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Sujit K Ghosh

Publications and source records attributed to Sujit K Ghosh.

14 recordsLinked to original sources

Physiologically-based pharmacokinetic modeling of genistein in rats, Part I: Model development.

Genistein is a phytoestrogen-a plant-derived compound that binds to and activates the estrogen receptor-occurring at high levels in soy beans and food products, leading to widespread human exposure. The numerous scientific publications available describing genistein's dosimetry, mechanisms of action, and identified or putative health effects in both experimental animals and humans make it ideal for examination as an example of endocrine-active compound (EAC). We developed a physiologically-based pharmacokinetic (PBPK) model to quantify the internal, target-tissue dosimetry of genistein in adult rats. Complexities of the model include enterohepatic circulation, binding of both genistein and its conjugates to plasma proteins, and the multiple compartments used to describe transport through the bile duct and gastrointestinal tract. Other aspects of the model are simple perfusion-limited transport to the tissue groups and first-order rates of metabolism, uptake, and excretion. We describe here the model structure and initial calibration of the model by fitting to a large data set for Wistar rats. The model structure can be readily extrapolated to describe genistein dosimetry in humans or modified to describe the dosimetry of other phytoestrogens and phenolic EACs. The model does a fair job of capturing the pharmacokinetics. Although it does not describe the interindividual variability and we have not identified a single set of parameters that provide a good fit to the data for both oral and intravenous exposures, we believe it provides a good initial attempt at PBPK modeling for genistein, which can serve as a template for other phytoestrogens and in the design of future experiments and research that can be used to fill data gaps and better estimate model parameters.

Animals↗

Spatial association between speciated fine particles and mortality.

Particulate matter (PM) has been linked to a range of serious cardiovascular and respiratory health problems, including premature mortality. The main objective of our research is to quantify uncertainties about the impacts of fine PM exposure on mortality. We develop a multivariate spatial regression model for the estimation of the risk of mortality associated with fine PM and its components across all counties in the conterminous United States. We characterize different sources of uncertainty in the data and model the spatial structure of the mortality data and the speciated fine PM. We consider a flexible Bayesian hierarchical model for a space-time series of counts (mortality) by constructing a likelihood-based version of a generalized Poisson regression model that combines methods for point-level misaligned data and change of support regression. Our results seem to suggest an increase by a factor of two in the risk of mortality due to fine particles with respect to coarse particles. Our study also shows that in the Western United States, the nitrate and crustal components of the speciated fine PM seem to have more impact on mortality than the other components. On the other hand, in the Eastern United States, sulfate and ammonium explain most of the fine PM effect.

Air Pollutants↗

Spatial analysis of Aedes albopictus (Diptera: Culicidae) oviposition in suburban neighborhoods of a Piedmont community in North Carolina.

Temporal and spatial distribution of egg-laying by Aedes albopictus (Skuse) (Diptera: Culicidae) was investigated in suburban neighborhoods in Raleigh, NC, by using oviposition traps (ovitraps) at fixed sampling stations during the 2002 and 2003 mosquito seasons. Variations in the phenology of oviposition between the two mosquito seasons resulted from differences in the patterns and amounts of rainfall early in the season. Aerial images of each study neighborhood were digitized, and the proportions of specific types of land cover within buffer zones encompassing ovitraps were estimated. Retrospective analyses showed that in some neighborhoods, oviposition intensity was significantly associated with specific types of land cover. However, in general, it seemed that gravid Ae. albopictus searched throughout the landscape for water-filled containers in which to lay eggs. Peridomestic surveys were carried out concurrently with ovitrap collections to estimate production of Ae. albopictus pupae in discarded water-filled containers and the abundance of females in vegetation that made up the resting habitat. Results of linear regression analyses indicated that the mean standing crop of pupae (total and per container) per residence was not a significant predictor of mean egg densities in ovitraps. However, the mean standing crop of adult females was a significant but weak predictor variable, because the magnitude and sign of regression coefficients varied between neighborhoods. Linear spatial regression analyses revealed that oviposition intensity was not spatially dependent on pupal standing crop or the numbers of pupae-positive containers distributed peridomestically. However, a weak spatial dependence on the standing crop of adult females was found in some neighborhoods. Based on spherical variogram models, kriging was carried out to predict the spatial patterns of oviposition in suburban neighborhoods. Focal areas of high and low oviposition intensity were evident in most neighborhoods; however, the spatial patterns of oviposition changed between mosquito seasons. Kriging predictions were evaluated, using cross-validation, by systematically removing each data point from our data set and predicting the removed point by using the remaining points. The root mean square (standardized) error values of best fitting variogram models approximated 1, and plots of standardized PRESS residuals showed no distinct pattern for most neighborhoods, indicating that predictions of the spatial distribution of oviposition intensity were valid. Spherical variogram models are a satisfactory method for describing the spatial distribution of Ae. albopictus oviposition, and kriging can be a useful technique for predicting oviposition intensity at locations that have not been sampled.

Aedes↗

Internucleotide movements during formation of 16 S rRNA-rRNA photocrosslinks and their connection to the 30 S subunit conformational dynamics.

UV light-induced RNA photocrosslinks are formed at a limited number of specific sites in the Escherichia coli and in other eubacterial 16 S rRNAs. To determine if unusually favorable internucleotide geometries could explain the restricted crosslinking patterns, parameters describing the internucleotide geometries were calculated from the Thermus thermophilus 30 S subunit X-ray structure and compared to crosslinking frequencies. Significant structural adjustments between the nucleotide pairs usually are needed for crosslinking. Correlations between the crosslinking frequencies and the geometrical parameters indicate that nucleotide pairs closer to the orientation needed for photoreaction have higher crosslinking frequencies. These data are consistent with transient conformational changes during crosslink formation in which the arrangements needed for photochemical reaction are attained during the electronic excitation times. The average structural rearrangement for UVA-4-thiouridine (s4U)-induced crosslinking is larger than that for UVB or UVC-induced crosslinking; this is associated with the longer excitation time for s4U and is also consistent with transient conformational changes. The geometrical parameters do not completely predict the crosslinking frequencies, implicating other aspects of the tertiary structure or conformational flexibility in determining the frequencies and the locations of the crosslinking sites. The majority of the UVB/C and UVA-s4U-induced crosslinks are located in four regions in the 30 S subunit, within or at the ends of RNA helix 34, in the tRNA P-site, in the distal end of helix 28 and in the helix 19/helix 27 region. These regions are implicated in different aspects of tRNA accommodation, translocation and in the termination reaction. These results show that photocrosslinking is an indicator for sites where there is internucleotide conformational flexibility and these sites are largely restricted to parts of the 30 S subunit associated with ribosome function.

Base Pairing↗

Metal-organic framework H-bonded like a polycatenane: coexistence of acyclic water trimer and nonamer.

Pyridine-2,6-dicarboxylic acid and 1,2-di-4-pyridylethylene react hydrothermally with nickel(II) nitrate, forming a metal-organic framework that forms a polycatenane-like structure through H-bonding interactions between water molecules and carboxylate O atoms with void spaces. Discrete acyclic trimeric and nonameric water clusters occupy the voids in the structures. X-ray powder diffraction and X-ray structure analysis have been used to characterize this compound. Crystal data for 1 {(3dpeH(2))[Ni(pdc)(2)](3).15H(2)O}: monoclinic space group P2(1)/c, a = 24.730(5) Angstroms, b = 19.895(2) Angstroms, c = 17.257(4) Angstroms, beta = 104.832(5) degrees, V = 8208(4) Angstroms(3), Z = 4, R1 = 0.0429, wR2 = 0.1072, and S = 1.051.

Journal Article↗

Mn(II) staircase structures stitched by water clusters to a 3D metal-organic open framework: X-ray structural and magnetic studies.

4-Hydroxypyridine-2,6-dicarboxylic acid (chelidamic acid, cdaH2) reacts with Mn(OAc)2 x 4H2O to form a 1D staircase structure with dimeric Mn(II) units connected by water clusters to form a 3D framework, {[Mn2(cda)2 x 4H2O] x 4H2O}n, 1, in aqueous pyridine at room temperature. The compound crystallizes in the triclinic space group P1 with a = 9.495(3), b =10.733(5), c = 11.065(4) A, alpha = 87.42(5), beta = 74.14(5), gamma = 80.07(2) degrees, U = 1068.5(9) A3, Z = 2, rho(calcd) = 1.915 g cm(-3), T = 100 K, mu = 1.28 mm(-1), R1 = 0.0453 (I > 2sigma(I)), wR2 = 0.1046, GOOF = 1.282. Upon removal of the water molecules by heating, the 3D structure breaks down. Thermogravimetric analysis, infrared, X-ray powder diffraction studies, and X-ray crystallography were performed to characterize this compound. Since the coordination polymer has diaqua-bridged Mn(II) centers, it was subjected to variable-temperature magnetic studies.

Journal Article↗

Coordination polymers of La(III) as bunched infinite nanotubes and their conversion into an open-framework structure.

Pyridine-2,6-dicarboxylic acid (pdcH2) reacts with LaCl3 x 7H2O under hydrothermal conditions followed by evaporation at room temperature to give a metal-organic framework structure of the empirical formula, [La(pdc)(H2O)4] x Cl (1), in the form of infinitely long bunched nanotubes. The chloride ions and water molecules occupy the tubular as well as the inter-tubular spaces. When La(NO3)3 x 7H2O is used in place of LaCl3 x 6H2O, a similar structure is formed with the empirical formula, [La(pdc)(H2O)4] x NO3 (2), where water molecules and the nitrate anions occupy the voids as in the case of 1. When an aqueous solution of AgNO3 is added to an aqueous solution of 1, the Cl- ions are replaced completely by NO3- ions to form 2; thus, the tubular structure is conserved. However, when AgBF4 is used in place of AgNO3, the tubular structure breaks down, and a new 3-D MOF structure, [La(pdc)(pdcH)(H2O)2] x 4H2O (3), is formed where the cavities are occupied by hexameric and dimeric water clusters. Structure 3 is also formed as the sole product when La(OAc)3 x xH2O is treated with pyridine-2,6-dicarboxylic acid following the method adopted for 1 and 2. Formation of the tubular structure depends on the molar ratio of the ligand and the metal. When higher than 1 equiv of the metal is taken, a linear coordination polymer, [La2(pdc)3(H2O)6] x 2H2O (4), is formed. This study provides the first nanotubular structure of a pure lanthanide metal.

Journal Article↗

Structure of a discrete hexadecameric water cluster in a metal-organic framework structure.

Pyrazine-2,3,5,6-tetracarboxylic acid (pytcH(4)) reacts with Cu(NO(3))(2)x6H(2)O in 1:2 molar ratio in the presence of pyridine (py) vapor to form blue crystals of a coordination polymer with the empirical formula [Cu(2.5)(pytc)(py)(8)(NO(3)(-))x10H(2)O](n). Four such polymeric chains gather around a hexadecameric water cluster to form an overall 3D metal-organic framework structure. Once the water molecules are removed, the 3D structure breaks down. It presents a new mode of association of water molecules not predicted theoretically or found experimentally.

Journal Article↗

Reactivity of pyridine-2,4,6-tricarboxylic acid toward Zn(II) salts under different reaction conditions.

Pyridine-2,4,6-tricarboxylic acid (ptcH(3)) readily reacts with a Zn(II) salt at room temperature to form different products depending upon the presence or absence of pyridine in the reaction mixture. In the presence of pyridine, the ligand breaks to form infinitely zigzag coordination polymers with the empirical formula [Zn(Ox)(py)(2)]n(Ox = oxalate, py = pyridine). The backbone is formed from Zn(II)-oxalate where two pyridine molecules are coordinated to each Zn(II) ion giving it hexacoordination. The orientation of the bound pyridines is slightly different when Zn(II)-nitrate is used compared to that when Zn(II)-sulfate (or acetate) salt is used. In absence of pyridine, the ligand remains intact and forms a mixture of a carboxylate-bridged coordination polymer and a discrete carboxylate-bridged 12-membered metallomacrocycle.

Hydrogen Bonding↗

Puckered-boat conformation hexameric water clusters stabilized in a 2D metal-organic framework structure built from CuII and 1,2,4,5-benzenetetracarboxylic acid.

1,2,4,5-Benzenetetracarboxylic acid (btcH(4)) reacts with Cu(NO(3))(2).6H(2)O to form 2D coordination polymeric structure [[Cu(2)(btc)(Py)(4).2H(2)O].4H(2)O](n), 1, in the presence of pyridine from water at room temperature. Puckered-boat-shaped hexameric water clusters resulting from four free water molecules and two water molecules coordinating to metal ions join these sheets to make a 3D network. These water clusters behave as pillars to join those sheets which is the key factor stabilizing the 3D network. Thermal analysis, X-ray powder diffraction, and X-ray structure analysis have been used to characterize this compound. Crystal data for 1 follow: triclinic space group P1, a = 8.905(3) A, b = 11.137(4) A, c = 17.484(2) A, alpha = 82.342(6) degrees, beta = 81.312(3) degrees, gamma = 82.361(4) degrees V= 1687.5(1)A(3), Z = 2, R1 = 0.0331, wR2 = 0.0886, S =1.066.

Journal Article↗

Interval estimation of genetic susceptibility for retrospective case-control studies.

BACKGROUND: This article describes classical and Bayesian interval estimation of genetic susceptibility based on random samples with pre-specified numbers of unrelated cases and controls. RESULTS: Frequencies of genotypes in cases and controls can be estimated directly from retrospective case-control data. On the other hand, genetic susceptibility defined as the expected proportion of cases among individuals with a particular genotype depends on the population proportion of cases (prevalence). Given this design, prevalence is an external parameter and hence the susceptibility cannot be estimated based on only the observed data. Interval estimation of susceptibility that can incorporate uncertainty in prevalence values is explored from both classical and Bayesian perspective. Similarity between classical and Bayesian interval estimates in terms of frequentist coverage probabilities for this problem allows an appealing interpretation of classical intervals as bounds for genetic susceptibility. In addition, it is observed that both the asymptotic classical and Bayesian interval estimates have comparable average length. These interval estimates serve as a very good approximation to the "exact" (finite sample) Bayesian interval estimates. Extension from genotypic to allelic susceptibility intervals shows dependency on phenotype-induced deviations from Hardy-Weinberg equilibrium. CONCLUSIONS: The suggested classical and Bayesian interval estimates appear to perform reasonably well. Generally, the use of exact Bayesian interval estimation method is recommended for genetic susceptibility, however the asymptotic classical and approximate Bayesian methods are adequate for sample sizes of at least 50 cases and controls.

Alleles↗

Self-assembly of lanthanide helicate coordination polymers into 3D metal-organic framework structures.

Pyridine-2,6-dicarboxylic acid (pdcH(2) ) reacts with nitrate salts of La(III), Ce(III), and Nd(III) under hydrothermal conditions to form three-dimensional network structures, 1-4. All the compounds crystallize in the monoclinic space group P2(1)/c with the following lattice parameters: [La(2)(pdc)(3).3H(2)O] 1, a = 10.966(3) A, b = 17.534(4) A, c = 13.578(2) A, beta = 100.23(3) degrees, V( )()= 2569.3(9) A(3), Z = 4, R1 = 0.052, wR2 = 0.143, S = 1.06; [Ce(2)(pdc)(3).3H(2)O] 2, a = 12.701(3) A, b = 9.979(1) A, c = 19.401(4) A, beta = 97.73(2) degrees, V( )()= 2436.6(8) A(3), Z = 4, R1 = 0.039, wR2 = 0.117, S = 1.30; [Ce(2)(pdc)(3).3H(2)O] 3, a = 10.961(5) A, b = 17.523(5) A, c = 13.505(2) A, beta = 100.89(3) degrees, V( )()= 2547.2(8) A(3), Z = 4, R1 = 0.040, wR2 = 0.103, S = 1.08; [Nd(2)(pdc)(3).3H(2)O] 4, a = 10.944(3) A, b = 17.448(5) A, c = 13.397(2) A, beta = 101.19(3) degrees, V( )()= 2569.3(9) A(3), Z = 4, R1 = 0.052, wR2 = 0.143, S = 1.06. Compounds 1, 3, and 4 form infinite single helical chains with large widths and pitches containing four metal ions per turn while 2 forms a different helix with smaller width and pitch containing two metal ions per turn. Each helix is further bonded on either side via carboxylate bridging producing three-dimensional metal-organic framework structures.

Journal Article↗

Coexistence of water dimer and hexamer clusters in 3D metal-organic framework structures of Ce(III) and Pr(III) with pyridine-2,6-dicarboxylic acid.

Ce(NO3)3.6H2O or Pr(NO3)3.6H2O and pyridine-2,6-dicarboxylic acid form a linear coordination polymeric structure under hydrothermal conditions. Hexameric water clusters join these linear chains through bonding to the metal ions. Other coordinated water and the carboxylate oxygen form an intricate array of hydrogen bonding resulting in a 3D network where each metal ion shows 9-coordination with an approximate D3 symmetry. Dimeric water clusters are also located in the void spaces. In the structure containing Pr(III), the water dimers are hydrogen-bonded to the hexamers, whereas in the Ce(III) structure, the dimers and the hexamers are far apart.

Journal Article↗