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Biomedical subjects

V Gopal

Publications and source records attributed to V Gopal.

At least 19 recordsLinked to original sources
PubMed2006

Equilibrium, kinetic and thermodynamic studies of adsorption of fluoride onto plaster of Paris.

Batch sorption system using plaster of Paris as an adsorbent was investigated to remove fluoride ions from aqueous solutions. The system variables studied include initial concentration of the sorbate, agitation time, adsorbent dose, pH, co-ions and temperature. The experimental data fitted well to the Freundlich and Langmuir isotherms. Thermodynamic parameters such as DeltaH degrees , DeltaS degrees and DeltaG degrees were calculated indicating that the adsorption was a spontaneous and exothermic. Kinetic studies reveal that the adsorption is first order. A mechanism involving three stages (external surface adsorption, intraparticle diffusion and final equilibrium) has been proposed for the adsorption of F(-) onto plaster of Paris. XRD patterns of the adsorbent were recorded to get a better in sight into the mechanism of adsorption process.

Adsorption↗
PubMed2003

Recycling and utilization of metabolic wastes for energy production is an index of biochemical adaptation of fish under environmental pollution stress.

The activity levels of lactate dehydrogenase and lactic acid were assessed in various tissues of the fish during exposure to lethal concentration of group-II Pyrethroids (deltamethrin, cypermethrin, fenvalerate and fluvalinate) for a period of 72 hours. The results showed steady increased levels in all the tissues (blood, muscle, brain and liver) with response pattern characteristic of their own. The increased LDH activity and lactic acid levels indicate the shifting of aerobic glycolysis to anaerobiosis and its further utilization for energy production during adaptation to toxic stress.

Adaptation, Physiological↗
PubMed2001

Design, synthesis, and transfection biology of novel cationic glycolipids for use in liposomal gene delivery.

The molecular structure of the cationic lipids used in gene transfection strongly influences their transfection efficiency. High transfection efficiencies of non-glycerol-based simple monocationic transfection lipids with hydroxyethyl headgroups recently reported by us (Banerjee et al. J. Med. Chem. 1999, 42, 4292-4299) are consistent with the earlier observations that the presence of hydroxyl functionalities in the headgroup region of a cationic lipid contributes favorably in liposomal gene delivery. Using simple sugar molecules as the source of multiple hydroxyl functionalities in the headgroup region of the transfection lipids, we have synthesized four novel simple monocationic transfection lipids, namely, 1-deoxy-1-[dihexadecyl(methyl)ammonio]-D-xylitol (1), 1-deoxy-1-[methyl(ditetradecyl)ammonio]-D-arabinitol (2), 1-deoxy-1-[dihexadecyl(methyl)ammonio]-D-arabinitol (3) and 1-deoxy-1-[methyl(dioctadecyl)ammonio]-D-arabinitol (4), containing hydrophobic aliphatic tails and the hydrophilic arabinosyl or xylose sugar groups linked directly to the positively charged nitrogen atom. Syntheses, chemical characterizations, and the transfection biology of these novel transfection lipids 1-4 are described in this paper. Lipid 1, the xylosyl derivative, showed maximum transfection on COS-1 cells. All the lipids showed transfection with cholesterol as colipid and not with dioleoylphosphatidylethanolamine (DOPE). Radioactive quantitation of free and complexed DNA combined with ethidium bromide exclusion measurements suggest that though nearly 70% of the DNA exists as complexed DNA, the DNA may not have condensed as was observed with other cationic lipids. Presence of additional (more than two) hydroxyl functionalities in the headgroup of the cationic lipids appears to have improved the transfection efficiency and made these lipids less cytotoxic compared to two-hydroxyl derivatives.

Animals↗
PubMed2001

Small worlds: how and why.

We investigate small-world networks from the point of view of their origin. While the characteristics of small-world networks are now fairly well understood, there is as yet no work on what drives the emergence of such a network architecture. In situations such as neural or transportation networks, where a physical distance between the nodes of the network exists, we study whether the small-world topology arises as a consequence of a tradeoff between maximal connectivity and minimal wiring. Using simulated annealing, we study the properties of a randomly rewired network as the relative tradeoff between wiring and connectivity is varied. When the network seeks to minimize wiring, a regular graph results. At the other extreme, when connectivity is maximized, a "random" network is obtained. In the intermediate regime, a small-world network is formed. However, unlike the model of Watts and Strogatz [Nature 393, 440 (1998)], we find an alternate route to small-world behavior through the formation of hubs, small clusters where one vertex is connected to a large number of neighbors.

Algorithms↗
PubMed2001

Effect of pyrethroids on carbohydrate metabolic pathways in common carp, Cyprinus carpio.

The activity levels of succinate dehydrogenase (SDH) and glucose-6-phosphate dehydrogenase (G6PD) were assessed in various tissues of Cyprinus carpio var communis which had been exposed to lethal concentrations of group-II pyrethroids (deltamethrin, cypermethrin, fenvalerate and fluvalinate) for a period of 72 h. The results indicated a steady decrease in SDH activity with a concomitant increase in G6PD activity. The decreased SDH activity indicated inhibition of SDH at mitochondrial level and the increased G6PD activity an enhancement of an alternative pathway of carbohydrate metabolism, viz the hexose monophosphate shunt (HMP) or pentose phosphate pathway as a biochemical adaptation to overcome the toxic stress.

Animals↗
PubMed2000

Scanning mutagenesis reveals roles for helix n of the bacteriophage T7 RNA polymerase thumb subdomain in transcription complex stability, pausing, and termination.

Deletions within the thumb subdomain (residues 335-408) of T7 RNA polymerase decrease elongation complex stability and processivity, but the structure of a T7RNAP initial transcription complex containing a 3-nucleotide RNA reveals no interactions between the thumb and the RNA or DNA. Modeling of a longer RNA in this structure, using a T7DNAP-primer-template structure as a guide, suggests that the phosphate ribose backbone of the RNA contacts a stretch of mostly positively charged side chains between residues 385 and 395 of helix N of the thumb. Scanning mutagenesis of this region reveals that alanine substitutions of Arg(391), Ser(393), and Arg(394) destabilize elongation complexes and that substitutions at 393 and 394 increase termination of transcripts 5 or more bases in length. The alpha-carbons of all 3 of these residues lie on the side of helix N, which faces into the template-binding cleft of the RNA polymerase, and modeling suggests that they can contact the RNA 4-5 bases away from the 3'-end. Alanine substitutions of other residues within 385-395 do not have marked effects on transcription complex stability, but alanine substitutions of Asp(388) and Tyr(385) reduce pausing and termination at the T7 concatemer junction. Both of these side chains lie on the outer side of helix N, pointing away from the template binding cleft. The thumb subdomain of T7RNAP therefore has roles both in transcription complex stabilization and in pausing and termination at the T7 concatemer junction.

Amino Acid Sequence↗
PubMed2000

Distribution of particulate matter and tissue remodeling in the human lung.

We examined the relationship between intrapulmonary particle distribution of carbonaceous and mineral dusts and remodeling of the airways along anatomically distinct airway paths in the lungs of Hispanic males from the central valley of California. Lung autopsy specimens from the Fresno County Coroner's Office were prepared by intratracheal instillation of 2% glutaraldehyde at 30 cm H(2)O pressure. Two distinct airway paths into the apico-posterior and apico-anterior portions of the left upper lung lobe were followed. Tissue samples for histologic analysis were generally taken from the intrapulmonary second, fourth, sixth, and ninth airway generations. Parenchymal tissues beyond the 12th airway generation of each airway path were also analyzed. There was little evidence of visible particle accumulation in the larger conducting airways (generations 2-6), except in bronchial-associated lymphoid tissues and within peribronchial connective tissue. In contrast, terminal and respiratory bronchioles arising from each pathway revealed varying degrees of wall thickening and remodeling. Walls with marked thickening contained moderate to heavy amounts of carbonaceous and mineral dusts. Wall thickening was associated with increases in collagen and interstitial inflammatory cells, including dust-laden macrophages. These changes were significantly greater in first-generation respiratory bronchioles compared to second- and third-generation respiratory bronchioles. These findings suggest that accumulation of carbonaceous and mineral dust in the lungs is significantly affected by lung anatomy with the greatest retention in centers of lung acini. Furthermore, there is significant remodeling of this transitional zone in humans exposed to ambient particulate matter.

Adolescent↗
PubMed1999

Characterization of structural features important for T7 RNAP elongation complex stability reveals competing complex conformations and a role for the non-template strand in RNA displacement.

We have characterized the roles of the phage T7 RNA polymerase (RNAP) thumb subdomain and the RNA binding activity of the N-terminal domain in elongation complex (EC) stability by evaluating how disrupting these structures affects the dissociation rates of halted ECs. Our results reveal distinct roles for these elements in EC stabilization. On supercoiled or partially single-stranded templates the enzyme with a deletion of the thumb subdomain is exceptionally unstable. However, on linear duplex templates the polymerase which has been proteolytically cleaved within the N-terminal domain is the most unstable. The differences in the effects of these RNAP modifications on the stability of ECs on the different templates appear to be due to differences in EC structure: on the linear duplex templates the RNA is properly displaced from the DNA, but on the supercoiled or partially single-stranded templates an extended RNA:DNA hybrid makes a larger contribution to the conformational state of the EC. The halted EC can therefore exist either in a conformation in which the RNA is displaced from the DNA and forms an interaction with the RNAP, or in a conformation in which a more extended RNA:DNA hybrid is present and the RNA:RNAP interaction is less extensive. The partitioning between these competing conformations appears to be a function of the energetics of template reannealing and the relative strengths of the RNA:RNAP interaction and the RNA:DNA hybrid.

Bacteriophage T7↗
PubMed1997

Mutations in the 1.1 subdomain of Escherichia coli sigma factor sigma70 and disruption of its overall structure.

Among various group I sigma factors, two amino acids, Val55 and Ala59 are the conserved amino acids in the 1.1 hydrophobic subdomain. These two sites have been mutated to generate variants designated as [Gly55]sigma70 and [Gly59]sigma70, where glycine replaces valine and alanine, respectively. The function of these sigma mutants is reported here. The molecular mass of these proteins determined on denaturing gels was 70 kDa, which is the expected calculated molecular mass; wild-type sigma70 has an apparent molecular mass of 87 kDa. However, [Gly434]sigma70, which contains a mutation at the DNA-binding rpoD box region, also migrates as a 70-kDa protein on SDS/PAGE. Circular dichroism spectral analysis indicated that both [Gly55]sigma70 and [Gly59]sigma70 have reduced helicity (20%) compared to wild-type sigma70 (50%). Binding of sigma factors with the hydrophobic, surface active probe 1-anilinonapthalene-8-sulphonate, has shown that more hydrophobic surfaces are available/exposed in [Gly55]sigma70, [Gly59]sigma70 as well as in [Gly434]sigma70 in comparison to wild-type sigma70. Time-resolved emission spectroscopic studies have suggested transient binding between these mutants and DNA. The different holoenzyme RNA polymerases generated upon reconstituting these mutants independently with core RNA polymerase (alpha2beta beta') have shown reduced transcriptional activity in comparison to the enzyme containing wild-type sigma factor. However, another mutation (Val-->Gly) in the hydrophobic subdomain 1.2 at position 83, which is designated as [Gly83]sigma70, has similar properties as the wild-type with respect to its mobility on denaturing gels, circular dichroism profile, and transcriptional activity when reconstituted with core RNA polymerase. It appears that the 1.1 subdomain in sigma70 may interact hydrophobically with the 2.3/2.4 DNA-binding region.

Amino Acid Sequence↗
PubMed1997

Recognition of promoter DNA by subdomain 4.2 of Escherichia coli sigma 70: a knowledge based model of -35 hexamer interaction with 4.2 helix-turn-helix motif.

In Escherichia coli, subdomains 2.4 and 4.2 of the primary transcription factor sigma 70 are the most highly conserved regions and are responsible for the recognition of -10 and -35 promoter elements respectively. Mutational studies provide evidence to this end and indicate that the side chains of subdomain 4.2 make specific contacts with the nucleotides at -35. Subdomain 4.2 is highly conserved among group-1 sigma factors and is strongly homologous to the classical helix-turn-helix (HTH) motif shared by bacteriophage lembda cl, Cro, the CAP protein and other homeodomain proteins, suggesting that sigma factor also belongs to the HTH class of proteins. In this study, a single point mutation of the conserved hydrophobic residue valine at position 576, in the 4.2 subdomain results in a mutant that is transcriptionally inefficient although conformationally similar to wild-type sigma. The mutant sigma, like wild-type, migrates as a 87 kDa protein on SDS gels and has 50% helicity. However, transcription at "extended -10 promoter' by RNA polymerase containing mutant sigma 70-V576G, synthesized appreciable amount of RNA product, when compared with that generated by sigma 70-W434G, a mutation in -10 DNA binding domain. A model of HTH motif for the conserved 20 residue region of 4.2 domain of E. coli sigma 70 as well as its mutant sigma 70-V576G and sigma 70-V576T were constructed based on five other homologous HTH motifs from DNA-protein complexes for which X-ray or NMR structure is available. A B-DNA structure was designed for -35 region using sequence dependent base pair parameters. The modeled HTH structure was docked into the major groove formed by the -35 hexamer DNA using the DNA-recognition rules and amino acid-nucleotide base contact information of homologous DNA-protein complexes. Analysis of the residue contact information of the model was tested and found to have good agreement with the experimental reports.

Amino Acid Sequence↗
PubMed1995

Distribution of cell cycle times amongst the leukemia cells within individual patients with acute myelogenous leukemia.

Seventeen patients with AML received infusions of BrdUrd to permit measurement of the cell parameters of leukemia cells in vivo. The range of S-phase times was measured by using a two color BrdUrd/Pl analysis to determine the range of BrdUrd incorporation into cells which had been in S-phase throughout the entire duration of BrdUrd administration. These data were, in turn, used to calculate the range of cell cycle times amongst the leukemia cells present within individual patients. The range of cell cycle times amongst the leukemia cells present within individual patients differs between patients, with some leukemia cell populations characterized by narrow and others by broad ranges. In general, the longer the mean cell cycle time (between 27 and 112 h) the broader the range of cell cycle times. These differences may help to explain, in part, the differences in response to therapy among patients whose mean leukemia cell kinetic parameters are similar.

Bromodeoxyuridine↗
PubMed1995

Time-resolved emission spectroscopy as a tool to follow nucleic acid-protein interaction.

Fluorescence spectroscopy is undoubtedly a useful tool to study the structural and functional aspects of nucleic acids-protein interactions as well as the catalytic functions of particular residues of multi-subunit enzyme complexes. The dynamic interaction of nucleic acids and proteins occurring at nanosecond time scale can now be monitored by making life-time measurements or by time-resolved emission spectroscopy. These measurements are made by exploiting the intrinsic fluorescent residues in proteins i.e. W or by the use of extrinsic fluorophores which are tagged on to particular residues and that are sensitive to the microenvironment changes. In this study we describe the use of time resolved emission spectroscopy to (a) analyse the transient binding between sigma 70 and DNA by monitoring the quenching of W residues and (b) monitor the various states which nucleosomes of active, inducible or inactive chromatin may adopt in vivo.

Animals↗
PubMed1994

A point mutation at the junction of domain 2.3/2.4 of transcription factor sigma 70 abrogates productive transcription and restores its expected mobility on a denaturing gel.

Region 2 of eubacterial sigma factors is highly conserved and the subdomain 2.4 is involved in -10 promoter recognition. An evolutionary conserved "RpoD box" has been identified at the junction of subdomain 2.3/2.4 in class I and class II sigma factors and there are two tryptophan residues at position 433 and 434 which can be used as intrinsic fluorescent markers to study their structure-function relationship. Site-directed mutagenesis of these two tryptophan residues has been carried out to generate three variants of sigma 70 of Escherichia coli RNA polymerase. These are W433F, W433G and W434G. sigma 70-W433F is found to be indistinguishable from the native sigma factor by both structural and functional analysis. sigma 70-W433G shows anomalous mobility on SDS-PAGE like the native sigma factor, is alpha-helical in conformation (50% helicity) although found to be less active in total transcription when reconstituted with core RNA polymerase. Free sigma 70-W434G, unlike the native sigma factor, shows the expected mobility of a 70 kDa protein on SDS-PAGE and has 20% helicity. Time-resolved fluorescence analysis indicates that free sigma 70-W434G has DNA binding ability, and displays a normal abortive initiation reaction but a decreased level of productive transcription after reconstitution with core RNA polymerase. A model is proposed in which tryptophan at position 434 interacts with the hydrophobic 1.1 domain of sigma 70 giving rise to the stability of the protein under denaturing conditions.

Amino Acid Sequence↗
PubMed1994

Regrowth resistance in leukemia and lymphoma: the need for a new system to classify treatment failure and for new approaches to treatment.

Treatment failure in drug sensitive malignancies is a complex phenomenon resulting from both drug resistance and from the rapid regrowth of malignant cells ('regrowth resistance'). Attempts to overcome regrowth resistance during the treatment of the aggressive lymphomas by increasing the frequency of cytotoxic therapy appears to have failed. An alternative approach of significant potential would be to administer biologically active agents to directly slow the regrowth of neoplastic cells between courses of full dose cytotoxic therapy. To facilitate this approach a new system for classifying treatment failure in the leukemias and lymphomas is needed so that the extent of regrowth resistance and the effects of treatment on regrowth resistance can be directly assessed. Accordingly, a new classification system is proposed.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed1994

The study of acute leukemia cells by means of acridine orange staining and flow cytometry.

The studies described here explored the staining of acute leukemia cells with acridine orange (AO). The red fluorescence curve of AML specimens was usually bimodal, suggesting the presence of subpopulations of cells which have different RNA contents. In almost every AML specimen, small leukemic blast cells comprised at least part of the "low RNA content" subpopulation. Residual granulocytes and lymphocytes also contributed to this population. Frequently, the green fluorescence, indicative of the binding of AO to DNA, was slightly less in these cells than in the majority of cells present. There was no evidence however, that the leukemia cells with these characteristics represented a G0 or kinetically quiescent population of cells. In ALL specimens, the presence of multiple cytogenetically distinct clones was easily detectable in AO stained specimens. The red fluorescence curve of G0/G1 ALL cells was unimodal.

Acridine Orange↗
PubMed1993

Clonogenic potential of myeloid leukaemia cells in vitro is restricted to leukaemia cells expressing the CD34 antigen.

Cells from patients with acute myeloid leukaemia (AML) or chronic myeloid leukaemia (CML) were separated into CD34-enriched and CD34-depleted subpopulations. The clonogenic capacities of these two subpopulations were then compared to each other and to the original unseparated cell population. In every study, the CD34-enriched subpopulation demonstrated a substantial increase in clonogenicity in vitro in comparison with the original cell population, while the reverse was the case for the CD34-depleted subpopulations. For reasons not clear at present, the enrichment for clonogenic cells far exceeded the enrichment for cells expressing the CD34 antigen. Additionally, the clonogenic potential was found to be unrelated to the level of myc expression in the various cell populations.

Antigens, CD↗
PubMed1993

Effects of rhGM-CSF on myeloid clonogenic cells in acute myelogenous leukemia patients.

The effects of rhGM-CSF in vivo on the myeloid clonogenic cells present in 6 AML patients was evaluated. The relative number of clonogenic cells fell in 4 of the 6 patients. The effects of rhGM-CSF on the percentage of clonogenic cells in S phase and the sensitivity of clonogenic cells to cytosine arabinoside varied among the patients. These effects were not related to the effects of rhGM-CSF on the white blood cell count or on the proliferative rate of the leukemia cell population as a whole.

Adult↗