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Biomedical subjects

A Sarkar

Publications and source records attributed to A Sarkar.

At least 37 records · Page 2Linked to original sources
PubMed2001

Removal of DNA-bound proteins by DNA twisting.

We present a simple model of how local torsional stress in DNA can eject a DNA-bound protein. An estimate of the torque tau(*) required to eject a typical DNA-bound protein is made through a two-state model of the equilibrium between the bound and unbound states of the protein. For the familiar case of a nucleosome octamer bound to double-stranded DNA, we find this critical torque to be approximately equal to 9k(B)T. More weakly bound proteins and large (approximately equal to kilobase) loops of DNA are shown to be destabilized by smaller torques of only a few k(B)T. We then use our model to estimate the maximum range R(max) at which a protein can be removed by a transient source of twisting. We model twist strain propagation along DNA by simple dissipative dynamics in order to estimate R(max). Given twist pulses of the type expected to be generated by RNA polymerase and DNA gyrase, we find R(max) approximately equal to 70 and 450 bp, respectively, for critical torques of approximately equal to 2k(B)T.

DNA↗
PubMed2001

Black tea is a powerful chemopreventor of reactive oxygen and nitrogen species: comparison with its individual catechin constituents and green tea.

Production of black tea [BT] results in biotransformation of catechins of green tea [GT] to theaflavins and thearubigins. BT was found to be more efficient than GT and its individual catechin constituents in proportionate amounts in abrogating production of NO and O2(-) in activated murine peritoneal macrophages. In a reconstitution system of BT that is free of all catechins, stepwise addition of catechins showed that though all the constituents contributed to the overall effect of BT, theaflavin was the most powerful in abrogating NO production. RT-PCR analysis also showed theaflavin to be the most important constituent in down-regulating synthesis of iNOS. Clearly, BT containing theaflavin is an excellent chemopreventor against reactive oxygen and nitrogen species.

Animals↗
PubMed2001

Structural transitions in DNA driven by external force and torque.

Experiments on single DNA molecules have shown that abrupt transitions between states of different extensions can be driven by stretching and twisting. Here we show how a simple statistical-mechanical model can be used to globally fit experimental force-extension data of Léger et al. [Phys. Rev. Lett. 83, 1066 (1999)], over a wide range of DNA molecule twisting. We obtain the mean twists, extensions, and free energies of the five DNA states found experimentally. We also predict global force-torque and force-linking number phase diagrams for DNA. At zero force, the unwinding torque for zero-force structural transition from the double helix to an unwound structure is found to be approximately -2kBT, while the right-handed torque needed to drive DNA to a highly overwound state approximately 7kBT.

Base Pairing↗
PubMed2001

Conformationally restricted analogues of 1N,14N-bisethylhomospermine (BE-4-4-4): synthesis and growth inhibitory effects on human prostate cancer cells.

Twelve analogues of 1N,14N-bisethylhomospermine (BE-4-4-4) with restricted conformations were synthesized in the search for cancer chemotherapeutic agents with higher cytotoxic activities and lower systemic toxicities than BE-4-4-4. The central butane segment of BE-4-4-4 was replaced with a 1,2-substituted cyclopropane ring, a 1,2-substituted cyclobutane ring, and a 2-butene residue. In each case, the cis/trans-isomeric pair was synthesized. Cis-monounsaturation(s) was also introduced at the outer butane segment(s) of BE-4-4-4. The two possible cis-dienes and a cis-triene formally derived from the tetraazaeicosane skeleton of BE-4-4-4 were also prepared. Four cultured human prostate cancer cell lines (LnCap, DU145, DuPro, and PC-3) were treated with the new tetramines to examine their effects on cell growth with a MTT assay. One representative cell line (DuPro) was selected to further study the cellular uptake of the novel tetramines, their effects on intracellular polyamine pools, and their cytotoxicity. All tetramines entered the cells, reduced cellular putrescine and spermidine pools while exerting only a small effect on the spermine pool, inhibited cell growth, and killed 2-3 logs of cells after 6 days of treatment at 10 microM. Four new tetramines, the two cyclopropyl isomers, the trans-cyclobutyl isomer, and the (5Z)-tetraazaeicosene, were more cytotoxic than their saturated counterpart (BE-4-4-4). Their cytotoxicity, however, could not be correlated either with their cellular uptake or with their ability to deplete intracellular polyamine pools. We attribute their cytotoxicity to their specific molecular structures. The cytotoxicity was markedly reduced when the central butane segment was deprived of its rotational freedom by replacing it with a double bond. Introduction of a triple bond or a benzene-1,2-dimethyl residue at the central segment of the polyamine chain, led to complete loss of biological activity. The conformationally restricted alicyclic derivatives were not only more cytotoxic than was the freely rotating BE-4-4-4 by several orders of magnitude but also had much lower systemic toxicities than the latter. Thus, we obtained new tetramines with a wider therapeutic window than BE-4-4-4.

Antineoplastic Agents↗
PubMed2001

cis-Unsaturated analogues of 3,8,13,18,23-pentaazapentacosane (BE-4-4-4-4): synthesis and growth inhibitory effects on human prostate cancer cell lines.

From the results of our previous physicochemical studies of polyamine-nucleic acid interactions, we concluded that polyamine analogues in cisoidal conformation are capable of wrapping around the major groove of the double helix, of displacing natural polyamines from their nucleic acid binding sites, and of inhibiting cell division. On the basis of this hypothesis, nine unsaturated pentamines, formally derived from the cytotoxic pentamine 3,8,13,18,23-pentaazapentacosane (BE-4-4-4-4), were prepared in an attempt to increase antineoplastic activity. Cis-double bonds were introduced in all possible sites in the saturated pentaazapentacosane structure of BE-4-4-4-4 to yield two pentacosenes, four pentacosadienes, two pentacosatrienes, and one pentacosatetraene. Cis-double bonds should also provide good targets for mixed-function oxidases that might eliminate the accumulation of unsaturated pentamines in serum, thereby reducing systemic toxicity in animals. We determined the ability of these new pentamines to inhibit growth in four cultured human prostate cancer cell lines (LnCap, DU145, PC-3, and DuPro) using a MTT assay. LnCap and DU145 cells were very sensitive, PC-3 cells were relatively resistant, and DuPro cells were intermediate in sensitivity to most of these synthetic pentamines. In all cell lines, pentamines that had unsaturation(s) at the end of the chain showed the highest cell growth inhibitory effects. The cellular uptake, effects on cellular polyamine levels, and cytotoxicity of these pentamines on one representative prostate cancer cell line (DuPro) were further examined with a colony-forming efficiency (CFE) assay. The pentamines with unsaturation(s) at the end of the chain were once again the most cytotoxic among both the saturated (BE-4-4-4-4) and unsaturated analogues. Appreciable amounts of all pentamines entered DuPro cells and depleted cellular polyamine pools by day 6 of treatment. For most pentamines, however, cell growth inhibitory and cytotoxic effects could not be directly correlated either with their cellular uptake or with their ability to deplete cellular polyamine pools. The position of the double bonds in the aliphatic backbone seems to be the most important determinant of cytotoxicity. For some pentamines, however, depletion of cellular polyamines may add to their efficacy.

Antineoplastic Agents↗
PubMed2001

1alpha, 25-Dihydroxyvitamin D3 suppresses the effect of streptozotocin-induced diabetes during chemical rat liver carcinogenesis.

The effect of streptozotocin-induced diabetes in male Sprague-Dawley rats was investigated to ascertain whether it has had any modulating role in hepatocarcinogenesis. Hepatocarcinogenesis was initiated with a single sub-necrogenic dose of diethylnitrosamine (DEN) (125 mg/kg body weight, i.p.) whilst acute diabetes was produced with a single i.p. injection of streptozotocin (STZ) (65 mg/kg body weight). STZ was administered either before or after initiation with DEN at 3-week intervals. With this basic experimental regimen, the effect of an antioxidant vitamin, 1alpha, 25-dihydroxyvitamin D3 (VD) (0.3 microg/ 0.1 ml propylene glycol per os twice a week), was investigated with effect from 4 weeks prior to the exposure of DEN or STZ. Primary routine histopathology, hepatic nodular morphometric analysis and major preneoplastic antioxidant and drug metabolising enzymes were tested either with or without VD treatment in different experimental and control groups. Observation of the hepatic nodulogenesis, pathology and level of the antioxidant and drug metabolising enzyme pattern of the tissue showed a marked protection in different experimental groups of rats treated with VD. It may be that VD could elicit an anticarcinogenic potential in the aforesaid regimen by resetting the effects of these biomarkers induced by DEN and/or STZ. We further propose that STZ, when administered 3 weeks after DEN, caused massive damage where its action in vivo could be comparable with any known promoter that could propel the process of carcinogenesis more efficiently than when it was applied before the carcinogen.

Alkylating Agents↗
PubMed2001

Role of a ferredoxin gene cotranscribed with the nifHDK operon in N(2) fixation and nitrogenase "switch-off" of Azoarcus sp. strain BH72.

The endophytic diazotroph Azoarcus sp. strain BH72 is capable of infecting rice roots and of expressing the nitrogenase (nif) genes there. In order to study the genetic background for nitrogen fixation in strain BH72, the structural genes of nitrogenase (nifHDK) were cloned and sequenced. The sequence analysis revealed an unusual gene organization: downstream of nifHDK, a ferredoxin gene (fdxN; 59% amino acid sequence identity to R. capsulatus FdxN) and open reading frames showing 52 and 36% amino acid sequence identity to nifY of Pseudomonas stutzeri A15 and ORF1 of Azotobacter vinelandii were located. Northern blot analysis, reverse transcriptase PCR and primer extension analysis revealed that these six genes are located on one transcript transcribed from a sigma(54)-type promoter. Shorter transcripts sequentially missing genes of the 3' part of the full-length mRNA were more abundantly detected. Mutational analyses suggested that FdxN is an important but not the essential electron donor for dinitrogenase reductase. An in-frame deletion of fdxN resulted in reduced growth rates (59% +/- 9%) and nitrogenase activities (81%) in nitrogen-fixing pure cultures in comparison to the wild type. Nitrogenase activity was fully complemented in an fdxN mutant which carried a nifH promoter-driven fdxN gene in trans. Also, in coculture with the ascomycete Acremonium alternatum, where strain BH72 develops intracytoplasmic membrane stacks, the nitrogenase activity in the fdxN deletion mutant was decreased to 56% of the wild-type level. Surprisingly, the fdxN deletion also had an effect on the rapid "switch-off" of nitrogenase activity in response to ammonium. Wild-type strain BH72 and the deletion mutant complemented with fdxN in trans showed a rapid reversible inactivation of acetylene reduction, while the deletion mutant did not cease to reduce acetylene. In concordance with the hypothesis that changes in the redox state of NifH or electron flux towards nitrogenase may be involved in the mechanism of physiological nitrogenase switch-off, our results suggest that the ferredoxin may be a component involved in this process.

Azoarcus↗
PubMed2001

Detergent-mediated destaining of coomassie brilliant blue-stained SDS polyacrylamide gels.

A simple and one-step detergent-mediated destaining procedure for SDS Polyacrylamide gels for proteins is described. Suspension (5%, w/v) of a commercially available household detergent, Vim Ultra, has been found to be very efficient in destaining polyacrylamide gels without interfering with the resolution of proteins. As compared to the routinely used solvent (methanol-acetic acid-water)-mediated destaining procedure, the present method is economical and user-friendly.

Detergents↗
PubMed2000

Anticlastogenic potential of 1alpha,25-dihydroxyvitamin D3 in murine lymphoma.

Vitamin D3, having gained scientific interest for so long because of its role in mineral homeostasis, has now received great importance as a possible antitumor agent. This study was undertaken in an attempt to visualize the possible anticlastogenic potential of the vitamin in an ascitic mouse lymphoma model namely, Dalton's lymphoma. Frequencies of structural type chromosomal aberrations, sister chromatid exchanges and micronucleus assays have been chosen as the genotoxic endpoints in the proposed investigation. All these cytogenetic markers have been found to be markedly elevated during the progression of lymphoma in bone marrow cells. Vitamin D3 effectively suppressed the frequencies of chromosomal aberrations and sister chromatid exchanges in the lymphoma-bearing mice during the entire phase of tumor growth that significantly coupled with almost two-fold increase in survival time (37 +/- 2 and 68 +/- 2 days in lymphoma controls and vitamin D3-treated lymphoma-bearing mice, respectively), thus substantiating the antineoplastic efficacy of this secosteroid. The outcome of this study also is clearly reflected in the depletion of circulating (serum) vitamin D3 levels in the lymphoma control mice compared with normal (vehicle) controls while a still higher level was maintained in the VD3-treated lymphoma mice. This anticlastogenic property of the vitamin has so far been neglected and this is the first attempt to unravel the vitamin D3's effect in combating tumor development in vivo by limiting the frequencies of chromosomal aberrations, sister chromatid exchanges and micronuclei at least in transplantable murine model studied herein.

Animals↗
PubMed2000

Further evidence for chemopreventive potential of beta-carotene against experimental carcinogenesis: diethylnitrosamine-initiated and phenobarbital-promoted hepatocarcinogenesis is prevented more effectively by beta-carotene than by retinoic acid.

The comparative effectiveness of beta-carotene (BC) and retinoic acid (RA) was investigated against two-stage rat liver carcinogenesis initiated by a single injection of diethylnitrosamine (DEN, 200 mg/kg i.p.) followed by promotion with phenobarbital (PB, 0.05%) in a basal diet. BC (500 mg/kg) or RA (200 mg/kg) was administered per os daily throughout the entire experiment, before the initiation, or during the promotional stage. Treatment with BC throughout the experiment or before initiation significantly reduced the incidence (p < 0.01), multiplicity (p < 0.05), and size of visible subcapsular hepatocyte nodules (HNs) and reduced (p < 0.001 or 0.05) nodular volume as a percentage of liver volume. The results with RA were of lesser extent than those observed with BC. There was a considerable depletion of hepatic BC and total vitamin A (retinol + ester) in HNs and nonnodular surrounding parenchyma (NNSP) of rats subjected to the DEN-PB regimen than their control counterparts. Treatment with BC significantly elevated hepatic BC and total vitamin A contents in HNs and NNSP compared with DEN-PB control, and the elevation was proportional to the duration of BC treatment. Long-term BC or RA treatment elicited a substantial decrement in reduced glutathione content and gamma-glutamyltranspeptidase activity and an increment in cytochrome P-450 content and glutathione peroxidase and glutathione S-transferase activities in the HNs and NNSP, which were otherwise reversed in rats that received DEN-PB treatment alone. Our results suggest that BC or RA has the potential to inhibit DEN-induced hepatocarcinogenesis through selective modulation of the antioxidant defense system and xenobiotic detoxification in the liver. It is also apparent that the beneficial effect of BC or RA is primarily exerted on the initiation phase and secondarily during the promotional stage of DEN-initiated rat liver carcinogenesis and that BC affords a better chemopreventive response than RA.

Alkylating Agents↗
PubMed1999

Sediment deposition rates on the continental margins of the eastern Arabian Sea using 210Pb, 137Cs and 14C.

Eight gravity cores from the active eastern continental margins of the Arabian Sea were dated using 210Pbxs, 137Cs and 14C. The short-term (< or = 100 years) sedimentation rates range from 0.06 to 0.66 cm/year where as the long-term (> or = 1000 years) ones using AMS 14C on planktonic foraminifera varied from 0.004 to 0.13 cm/year. For long-term chronology (< or = 50,000 years) AMS dating of well-cleaned planktonic foraminifera is most suited.

Animals↗
PubMed1999

Inhibition of early DNA-damage and chromosomal aberrations by Trianthema portulacastruml. In carbon tetrachloride-induced mouse liver damage.

The underlying molecular mechanisms of the antihepatotoxic activity of Trianthema portulacastrum by monitoring its effect on mouse liver DNA-chain break, sugar-base damage and chromosomal aberrations, during chronic or acute treatment with carbon tetrachloride (CCl(4)) have been studied. Daily oral feeding with the ethanolic extract (150 mg/kg basal diet, per os) was given 2 weeks before CCl(4)treatment and continued until the end of the experiment (13 weeks). T. portulacastrum extract offer unique protection (P< 0.05-0. 001) against the induction of liver-specific structural-type chromosomal anomalies 15, 30 or 45 days after the last CCl(4)insult, compared to control mice. This was further evidenced by extract-mediated protection (15 days prior feeding following a single necrogenic dose of CCl(4)) of the generation of DNA chain-break and Fe-sugar-base damage assays. The observed hepatoprotective mechanism could be due to its ability to counteract oxidative injury to DNA in the liver of mouse.

Acute Disease↗
PubMed1999

Effect of cerebellar modulation on rat gastric secretion and enterochromaffin-like cell.

Effect of cerebellar lesion and vestibular stimulation (VS) on the activity and alternation of ECL-cells along with changes in gastric volume and acid secretion was studied. The results suggest that cerebellar lesion caused increased gastric volume and acid secretion and tended to decrease ECL-cell density. On the other hand VS of nodular lesioned rats resulted in decrease of above parameter which became marked only after 21 days of nodular lesion.

Animals↗
PubMed1999

Changes of gastroduodenal peroxidase activity of rats by cerebellar modulation.

The effect of vestibulo-cerebellar lesion and its stimulation by rotation on gastric and duodenal peroxidase activity of rats was studied. Vestibulocerebellar lesion by kainic acid produced gastroduodenal ulceration and peroxidase activity of these tissues were decreased. Mucosal thickness of gastric and duodenal tissue were also decreased. It was observed that when vestibulo-cerebellar lesioned rats were subjected to vestibular stimulation, the peroxidase activity was increased together with increased mucosal thickness of gastric and duodenal tissue. At the same time, it was noted that the severity of ulceration was decreased. We conclude that the study of peroxidase activity is a sensitive and potentially useful estimate of gastric and duodenal injury produced by cerebellar lesion that can be valuable in assessing ulcerogenesis and healing.

Animals↗