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Biomedical subjects

N Kannan

Publications and source records attributed to N Kannan.

At least 19 recordsLinked to original sources
PubMed2007

HOXA1-stimulated oncogenicity is mediated by selective upregulation of components of the p44/42 MAP kinase pathway in human mammary carcinoma cells.

Expression of homeobox A1 (HOXA1) results in oncogenic transformation of immortalized human mammary epithelial cells with aggressive tumor formation in vivo. However, the mechanisms by which HOXA1 mediates oncogenic transformation is not well defined. To identify molecules that could potentially be involved in HOXA1-mediated oncogenic transformation, microarray analysis was utilized to characterize and compare the gene expression pattern in response to forced expression or depletion of HOXA1 in human mammary carcinoma cells. Gene expression profiling identified that genes involved in the p44/42 mitogen-activated protein (MAP) kinase activation pathway (GRB2, MAP kinase kinase (MEK1) and SDFR1) or p44/42 MAP kinase-regulated genes (IER3, EPAS1, PCNA and catalase) are downstream expression targets of HOXA1. Forced expression of HOXA1 increased GRB2 and MEK1 mRNA and protein expression and increased p44/42 MAP kinase phosphorylation, activity and Elk-1-mediated transcription. Use of a MEK1 inhibitor demonstrated that increased p44/42 MAP kinase activity is required for the HOXA1-mediated increase in cell proliferation, survival, oncogenicity and oncogenic transformation. Thus, modulation of the p44/42 MAP kinase pathway is one mechanism by which HOXA1 mediates oncogenic transformation of the human mammary epithelial cell.

Breast Neoplasms↗
PubMed2006

Predicting diffuse-source transfers of surfactants to surface waters using SWAT.

Chemicals present in domestic wastewater can adsorb to solid phase materials during sewage treatment. If biosolids (or sewage sludge) are applied to land, these chemicals can be transferred to soil. Under some circumstances they can also be transferred to surface waters during storm events either in solution or attached to sediment. In this paper we describe the utility of the SWAT 2000 model to estimate diffuse-source surface water exposure to "down-the-drain" chemicals. The model was applied hypothetically to predict the behaviour of linear alkylbenzene sulphonate (LAS), an anionic surfactant commonly used in household detergents, in a small catchment in Bedfordshire, UK, where it has previously been successfully validated for stream flow, sediments and pesticides. LAS transfers were estimated for two scenarios: (1) realistic and (2) reasonable worst case, based on assumptions on sludge application rates and the concentration of LAS in sludge. In addition, the sensitivity of the model output to the proportion of the catchment to which sludge is applied was established. Soil wetness and the total quantity of biosolids applied were the biggest determinants of chemical transport from the catchment. The potential of SWAT as a higher-tier tool in environmental risk assessments is discussed.

Diffusion↗
PubMed2006

Comparison of treatment potential of electrocoagulation of distillery effluent with and without activated Areca catechu nut carbon.

Physico-chemical characteristics of distillery effluent samples have been determined. The water quality parameters (WQPs) measured are colour, pH, electrical conductivity, turbidity, total dissolved solids (TDS), chloride, total hardness (THA), calcium, iron, bio-chemical oxygen demand (BOD) and chemical oxygen demand (COD). Almost all the values of WQPs of the distillery effluents have been found to be very high and well above the permissible limit suggested by Bureau of Indian Standards (BIS). Electrocoagulation (EC) technique is employed to treat the distillery effluents. Removal efficiency of WQPs is compared by adopting EC technique with and without the addition of indigenously prepared activated areca nut [botanical name: Areca catechu; kotta pakku, in (vernacular)] carbon (AAC). About 99% of turbidity has been removed in both the cases. The experimental results also revealed that the WQPs like EC, TDS, etc. of the effluents could be reduced. Loss of weight of sacrificial electrode (anode) is also ascertained. EC with AAC is found to be more effective than EC without AAC.

Aluminum↗
PubMed2004

Optimisation of process parameters for adsorption of metal ions on straw carbon by using response surface methodology.

Optimisation of process parameters for adsorption of metal ions viz., Cu2+, Cd2+ and Ni2+ ions on Straw Carbon (SC) was carried out by using Box-Behnken statistics and analysis of variance methods. Response surface methodology with three levels of initial pH (4, 5, 6), dose (8, 10, 12 gl(-1)) and particle size (0.075, 0.090, 0.106m micron) were used in the identification of significance of the effects and interactions in adsorption studies. Response surface methodology requires no assumption and identifies the principal experimental variables and their interactions which have the greatest effect on adsorption. The optimum process parameters for maximum adsorption of Ni2+, Cu2+ and Cd2+ were obtained by this procedure.

Adsorption↗
PubMed2004

Effects of injection of serotonin into nucleus caudatus on food and water intake and body weight in albino rats.

Serotonin is known to inhibit food and water intake. However, the effect of its injection into nucleus caudatus on food and water intake is not known. In the present study, serotonin hydrochloride, buspirone (the serotonin 5-HT1A agonist) and ondensetron (the 5HT3 antagonist) were injected into nucleus caudatus through stereotaxically implanted cannulae in three different dosages (1, 2 and 5 microg) and their effects on 24 h food and water intake, and body weight were recorded. The injection of serotonin hydrochloride resulted in a dose- dependent decrease in food intake attaining maximum of 27.3% at 5 microg dose, whereas water intake and body weight were decreased 12% and 4.3% respectively only at the highest does. Buspirone elicited a dose dependent inhibition of food and water intake and body weight (22.3%, 19.8% and 5.1% respectively), whereas ondensetron elicited an increase in food and water intake (37.8% and 36.3% respectively) without significantly altering bodyweight. It was concluded that serotonin hydrochloride injected into nucleus caudatus inhibits food and water intake significantly. These effects are mediated via 5-HT1A and 5HT3 receptors. The effect of injections of 5-HT1A receptor agonist is more pronounced on water intake. The effect of injections of 5HT3 receptor antagonist is also more pronounced on water intake.

Animals↗
PubMed2002

Analysis of homodimeric protein interfaces by graph-spectral methods.

The quaternary structures impart structural and functional credibility to proteins. In a multi-subunit protein, it is important to understand the factors that drive the association or dissociation of the subunits. It is a well known fact that both hydrophobic and charged interactions contribute to the stability of the protein interface. The interface residues are also known to be highly conserved. Though they are buried in the oligomer, these residues are either exposed or partially exposed in the monomer. It is felt that a systematic and objective method of identifying interface clusters and their analysis can significantly contribute to the identification of a residue or a collection of residues important for oligomerization. Recently, we have applied the techniques of graph-spectral methods to a variety of problems related to protein structure and folding. A major advantage of this methodology is that the problem is viewed from a global protein topology point of view rather than localized regions of the protein structure. In the present investigation, we have applied the methods of graph-spectral analysis to identify side chain clusters at the interface and the centers of these clusters in a set of homodimeric proteins. These clusters are analyzed in terms of properties such as amino acid composition, accessibility to solvent and conservation of residues. Interesting results such as participation of charged and aromatic residues like arginine, glutamic acid, histidine, phenylalanine and tyrosine, consistent with earlier investigations, have emerged from these analyses. Important additional information is that the residues involved are a part of a cluster(s) and that they are sequentially distant residues which have come closer to each other in the three-dimensional structure of the protein. These residues can easily be detected using our graph-spectral algorithm. This method has also been used to identify important residues ('hot spots') in dimerization and also to detect dimerization sites on the monomer. The residues predicted using the present algorithm have correlated well with the experiments indicating the efficacy of this method in predicting residues involved in dimer stability.

Algorithms↗
PubMed2001

Clusters in alpha/beta barrel proteins: implications for protein structure, function, and folding: a graph theoretical approach.

The alpha/beta barrel fold is adopted by most enzymes performing a variety of catalytic reactions, but with very low sequence similarity. In order to understand the stabilizing interactions important in maintaining the alpha/beta barrel fold, we have identified residue clusters in a dataset of 36 alpha/beta barrel proteins that have less than 10% sequence identity within themselves. A graph theoretical algorithm is used to identify backbone clusters. This approach uses the global information of the nonbonded interaction in the alpha/beta barrel fold for the clustering procedure. The nonbonded interactions are represented mathematically in the form of an adjacency matrix. On diagonalizing the adjacency matrix, clusters and cluster centers are obtained from the highest eigenvalue and its corresponding vector components. Residue clusters are identified in the strand regions forming the beta barrel and are topologically conserved in all 36 proteins studied. The residues forming the cluster in each of the alpha/beta protein are also conserved among the sequences belonging to the same family. The cluster centers are found to occur in the middle of the strands or in the C-terminal of the strands. In most cases, the residues forming the clusters are part of the active site or are located close to the active site. The folding nucleus of the alpha/beta fold is predicted based on hydrophobicity index evaluation of residues and identification of cluster centers. The predicted nucleation sites are found to occur mostly in the middle of the strands. Proteins 2001;43:103-112.

Algorithms↗
PubMed2001

Stabilizing interactions in the dimer interface of alpha-subunit in Escherichia coli RNA polymerase: a graph spectral and point mutation study.

The formation of alpha(2) dimer in Escherichia coli core RNA polymerase (RNAP) is thought to be the first step toward the assembly of the functional enzyme. A large number of evidences indicate that the alpha-subunit dimerizes through its N-terminal domain (NTD). The crystal structures of the alpha-subunit NTD and that of a homologous Thermus aquaticus core RNAP are known. To identify the stabilizing interactions in the dimer interface of the alpha-NTD of E. coli RNAP, we identified side-chain clusters by using the crystal structure coordinates of E. coli alpha-NTD. A graph spectral algorithm was used to identify side-chain clusters. This algorithm considers the global nonbonded side-chain interactions of the residues for the clustering procedure and is unique in identifying residues that make the largest number of interactions among the residues that form clusters in a very quantitative way. By using this algorithm, a nine-residue cluster consisting of polar and hydrophobic residues was identified in the subunit interface adjacent to the hydrophobic core. The residues forming the cluster are relatively rigid regions of the interface, as measured by the thermal factors of the residues. Most of the cluster residues in the E. coli enzyme were topologically and sequentially conserved in the T. aquaticus RNAP crystal structure. Residues 35F and 46I were predicted to be important in the stability of the alpha-dimer interface, with 35F forming the center of the cluster. The predictions were tested by isolating single-point mutants alpha-F35A and alpha-I46S on the dimer interface, which were found to disrupt dimerization. Thus, the identified cluster at the edge of the dimer interface seems to be a vital component in stabilizing the alpha-NTD.

Algorithms↗
PubMed2001

Differential effects of two lots of aroclor 1254: congener-specific analysis and neurochemical end points.

Aroclor 1254 is a widely studied commercial polychlorinated biphenyl (PCB) mixture which, by definition, contains 54% chlorine by weight. Recent reports indicate substantial differences in the congener composition among Aroclor lots and hence their biologic effects. We designed the current study to compare the effects of two lots of Aroclor 1254 (lots 6024 and 124-191). We analyzed these two lots for PCB congeners, polychlorinated dibenzofurans (PCDFs), polychlorinated naphthalenes (PCNs), and polychlorinated dibenzodioxins (PCDDs). We used previously established techniques for analyzing intracellular Ca(2+) buffering and protein kinase C (PKC) translocation to test their biologic activity in neuronal preparations. PCB congener-specific analysis indicated that ortho and non-ortho congeners in these two lots varied in their percent contribution. Among all congeners, the percentages of non-ortho congeners (PCBs 77, 81, 126, and 169) were higher in lot 6024 (2.9% of total) than in lot 124-191 (0.02% of total). We detected no dioxins in these two lots (< 2 ppb). Although there are some differences in the congener composition, total PCNs were similar in both lots: 171 ppm in lot 6024 and 155 ppm in lot 124-191. However, total PCDFs were higher in lot 6024 (38.7 ppm) than in lot 124-191 (11.3 ppm). When we tested these two Aroclors on Ca(2+) buffering and PKC translocation in brain preparations, the effects were significantly different. Although lot 124-191 was more potent on PKC translocation than lot 6024, lot 6024 was slightly more active on Ca(2+) buffering than lot 124-191. These effects could not be attributed to the differences in the percentage of non-ortho congeners or PCDFs because they were inactive on these two parameters. The effects could not be attributed to PCNs because the levels were almost similar. The effects seen with two lots of Aroclor 1254 in neuronal cells were also not predicted based on the TCDD toxic equivalents (TEQs), although TEQs predicted the effects on ethoxyresorufin-O-deethylase (EROD) or methoxyresorufin-O-deethylase (MROD) activities. It is possible that the differential effects seen in neuronal cells could be caused by differences in the composition of ortho-congeners in these two mixtures, because PCBs with ortho-lateral substitutions can exhibit different activities on the selected neurochemical end points. Because of these differential effects with different lot numbers, the composition of Aroclor mixtures used in investigations should be disclosed.

Animals↗
PubMed2001

Differential effects of two lots of aroclor 1254 on enzyme induction, thyroid hormones, and oxidative stress.

Aroclor 1254 is a commercial mixture of polychlorinated biphenyls (PCBs), which is defined as being 54% chlorine by weight. However, the congener composition varies from lot to lot. Two lots which have been used in toxicity studies, 124-191 and 6024 (AccuStandard), were analyzed for their congener composition. Lot 6024 has approximately 10 times the dioxin toxic equivalents (TEQ) of lot 124-191. The purpose of this study was to determine if the difference in the TEQ of the two lots explains the different in vivo responses seen on a weight basis. Male Long-Evans rats (70 days old) were treated orally with a single dose of 0-1,000 mg/kg of each lot. Hepatic ethoxy-, methoxy-, and pentoxyresorufin O-deethylase (EROD, MROD, and PROD, respectively) activities as well as serum thyroxine (T(4)) concentrations and measures of oxidative stress were determined 4 days after treatment. Results, on a weight basis, indicate that lot 6024 led to a greater induction of EROD, MROD, and PROD but not total T(4) reduction. The differences in TEQ between the lots explained the differential induction of EROD and MROD but did not account for the induction of PROD nor decreases in T(4). PROD induction is not due to dioxin-like congeners, whereas the decrease in serum T(4) levels may involve multiple mechanisms. Effects on the antioxidants ascorbic acid and uric acid were seen only at the highest mass dose for both lots and were not explained by the difference in TEQ. These results illustrate that the differences in the TEQ explain the differences in the strict dioxin-like effects (EROD, MROD induction), but the non-dioxin-like congeners cause other effects that are not associated with the aryl hydrocarbon receptor (e.g., PROD). In addition, supra-additive effects also occur in the mixture (T(4), oxidative stress). Thus, current results demonstrate that overall toxicity cannot be predicted on the basis of the TEQ values. It is also critical that the lot number is reported in studies conducted with Aroclor 1254 because the congener composition and therefore the effects observed can be very different.

Administration, Oral↗
PubMed2001

The effect of exposure to 35,000 ft on incidence of altitude decompression sickness.

INTRODUCTION: Exposure to 35,000 ft without preoxygenation (breathing 100% oxygen prior to decompression) can result in severe decompression sickness (DCS). Exercise while decompressed increases the incidence and severity of symptoms. Clarification of the level of activity vs. time to symptom onset is needed to refine recommendations for current operations requiring 35,000-ft exposures. Currently, the U.S. Air Force limits these operations to 30 min following 75 min of preoxygenation. The objective of this study was to determine the effect of exercise intensity on DCS incidence and severity at 35,000 ft. METHODS: Following 75 or 90 min of ground-level preoxygenation, 54 male and 38 female subjects were exposed to 35,000 ft for 3 h while performing strenuous exercise, mild exercise, or seated rest. The subjects were monitored for venous gas emboli (VGE) with an echo-imaging system and observed for signs and symptoms of DCS. RESULTS: Exposures involving strenuous and mild exercise resulted in higher incidence (p < 0.05) and earlier onset of symptoms (p < 0.05) of DCS than exposure at rest. Mild and strenuous exercise during exposure did not differ in incidence or rate of onset. Incidence at 30 min of exposure was 8% at rest and 23% while exercising. CONCLUSION: The results showed that current guidelines for 35,000-ft exposures keep DCS risk below 10% at rest. Exercise, even at mild levels, greatly increases the incidence and rate of onset of DCS.

Aerospace Medicine↗
PubMed2000

Aromatic clusters: a determinant of thermal stability of thermophilic proteins.

A number of factors have been elucidated as responsible for the thermal stability of thermophilic proteins. However, the contribution of aromatic interactions to thermal stability has not been systematically studied. In the present investigation we used a graph spectral method to identify aromatic clusters in a dataset of 24 protein families for which the crystal structures of both the thermophilic and their mesophilic homologues are known. Our analysis shows a presence of additional aromatic clusters or enlarged aromatic networks in 17 different thermophilic protein families, which are absent in the corresponding mesophilic homologue. The additional aromatic clusters identified in the thermophiles are smaller in size and are largely found on the protein surface. The aromatic clusters are found to be relatively rigid regions of the surface and often the additional aromatic cluster is located close to the active site of the thermophilic enzyme. The residues in the additional aromatic clusters are preferably mutated to Leu, Ser or Ile in the mesophilic homologue. An analysis of the packing geometry of the pairwise aromatic interaction in the additional aromatic clusters shows a preference for a T-shaped orthogonal packing geometry. The present study also provides new insights for protein engineers to design thermostable and thermophilic proteins.

Enzyme Stability↗
PubMed2000

Logos for amino-acid preferences in different backbone packing density regions of protein structural classes.

A protein sequence can be classified into one of four structural classes, namely alpha, beta, alpha + beta and alpha/beta, based on its amino-acid composition. The present study aims at understanding why a particular sequence with a given amino-acid composition should fold into a specific structural class. In order to answer this question, each amino acid in the protein sequence was classified to a particular neighbor density based on the number of spatial residues surrounding it within a distance of 6.5 A. Each of the four structural classes showed a unique preference of amino acids in each of the neighbor densities. Residues which show a high compositional bias in a structural class are also found to occur in high neighbor densities. This high compositional bias towards specific residues in the four different structural classes of proteins appears to be caused by structural and functional requirements. The distribution of amino acids in different neighbor densities is graphically presented in a novel logo form which incorporates several features such as composition, the frequency of occurrence and color code for amino acids. The spatial neighbors of the residues in different neighbor densities and their secondary structural location are also represented in the form of logos. This representation helped in the identification of specific details of the whole data which may otherwise have gone unnoticed. It is suggested that the data presented in this study may be useful in knowledge-based structure modelling and de novo protein design.

Amino Acid Sequence↗
PubMed2000

The effect of staged decompression while breathing 100% oxygen on altitude decompression sickness.

INTRODUCTION: Space Shuttle extravehicular activity (EVA) requires decompression from sea level pressure (14.7 psia) to a 4.3 psia (30,300 ft) pressure suit. The transition currently involves altering the shuttle atmosphere to allow shirt-sleeve denitrogenation to occur during a 12 to 36-h staged decompression (SD) at 10.2 psia (9,800 ft) with an oxygen-enriched breathing gas (26.5% oxygen, 73.5% nitrogen). The denitrogenation provides protection from decompression sickness (DCS) during EVA in a 4.3 psia pressure suit. Our goal was to determine the highest altitude at which SD while breathing 100% oxygen (SD100) could provide effective protection from development of DCS symptoms after further decompression to 29,500 ft (4.5 psia). METHODS: There were 30 male subjects exposed to at least 6 of 11 conditions in random order on successive months to 29,500 ft for 4 h while performing mild exercise and being monitored for venous gas emboli (VGE) with an echo-imaging system. The subjects received 15 min of ground-level (GL) preoxygenation and an additional 60 or 120 min of SD100 at one of four altitudes between 8,000 ft (10.9 psia) and 18,000 ft (7.3 psia). Control exposures followed a 75- or 135-min ground-level preoxygenation. RESULTS: During SD100, one case of DCS occurred at 18,000 ft, but not at lower staging altitudes. Higher levels of VGE were observed during SD100 at 18,000 ft than during SD100 at any lower altitude. CONCLUSION: Staged decompression at 16,000 ft and below results in decompression risk during subsequent decompression to 29,500 ft similar to that following equivalent periods of ground-level preoxygenation.

Altitude Sickness↗
PubMed1999

Persistent chlorinated organic contaminants in harbour porpoises from the North Sea, the Baltic Sea and Arctic waters.

Individual chlorinated biphenyls (CBs) and chlorinated pesticides (p,p'-DDT and metabolites, HCHs and HCB) were determined in blubber samples of 40 harbour porpoises (Phocoena phocoena) of different age and sex from the North Sea, the Baltic Sea and Greenland coastal waters. Polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) were analysed in a selected group of animals. sigma CB concentrations (medians) in North Sea immature specimens were similar (14.9 micrograms/g lipid) to those from the Baltic Sea (17.0 micrograms/g lipid) and exceeding those in Greenland specimens by an order of magnitude (1.3 micrograms/g lipid). The median concentrations (microgram/g lipid) of HCB, p,p'-DDE, p,p'-DDD and gamma-HCH were in the order Greenland < North Sea < Baltic Sea. The highest concentrations of alpha-HCH (0.14 microgram/g lipid) were found in the Greenland population, and p,p'-DDT was detected only in this group. The North Sea and Baltic Sea populations were identified as distinctly separate on the basis of levels and compositions of these contaminants. The ecological risk associated with dioxin-like toxicity was dominated by the CB congeners 118 and 170; the PCDD/Fs were playing only a minor role.

Adipose Tissue↗