vth cranial nerve in a 4-year-old male child. The tumor was seen to involve the mandibular division of the trigeminal nerve in the infratemporal fossa and extend intracranially by eroding the base of middle cranial fossa. The mass was totally excised. In the tumor, bundles of axons intermingling with fascicles of relatively mature skeletal muscle were found. This type of hamartomatous lesions of neuroectodermal-mesenchymal origin could have arisen as the result of incorporation of mesenchymal tissue into nerve sheaths during embryogenesis or aberrant differentiation of neuroectodermal component into mesenchymal elements.

Child, Preschool↗
PubMed1999

Hypothalamic-pituitary-thyroid axis status of humans during development of ageing process.

We have investigated hypothalamic-pituitary-thyroid function in four groups of healthy elderly male humans. Group A (n=18, age range 20-45 years) served as healthy younger controls, group B (n=10, age range 50-60 years), group C (n=15, age range 60-70 years) and group D (n=16, age range 70-85 years) are the subjects of this study. Groups C and D showed significantly lower T3 and thyroid-stimulating hormone (TSH), and higher T4 levels with respect to controls. Evidence for TSH circadian modulation was found in group A (control) and group B subjects. The TRH-stimulated TSH peak was reduced among all elderly subjects with respect to controls and appeared to be pronounced with the ageing process. The maximal prolactin response was also inhibited with increasing age. Our study suggest that a resetting of the pituitary threshold for the TSH feed-back suppression along with complex alterations in peripheral thyroid hormone concentrations may, in turn, develop in older people and that appeared to manifest prominently among the oldest population. Additionally, the TSH nocturnal response appeared to be impaired with increasing age indicating an alteration of hypothalamic function.

Adult↗
PubMed1999

Phenotype-genotype correlation of in vitro SN-38 (active metabolite of irinotecan) and bilirubin glucuronidation in human liver tissue with UGT1A1 promoter polymorphism.

BACKGROUND: Hepatic uridine diphosphate glucuronosyltransferase (UGT) isoform 1A1 (UGT1A1) is primarily responsible for the glucuronidation of SN-38 (7-ethyl-10-hydroxycamptothecin), the active metabolite of the anticancer agent irinotecan. UGT1A1, also catalyzing the glucuronidation of bilirubin, has been shown to have reduced activity in Gilbert's syndrome. The presence of an additional TA repeat [(TA)7TAA] in the TATA sequence of UGT1A1 has been associated with Gilbert's syndrome. OBJECTIVE: To evaluate the relationship between UGT1A1 phenotypic activity and UGT1A1 promoter polymorphism. METHODS: Phenotypic measurements included in vitro SN-38 and bilirubin glucuronidation in human liver microsomes (n = 44). A recently developed genotyping test was used to determine TATA sequence polymorphisms in UGT1A1. Genotypes were assigned as follows: 7/7, homozygous for the (TA)7TAA allele; 6/6, homozygous for the (TA)6TAA allele; and 6/7, heterozygous with 1 of each allele. RESULTS: Nine percent of screened liver samples were found to be homozygous for allele 7 (7/7), 43% were homozygous for allele 6 (6/6), and 48% were heterozygous (6/7). Frequencies of (TA)7TAA and (TA)6TAA alleles were 0.33 and 0.67, respectively. A significant trend toward a decrease in SN-38 and bilirubin glucuronidation rates was found as the number of TA repeats increased (6/6 > 6/7 > 7/7). Glucuronidation rates of both substrates were significantly lower in the 7/7 and 6/7 groups compared with the 6/6 group. CONCLUSIONS: The results indicate a significant association of UGT1A1 phenotype and genotype based on in vitro phenotypic measurements. The clinical significance of our finding remains to be established.

Antineoplastic Agents, Phytogenic↗
PubMed1999

A distributed model of the saccade system: simulations of temporally perturbed saccades using position and velocity feedback.

Interrupted saccades, movements that are perturbed in mid-flight by pulsatile electrical stimulation in the omnipause neuron region, are known to achieve final eye displacements with accuracies that are similar to normal saccades even in the absence of visual input following the perturbation. In an attempt to explain the neurophysiological basis for this phenomenon, the present paper describes a model of the saccadic system that represents the superior colliculus as a dynamic two-dimensional, topographically arranged array of laterally interconnected units. A distributed feedback pathway to the colliculus from downstream elements, providing both eye position and velocity signals is incorporated in the model. With the help of a training procedure based on a genetic algorithm and gradient descent, the model is optimized to produce both the normal as well as slow saccades with similar accuracy. The slow movements are included in the training set to mimic the accurate saccades that occur despite alterations in alertness, as well as following various degenerative oculomotor diseases. Although interrupted saccades were not included in the training set, the model is able to produce accurate movement of this type as an emergent property for a wide range of perturbed eye velocity trajectories. Our model demonstrates for the first time, that by means of an appropriate feedback mechanism, a single-layered dynamic network can be made to retain a distributed memory of the remaining ocular displacement error even for interrupted and slow saccades. These results support the hypothesis that saccades are controlled by error feedback of signals that code efference copies of eye motion, and further, suggest a possible answer to a long standing question about the kind of the feedback signal, if any, that is received by the superior colliculus during saccadic eye movements.

Journal Article↗
PubMed1999

Oxidant, mitochondria and calcium: an overview.

Mitochondria are active in the continuous generation of reactive oxygen species (ROS), (e.g., superoxide), thereby favouring a situation of mitochondrial oxidative stress. Under oxidative stress--for example, ischaemia-reoxygenation injury to cells--mitochondria form superoxide, which in turn is converted to hydrogen peroxide and the potent reactive species, hydroxyl radical. Alternatively, mitochondrial superoxide may react with nitric oxide to form potent oxidant peroxynitrite and as a consequence, mitochondrial function is altered. An increase in the release of calcium from mitochondria by oxidants stimulates calcium-dependent enzymes such as calcium-dependent proteases, nucleases, and phospholipases, which subsequently trigger apoptosis of the cells. In principle, calcium can leave mitochondria by different ways: by non-specific leakage through the inner membrane by "pore formation," by changes in the membrane lipid phase, by reversal of the uniport influx carrier, by the specific calcium/hydrogen (or sodium) antiport system, by channel-mediated release pathways, or by a combination of two or more of these pathways. Additionally, the release of calcium from mitochondria can also occur either by oxidation of internal nicotinamide adenine nucleotides to ADP ribose and nicotinamide or by oxidation of thiols in membrane proteins. Once calcium efflux has been triggered, a series of common pathways of apoptosis are initiated, each of which may be sufficient to destroy the cell. Apoptosis requires the active participation of cellular components, and several genes have been suggested to control apoptosis. The proto-oncogene bcl-2 suppresses apoptosis through mitochondrial effects. Overexpression of bcl-2 in the mitochondrial membrane inhibits calcium efflux, but the underlying mechanisms are not clearly known. Further studies are needed to explore the nature of the apoptosis-inducing pathways, the precise mechanisms of calcium efflux, the molecular partners of bcl-2 oncoproteins at the level of the outer-inner membrane contact sites, the molecular biology of the apoptosis-inducing factor formation and release, and the essential molecular targets of apoptosis-inducing proteases. Clarification of these issues might facilitate the understanding of mitochondrial response on cellular calcium dynamics under oxidant stress.

Adenosine Diphosphate↗
PubMed1999

TNF-alpha induced altered signaling mechanism in human neutrophil.

In the present study we investigated the TNF-alpha induced signal transduction mechanism in human neutrophil. Exogenously added TNF-alpha affects both PKC activity and its translocation from cytosol to the membrane. Endogenous protein phosphorylation pattern is inhibited in TNF-alpha induced neutrophil in Ca-dependent and Ca-independent manner, including a major 47 and 66 kDa cytosolic proteins, which may be implicated in superoxide anion generation. However TNF-alpha dose dependently enhances the expression of zeta-PKC isotype but not the beta-PKC. Morphology and cell cytotoxicity are studied in TNF-alpha treated neutrophil to understand the TNF-alpha induced cell death or apoptosis and these experiment is further confirmed by DNA fragmentation analysis. These results clearly demonstrate that TNF-alpha induces cellular death of human neutrophil at least in part by enhanced expression of Ca-independent zeta-PKC. These observations provide an insight towards understanding the function of zeta-PKC in apoptotic pathway.

Apoptosis↗