Biomedical subjects

S Ramaswamy

Publications and source records attributed to S Ramaswamy.

At least 19 recordsLinked to original sources

PubMed2001

Contributions of valine-292 in the nicotinamide binding site of liver alcohol dehydrogenase and dynamics to catalysis.

The participation of Val-292 in catalysis by alcohol dehydrogenase and the involvement of dynamics were investigated. Val-292 interacts with the nicotinamide ring of the bound coenzyme and may facilitate hydride transfer. The substitution of Val-292 with Ser (V292S) increases the dissociation constants for the coenzymes (NAD(+) by 50-fold, NADH by 75-fold) and the turnover numbers by 3-7-fold. The V292S enzyme crystallized in the presence of NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol has an open conformation similar to the structure of the wild-type apo-enzyme, rather than the closed conformation observed for ternary complexes with wild-type enzyme. The V292S substitution perturbs the conformational equilibrium of the enzyme and decreases the kinetic complexity, which permits study of the hydride transfer step with steady-state kinetics. Eyring plots show that the DeltaH for the oxidation (V(1)) of the protio and deuterio benzyl alcohols is 13 kcal/mol and that the kinetic isotope effect of 4.1 is essentially temperature-independent. Eyring plots for the catalytic efficiency for reduction of benzaldehyde (V(2)/K(p)) with NADH or NADD are distinctly convex, being temperature-dependent from 5 to 25 degrees C and temperature-independent from 25 to 50 degrees C; the kinetic isotope effect of 3.2 for V(2)/K(p) is essentially independent of the temperature. The temperature dependencies and isotope effects for V(1) and V(2)/K(p) are not adequately explained by semiclassical transition state theory and are better explained by hydride transfer occurring through vibrationally assisted tunneling.

Alcohol Dehydrogenase↗

PubMed2001

Androgen depletion activates telomerase in the prostate of the nonhuman primate, Macaca mulatta.

BACKGROUND: The activity of telomerase, an enzyme that synthesizes telomeric repeats at the ends of chromosomes, is not detectable in normal human prostate. However, the majority of human prostate cancers exhibit telomerase activity. Since androgens play a major role in prostate tumorigenesis, we investigated the effect of androgen-depletion on the expression of telomerase activity in the prostate. METHODS: Adult male rhesus monkeys were either bilaterally castrated or subjected to sham surgery (n = 5 each). Approximately 6 weeks later, the animals were killed and the different regions of the prostate gland were removed and frozen immediately. Telomerase activity was assayed using the telomeric repeat amplification protocol. RESULTS: All five regions of the prostate from sham operated control animals failed to exhibit telomerase activity. In the castrated monkey, all regions of the prostate, except for the anterior lobe, expressed high levels of telomerase activity. CONCLUSIONS: Our results indicate that in monkeys, androgen-ablation leads to up-regulation of telomerase activity. The negative-regulation of telomerase activity by androgens is probably lost during prostate tumorigenesis.

Androgens↗

PubMed2001

Active membrane fluctuations studied by micropipet aspiration.

We present a detailed analysis of the micropipet experiments recently reported by J-B. Manneville et al., [Phys. Rev. Lett. 82, 4356 (1999)], including a derivation of the expected behavior of the membrane tension as a function of the areal strain in the case of an active membrane, i.e., containing a nonequilibrium noise source. We give a general expression, which takes into account the effect of active centers both directly on the membrane and on the embedding fluid dynamics, keeping track of the coupling between the density of active centers and the membrane curvature. The data of the micropipet experiments are well reproduced by our expressions. In particular, we show that a natural choice of the parameters quantifying the strength of the active noise explains both the large amplitude of the observed effects and its remarkable insensitivity to the active-center density in the investigated range.

Bacteriorhodopsins↗

PubMed2001

Weak and strong dynamic scaling in a one-dimensional driven coupled-field model: effects of kinematic waves.

We study the coupled dynamics of the displacement fields in a one-dimensional coupled-field model for drifting crystals, first proposed by Lahiri and Ramaswamy [Phys. Rev. Lett. 79, 1150 (1997)]. We present some exact results for the steady state and the current in the lattice version of the model for a special subspace in the parameter space, within the region where the model displays kinematic waves. We use these results to construct the effective continuum equations corresponding to the lattice model. These equations decouple at the linear level in terms of the eigenmodes. We examine the long-time, large-distance properties of the correlation functions of the eigenmodes by using symmetry arguments, Monte Carlo simulations, and self-consistent mode-coupling methods. For most parameter values, the scaling exponents of the Kardar-Parisi-Zhang equation are obtained. However, for certain symmetry-determined values of the coupling constants the two eigenmodes, although nonlinearly coupled, are characterized by two distinct dynamic exponents. We discuss the possible application of the dynamic renormalization group in this context.

Journal Article↗

PubMed2001

Angiogenic role for glycodelin in tumorigenesis.

Angiogenesis plays an important role in neovascularization in tumors. Glycodelin, a hormone-responsive protein, has been detected in tumors of reproductive organs and is found in high levels in the plasma of subjects with gynecological malignancies. Glycodelin is also found in the endothelial cells of the umbilical cord and in the blood vessels of tumors. In this study, we tested whether glycodelin-rich amniotic fluid and a synthetic peptide derived from the sequence of glycodelin peptide (Gp) might promote angiogenic response by examining the migration and tube formation in human umbilical cord vein endothelial cells (HUVECs). Increased migration and tube formation of HUVECs were found in the presence of amniotic fluid and Gp, and this increase was blocked by antibody to Gp and by an anti-vascular endothelial growth factor (VEGF) antibody, suggesting that the angiogenic effects of glycodelin might be mediated by VEGF. The results also showed that Gp significantly increased the release of VEGF protein and mRNA expression in HUVECs, RL-95 (human endometrial carcinoma cells), OVCAR-3 (human ovarian adenocarcinoma cells), EM42 (human endometrial epithelial cells), THP-1 (human monocyte), and MCF-7 and MDA-MB-231 (human breast adenocarcinoma cells) cell lines. VEGF receptor Fit-1 mRNA expression in HUVECs was also increased in the presence of Gp. These findings, together with the suggestion from the literature that glycodelin may have immunosuppressive properties, suggest that glycodelin might play an important role in neovascularization during embryogenesis and tumor development.

Amino Acid Sequence↗

PubMed2001

Operation of the follicle-stimulating hormone (FSH)-inhibin B feedback loop in the control of primate spermatogenesis.

This paper reviews our current understanding of the function and operation of the follicle-stimulating hormone (FSH)-inhibin feedback loop in the male rhesus monkey (Macaca mulatta). Inhibin B is the major testicular inhibin in the monkey, and the pattern of secretion of this hormone during postnatal development is temporally coupled to that of gonadotropin. Inhibin B secretion by the Sertoli cell is stimulated by FSH and inhibited by luteinizing hormone (LH), the latter presumably acting via Leydig cell production of testosterone (T). The dynamics of the FSH-inhibin B feedback loop in the adult monkey is revealed following unilateral orchidectomy (UO). Interestingly, a sustained, 50% deficit in inhibin B secretion occurs after UO and this persistent error signal, in turn, results in elevated concentrations of FSH in the circulation. The elevated secretion of FSH appears to be the principal drive for the increased sperm output by the remaining testis. Available data for the functioning of the FSH-inhibin B feedback loop in the human male are placed in perspective, and a model for the negative feedback regulation of sperm number in primates is proposed.

Animals↗

PubMed2001

Crystal structure of sorbitol dehydrogenase.

Sorbitol dehydrogenase (SDH) is a distant relative to the alcohol dehydrogenases (ADHs) with sequence identities around 20%. SDH is a tetramer with one zinc ion per subunit. We have crystallized rat SDH and determined the structure by molecular replacement using a tetrameric bacterial ADH as search object. The conformation of the bound coenzyme is extended and similar to NADH bound to mammalian ADH but the interactions with the NMN-part have several differences with those of ADH. The active site zinc coordination in SDH is significantly different than in mammalian ADH but similar to the one found in the bacterial tetrameric NADP(H)-dependent ADH of Clostridiim beijerinckii. The substrate cleft is significantly more polar than for mammalian ADH and a number of residues are ideally located to position the sorbitol molecule in the active site. The SDH molecule can be considered to be a dimer of dimers, with subunits A-B and C-D, where the dimer interactions are similar to those in mammalian ADH. The tetramers are composed of two of these dimers, which interact with their surfaces opposite the active site clefts, which are accessible on the opposite side. In contrast to the dimer interactions, the tetramer-forming interactions are small with only few hydrogen bonds between side-chains.

Animals↗

PubMed2001

Definition of a novel binding site on CD8 cells for a conserved region of the MHC class Ib molecule Qa-1 that regulates IFN-gamma expression.

Natural killer (NK) cells and activated CD8 cells both express cytotoxic activity and produce substantial levels of IFN-gamma in response to viral and bacterial infections. In the case of NK cells, cellular activation and IFN-gamma expression are regulated by an interaction between NK receptors and MHC class Ib molecules, including HLA-E/Qa-1. We have used soluble tetrameric complexes of the murine class Ib molecule Qa-1 to define the significance of this interaction for CD8 cells. We find that all CD8 cells express a receptor for Qa-1 and that ligation of this receptor by Qa-1 results in up-regulation of IFN-gamma production.

Animals↗

PubMed2001

Structural basis for substrate specificities of cellular deoxyribonucleoside kinases.

Deoxyribonucleoside kinases phosphorylate deoxyribonucleosides and activate a number of medically important nucleoside analogs. Here we report the structure of the Drosophila deoxyribonucleoside kinase with deoxycytidine bound at the nucleoside binding site and that of the human deoxyguanosine kinase with ATP at the nucleoside substrate binding site. Compared to the human kinase, the Drosophila kinase has a wider substrate cleft, which may be responsible for the broad substrate specificity of this enzyme. The human deoxyguanosine kinase is highly specific for purine substrates; this is apparently due to the presence of Arg 118, which provides favorable hydrogen bonding interactions with the substrate. The two new structures provide an explanation for the substrate specificity of cellular deoxyribonucleoside kinases.

Adenosine Triphosphate↗

PubMed2001

Effect of centrally administered prolactin on gastric and duodenal ulcers in rats.

The effect of centrally administered prolactin on gastric acid secretion and experimentally-induced gastric and duodenal ulcers was studied. The acute gastric ulcer models used were pylorus ligation, indomethacin-induced and ethanol-induced gastric ulcers. Chronic gastric ulcers were induced using acetic acid and duodenal ulcers by cysteamine hydrochloride. In pylorus ligated rats, prolactin (1 microg/kg icv) produced 45% increase in gastric content volume, significant increase in free acidity (P < 0.001), total acidity (P < 0.001) and ulcer index (P < 0.001). It did not show any significant effect on ethanol-induced and indomethacin-induced gastric ulcers. Prolactin increased the ulcer index (P < 0.001) and ulcer score (P < 0.05) in acetic acid-induced chronic gastric ulcers. It also increased ulcer area (P < 0.05) in cysteamine-induced duodenal ulcers. Therefore, the proulcerogenic activity of prolactin was due to its gastric hypersecretory effect.

Acetic Acid↗

PubMed2001

Molecular classification of multiple tumor types.

Using gene expression data to classify tumor types is a very promising tool in cancer diagnosis. Previous works show several pairs of tumor types can be successfully distinguished by their gene expression patterns (Golub et al. 1999, Ben-Dor et al. 2000, Alizadeh et al. 2000). However, the simultaneous classification across a heterogeneous set of tumor types has not been well studied yet. We obtained 190 samples from 14 tumor classes and generated a combined expression dataset containing 16063 genes for each of those samples. We performed multi-class classification by combining the outputs of binary classifiers. Three binary classifiers (k-nearest neighbors, weighted voting, and support vector machines) were applied in conjunction with three combination scenarios (one-vs-all, all-pairs, hierarchical partitioning). We achieved the best cross validation error rate of 18.75% and the best test error rate of 21.74% by using the one-vs-all support vector machine algorithm. The results demonstrate the feasibility of performing clinically useful classification from samples of multiple tumor types.

Algorithms↗

PubMed2001

Effect of ATP sensitive potassium channel modifiers on antinociceptive effect of metoclopramide.

Metoclopramide, a prokinetic drug, has been documented to produce antinociceptive response in animal models through opioid pathways. Morphine has been shown to act through ATP sensitive potassium channels (KATP) to produce antinociceptive response. However, such a possibility has not been examined for metoclopramide. The present study investigated this using pharmacological tools. Acetic acid induced abdominal constriction assay procedure was utilized to assess antinociception. The results confirmed that metoclopramide has antinociceptive response. Glibenclamide, a KATP channel blocker, pretreatment antagonized this response. Where as, in minoxidil pretreated animals, metoclopramide elicited an enhanced antinociceptive response. Glibenclamide and minoxidil, which are known KATP channel blocker and opener respectively, interfered with metoclopramide antinociception. These finding are suggestive of a role for KATP channels in metoclopramide antinociception in mice.

Adenosine Triphosphate↗

PubMed2000

Effect of various essential oils on Callosobruchus maculatus (F.) (Coleoptera: Bruchidae).

Essential oils were extracted from four West African plant species [Tagetes minuta (Family Compositae), Hyptis suaveolens (Family Labiatae), white basil Ocimum canum (Family Labiatae), and sweet basil O. basilicum (Family Labiatae)] by steam distillation. The oil of the pepper Piper guineense (Family Piperaceae), was extracted from the fruits by hydro distillation and ethanol extraction. Mixed essential oil and total ethanol extract was used. Kaolin powder (clay) was mixed (aromatized) with these different oils. Cowpea weevils were reared on chickpeas and newly emerged males and females were deposited on uninfested seeds. Bioassays, i.e. fumigation with pure essential oils and aromatized kaolin powders, were carried out on adults and eggs. Twenty four hours after fumigation, 99 and 0% adult mortality were observed, respectively, as the result of treatments with Ocimum basilicum and the control. The application of powders aromatized with the same oils to weevil pairs resulted in a complete lack of oviposition, whereas 31, 56 and 76 eggs were laid in the controls after 24, 48 and 72 h, respectively. Application of aromatized powders did not have a significant effect on egg hatching (50 out of 110 with O. canum, 100 out of 115 with O. basilicum and 100 out of 130 in the control sample) but did have a significant impact on adult emergence: 0% for the two treatments compared with 100% in the controls. Our results suggest that plants of the genus Ocimum can be used as an alternative to synthetic insecticides.

Journal Article↗

PubMed2000

Selection of antibiotic-resistant bacterial mutants: allelic diversity among fluoroquinolone-resistant mutations.

To obtain a general framework for understanding selection of antibiotic-resistant mutants, allelic diversity was examined with about 600 fluoroquinolone-resistant mutants of mycobacteria. Selection at low fluoroquinolone concentration produced many low-level resistance mutants. Some of these contained mutations that conferred unselected antibiotic resistance; none contained alterations in the quinolone-resistance-determining region of the GyrA protein, the principal drug target. As selection pressure increased, a variety of GyrA variants became prevalent. High concentrations of antibiotic reduced the variety to a few types, and eventually a concentration was reached at which no mutant was recovered. That concentration defined a threshold for preventing the selection of resistance. The pattern of variants selected, which was also strongly influenced by antibiotic structure, readily explained the variants present in clinical isolates. Thus, resistance arises from selection of mutants whose identity depends on drug concentration and structure, both of which can be manipulated to restrict selection.

Alleles↗

PubMed2000

Neuropeptide Y: A hypothalamic brake restraining the onset of puberty in primates.

The adult reproductive axis is driven by an intermittent discharge of gonadotropin-releasing hormone (GnRH) generated by a network of hypothalamic neurons known as the GnRH pulse generator. Although this signal generator is operational in infant primates, puberty in these species is delayed by activation shortly after birth of a central neural mechanism that holds GnRH release in check during juvenile development. Here, we show that, in the male rhesus monkey, the postnatal pattern in GnRH pulse generator activity is inversely related to that in neuropeptide Y (NPY) gene and protein expression in the mediobasal hypothalamus and that central administration of an NPY Y(1) receptor antagonist to juvenile animals elicits precocious GnRH release. Cell imaging indicated that the developmentally regulated NPY neurons may be located in regions dorsal to the arcuate nucleus. These findings lead us to propose that NPY is a fundamental component of the neurobiological brake restraining the onset of puberty in primates.

Animals↗

PubMed2000

Nonequilibrium fluctuations, traveling waves, and instabilities in active membranes.

The stability of a flexible fluid membrane containing a distribution of mobile, active proteins (e.g., proton pumps) is shown to depend on the structure and functional asymmetry of the proteins. A stable active membrane is in a nonequilibrium steady state with height fluctuations whose statistical properties are governed by the protein activity. Disturbances are predicted to travel as waves at sufficiently long wavelength, with speed set by the normal velocity of the pumps. The unstable case involves a spontaneous, pump-driven undulation of the membrane, with clumping of the proteins in regions of high activity.

Kinetics↗

PubMed2000

Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding.

The three-dimensional structure of the aromatic hydroxylating enzyme naphthalene dioxygenase (NDO) from Pseudomonas sp. NCIB 9816-4 was recently determined. The refinement of the structure together with cyclic averaging showed that in the active site of the enzyme there is electron density for a flat aromatic compound. This compound appears to be an indole adduct, which in Escherichia coli is derived from tryptophan present in the rich culture medium. An indole-dioxygen adduct has been built which fits the electron density convincingly. Support for this interpretation was obtained from crystals of the enzyme purified from cells grown in the absence of tryptophan which had an empty substrate pocket. These types of crystals were soaked in indole solutions and the position of indole in this complex was similar to the corresponding part in the modelled indole-oxygen adduct. This suggests that a peroxide bound to iron end-on attacks the substrate and forms this intermediate. The substrate position has implications for the substrate specificity of the enzyme. Docking studies with indole, naphthalene and biphenyl inside the substrate pocket of NDO suggest the presence of subpockets where the one close to the active site iron is reserved for the binding of the aromatic ring which is hydroxylated upon catalysis. The plausible location for the binding of dioxygen is between this pocket and the catalytic iron. This is in accordance with the enantiospecificity of the products.

Amino Acid Sequence↗

PubMed2000

A transcript map of the chromosome 19q-arm glioma tumor suppressor region.

Allelic loss of the chromosome 19q arm is a frequent event in human diffuse gliomas, suggesting that it contains a tumor suppressor gene. Recent deletion mapping studies have broadly implicated a 1.6-Mb interval between D19S241E and D19S596, with a limited subset of tumors, suggesting that the region may be as narrow as 150 kb. Focusing on this smaller interval, we have used cDNA selection, exon amplification, and genomic sequencing to identify three novel transcripts (EHD2, GLTSCR1, and GLTSCR2) and to map two known genes (SEPW1 and CRX). A partial transcript map of 19 transcripts and two EST markers has been constructed for the 1.6-Mb interval D19S241E-D19S596. Ten of these transcripts, including the 5 mapped to the 150-kb deletion interval, have been examined for alterations in a panel of gliomas with allelic loss of 19q. Tumor-specific alterations have not been identified in the transcripts examined thus far. Collectively, these data should facilitate subsequent efforts to identify and characterize the remaining transcripts in the 1.6-Mb interval.

Base Sequence↗