The importance of modelling heterogeneity in complex disease: application to NIMH Schizophrenia Genetics Initiative data

As for other complex diseases, linkage analyses of schizophrenia (SZ) have produced evidence for numerous chromosomal regions, with inconsistent results reported across studies. The presence of locus heterogeneity appears likely and may reduce the power of linkage analyses if homogeneity is assumed. In addition, when multiple heterogeneous datasets are pooled, intersample variation in the proportion of linked families ( a) may diminish the power of the pooled sample to detect susceptibility loci, in spite of the larger sample size obtained. We compare the significance of linkage. findings obtained using allele- sharing LOD scores ( LODexp) - which assume homogeneity - and heterogeneity LOD scores ( HLOD) in European American and African American NIMH SZ families. We also pool these two samples and evaluate the relative power of the LODexp and two different heterogeneity statistics. One of these ( HLOD- P) estimates the heterogeneity parameter a only in aggregate data, while the second ( HLOD- S) determines a separately for each sample. In separate and combined data, we show consistently improved performance of HLOD scores over LODexp. Notably, genome-wide significant evidence for linkage is obtained at chromosome 10p in the European American sample using a recessive HLOD score. When the two samples are combined, linkage at the 10p locus also achieves genome-wide significance under HLOD- S, but not HLOD- P. Using HLOD- S, improved evidence for linkage was also obtained for a previously reported region on chromosome 15q. In linkage analyses of complex disease, power may be maximised by routinely modelling locus heterogeneity within individual datasets, even when multiple datasets are combined to form larger samples.

Effect of disrupted SOX18 transcription factor function on tumor growth, vascularization, and endothelial development

Background. The growth of solid tumors depends on establishing blood supply; thus, inhibiting tumor angiogenesis has been a long-term goal in cancer therapy. The SOX18 transcription factor is a key regulator of murine and human blood vessel formation. Methods: We established allograft melanoma tumors in wild-type mice, Sox18-null mice, and mice expressing a dominant-negative form of Sox18 (Sox18RaOp) (n = 4 per group) and measured tumor growth and microvessel density by immunohistochemical analysis with antibodies to the endothelial marker CD31 and the pericyte marker NG2. We also assessed the affects of disrupted SOX18 function on MCF-7 human breast cancer and human umbilical vein endothelial cell (HUVEC) proliferation by measuring BrdU incorporation and by MTS assay, cell migration using Boyden chamber assay, and capillary tube formation in vitro. All statistical tests were two-sided. Results: Allograft tumors in Sox18-null and Sox18RaOp mice grew more slowly than those in wild-type mice (tumor volume at day 14, Sox18 null, mean = 486 mm(3), 95% confidence interval [CI] = 345 mm(3) to 627 mm(3), p = .004; Sox18RaOp, mean = 233 mm(3), 95% CI = 73 mm(3) to 119 mm(3), p < .001; versus wild-type, mean = 817 mm(3), 95% CI = 643 mm(3) to 1001 mm(3)) and had fewer CD31- and NG2-expressing vessels. Expression of dominant-negative Sox18 reduced the proliferation of MCF-7 cells (BrdU incorporation: MCF-7(Ra) = 20%, 95% CI = 15% to 25% versus MCF-7 = 41%, 95% CI = 35% to 45%; P = .013) and HUVECs (optical density at 490 nm, empty vector, mean = 0.46 versus SOX18 mean = 0.29; difference = 0.17, 95% CI = 0.14 to 0.19; P = .001) compared with control subjects. Overexpression of wild-type SOX18 promoted capillary tube formation of HUVECs in vitro, whereas expression of dominant-negative SOX18 impaired tube formation of HUVECs and the migration of MCF-7 cells via the disruption of the actin cytoskeleton. Conclusions: SOX18 is a potential target for antiangiogenic therapy of human cancers.

The comparative characterization of structural heterogeneity of mesoporous activated carbon fibers (ACFs)

The comparative analysis of the most widely used methods of mesoporosity characterization of two activated carbon fibers is presented. Not only the older methods are used, i.e. Barrett, Joyner and Halenda (BJH), Dubinin (the so-called first variant-D-1ST and the so-called second variant-D-2ND), Dollimore and Heal (DH), and Pierce (P) but the recently developed ones, i.e. the method of Nguyen and Do (ND) and that developed by Do (Do) are also applied. Additionally, the method of the characterization of fractality is put to use (fractal analog of FHH isotherm). The results are compared and discussed. (C) 2002 Elsevier Science B.V. All fights reserved.

Proteomic analysis of k-casein micro-heterogeneity

The proteome of bovine milk is dominated by just six gene products that constitute approximately 95% of milk protein. Nonetheless, over 150 protein spots can be readily detected following two-dimensional electrophoresis of whole milk. Many of these represent isoforms of the major gene products produced through extensive posttranslational modification. Peptide mass fingerprinting of in-gel tryptic digests (using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) in reflectron mode with alpha-cyano-4-hydroxycinnamic acid as the matrix) identified 10 forms of K-casein with isoelectric point (pl) values from 4.47 to 5.81, but could not distinguish between them. MALDI-TOF MS in linear mode, using sinapinic acid as the matrix, revealed a large tryptic peptide (mass > 5990 Da) derived from the C-terminus that contained all the known sites of genetic variance, phosphorylation and glycosylation. Two genetic variants present as singly or doubly phosphorylated forms could be distinguished using mass data alone. Glycoforms containing a single acidic tetrasaccharide were also identified. The differences in electrophoretic mobility of these isoforms were consistent with the addition of the acidic groups. While more extensively glycosylated forms were also observed, substantial loss of N-acetylneuraminic acid from the glycosyl group was evident in the MALDI spectra such that ions corresponding to the intact glycopeptide were not observed and assignment of the glycoforms was not possible. However, by analysing the pl shifts observed on the two-dimensional gels in conjunction with the MS data, the number of N-acetylneuraminic acid residues, and hence the glycoforms present, could be determined.

Capillary phenomena in the framework of the two-dimensional density functional theory

We present results of application of the density functional theory (DFT) to adsorption and desorption in finite and infinite cylindrical pores accounting for the density distribution in radial and axial directions. Capillary condensation via formation of bridges is considered using canonical and grand canonical versions of the 2D DFT. The potential barrier of nucleation is determined as a function of the bulk pressure and the pore diameter. In the framework of the conventional assumptions on intermolecular interactions both 1D and 2D DFT versions lead to the same results and confirm the classical scenario of condensation and evaporation: the condensation occurs at the vapor-like spinodal point, and the evaporation corresponds to the equilibrium transition pressure. The analysis of experimental data on argon and nitrogen adsorption on MCM-41 samples seems to not completely corroborate this scenario, with adsorption branch being better described by the equilibrium pressure - diameter dependence. This points to the necessity of the further development of basic representations on the hysteresis phenomena.

Effects of surface heterogeneity on the adsorption of nitrogen on graphitized thermal carbon black

In this paper, we study the surface heterogeneity and the surface mediation on the intermolecular potential energy for nitrogen adsorption on graphitized thermal carbon black (GTCB). The surface heterogeneity is modeled as the random distribution of effective carbonyl functional groups on the graphite surface. The molecular parameters and the discrete charges of this carbonyl group are taken from Jorgensen, et al. (J. Am. Chem. Soc., (1984) 106, 6638) while those for nitrogen (dispersive parameters and discrete charges) are taken from Murthy et al. (Mol. Phys., (1983) 50, 531) in our Grand Canonical Monte Carlo (GCMC) simulation. The solid surface mediation in the reduction of intermolecular potential energy between two fluid molecules was taken from a recent work by Do et al. (Langmuir, (2004) 20, 7623). Our simulation results accounting for the surface heterogeneity and surface mediation on intermolecular potential energy were compared with the experimental data of nitrogen at 77 and 90 K. The solid-fluid dispersive parameters are determined from the Lorentz-Berthelot (LB) rule. The fraction of the graphite surface covered with carbonyl functional groups was then derived from the consideration of the Henry constant, and for the data of Kruk et al. (Langmuir, (1999) 15, 1435) we have found that 1% of their GTCB surface is covered with effective carbonyl functional groups. The damping constant, due to surface mediation, was determined from the consideration of the portion of the adsorption isotherm where the first layer is being completed, and it was found to take a value of 0.0075. With these parameters, we have found that the GCMC simulation results describe the data over the complete range of pressure substantially better than any other MC models in the literature. The implication of this work is demonstrated with local adsorption isotherms of 10 and 20 A slit pores. One was obtained without allowance for surface mediation, while the other correctly accounts for these factors. The two local isotherms differ substantially, and the implication is that if we used incorrect local isotherms (i.e. without the surface mediation) the pore size distribution would be incorrectly derived.

Nucleocapsid gene variability reveals two subgroups of Lettuce necrotic yellows virus

The complete nucleocapsid (N) genes of eight Australian isolates of Lettuce necrotic yellows virus (LNYV) were amplified by reverse transcription PCR, cloned and sequenced. Phylogenetic analyses of these sequences revealed two distinct subgroups of LNYV isolates. Nucleotide sequences within each subgroup were more than 96% identical but heterogeneity between groups was about 20% at the nucleotide sequence level. However, less than 4% heterogeneity was noted at the amino acid level, indicating mostly third nucleotide position changes and a strong conservation for N protein function. There was no obvious geographical or temporal separation of the subgroups in Australia.

Visualizing levels of osteoblast differentiation by a two-color promoter-GFP strategy: Type I collagen-GFPcyan and osteocalcin-GFPtpz

A 3.9 kb DNA fragment of human osteocalcin promoter and 3.6 kb DNA fragment of the rat collagen type1a1 promoter linked with visually distinguishable GFP isomers, topaz and cyan, were used for multiplex analysis of osteoblast lineage progression. Three patterns of dual transgene, expression can be appreciated in primary bone cell cultures derived from the transgenic mice and by histology of their corresponding bones. Our data support the interpretation that strong pOBCol3.6GFPcyan alone is found in newly formed osteoblasts, while strong pOBCol3.6GFPcyan and hOC-GFPtpz are present in osteoblasts actively making a new matrix. Osteoblasts expressing strong hOC-GFPtpz and weak pOBCol3.6GF-Pcyan are also present and may or may not be producing mineralized matrix. This multiplex approach reveals the heterogeneity within the mature osteoblast population that cannot be appreciated by current histological methods. It should be useful to identify and isolate populations of cells within an osteoblast lineage as they progress through stages of differentiation.

Characterization of two polymorphisms in the leukotriene C4 synthase gene in an Australian population of subjects with mild, moderate, and severe asthma

Background: The cysteinyl-leukotrienes (cys-LTs) are proinflammatory mediators that are important in the pathophysiology of asthma. LTC4 synthase is a key enzyme in the cys-LT biosynthetic pathway, and studies in small populations have suggested that a promoter polymorphism (A(-444)C) in the gene might be associated with asthma severity and aspirin intolerance. Objective: We sought to screen the LTC4 synthase gene for polymorphisms and to determine whether there is an association between these polymorphisms and asthma severity or aspirin sensitivity in a large, well-phenotyped population and to determine whether this polymorphism is functionally relevant. Methods: The coding regions of the LTC4 synthase gene were screened for polymorphisms and the A(-444)C polymorphism was analyzed in a large Australian white adult population of mild (n = 282), moderate (n = 236), and severe asthmatic subjects (n = 86) and nonasthmatic subjects (n = 458), as well as in aspirin-intolerant asthmatic subjects (n = 67). The functional activity of the promoter polymorphism was investigated by transient transfection of HL-60 cells with a promoter construct. Results: A new polymorphism was identified in intron 1 of the gene (IVS1-10c>a) but was not associated with asthma. Association studies showed that the A(-444)C polymorphism was weakly associated with asthma per se, but there was no association between the C-444 allele and chronic asthma severity or aspirin intolerance. A meta-analysis of all the genetic studies conducted to date found significant between-study heterogeneity in C-444 allele frequencies within different clinical subgroups. In vitro functional studies showed no significant differences in transcription efficiency between constructs containing the A(-444) allele or the C-444 allele. Conclusions: Our data confirm that, independent of transcriptional activity, the C-444 allele in the LTC4 synthase gene is weakly associated with the asthma phenotype, but it is not related to disease severity or aspirin intolerance.

Heterogeneity of physico-chemical properties in structured soils and its consequences

Structured soils are characterized by the presence of inter- and intra-aggregate pore systems and aggregates, which show varying chemical, physical, and biological properties depending on the aggregate type and land use system. How far these aspects also affect the ion exchange processes and to what extent the interaction between the carbon distribution and kind of organic substances affect the internal soil strength as well as hydraulic properties like wettability are still under discussion. Thus, the objective of this research was to clarify the effect of soil aggregation on physical and chemical properties of structured soils at two scales: homogenized material and single aggregates. Data obtained by sequentially peeling off soil aggregates layers revealed gradients in the chemical composition from the aggregate surface to the aggregate core. In aggregates from long term untreated forest soils we found lower amounts of carbon in the external layer, while in arable soils the differentiation was not pronounced. However, soil aggregates originating from these sites exhibited a higher concentration of microbial activity in the outer aggregate layer and declined towards the interior. Furthermore, soil depth and the vegetation type affected the wettability. Aggregate strength depended. on water suction and differences in tillage treatments.

Testing predictions of macroscopic binary diffusion coefficients using lattice models with site heterogeneity

Quantitatively predicting mass transport rates for chemical mixtures in porous materials is important in applications of materials such as adsorbents, membranes, and catalysts. Because directly assessing mixture transport experimentally is challenging, theoretical models that can predict mixture diffusion coefficients using Only single-component information would have many uses. One such model was proposed by Skoulidas, Sholl, and Krishna (Langmuir, 2003, 19, 7977), and applications of this model to a variety of chemical mixtures in nanoporous materials have yielded promising results. In this paper, the accuracy of this model for predicting mixture diffusion coefficients in materials that exhibit a heterogeneous distribution of local binding energies is examined. To examine this issue, single-component and binary mixture diffusion coefficients are computed using kinetic Monte Carlo for a two-dimensional lattice model over a wide range of lattice occupancies and compositions. The approach suggested by Skoulidas, Sholl, and Krishna is found to be accurate in situations where the spatial distribution of binding site energies is relatively homogeneous, but is considerably less accurate for strongly heterogeneous energy distributions.