Apolipoprotein E*3-Leiden transgenic mice as a test model for hypolipidaemic drugs

PURPOSE: We report an investigation into the distribution of proteoglycans (PGs) in normal, organ-cultured and dextran-treated human corneas. METHODS: Immunogold labeling was carried out at the electron microscope level to localize keratan sulphate (KS), chondroitin sulphate (CS), and heparan sulphate (HS) PGs. RESULTS: High levels of labeling for CS was found in the epithelium, endothelium, and keratocytes, with light labelling present in the basement membranes and the corneal stroma. Labeling for HS was present in the epithelium, endothelium, and keratocytes, with intense labeling present at the endothelium/Descemet's membrane interface and the epithelium/Bowman's layer interface. Large filaments were also observed in these regions in cuprolinic blue-stained specimens. Keratan sulphate was present at high levels in the stroma and the basement membranes with low levels present within the keratocytes, epithelium, and endothelium. The pattern of KS labeling along the collagen fibrils in the stroma sometimes showed evidence of periodicity. Organ-cultured corneas had extensive collagen-free "lakes," the interior of which immunolabeled positively for KS and showed staining with cuprolinic blue. The lakes were greatly reduced in the dextran-treated samples. CONCLUSION: This investigation determined the ultrastructural distribution of KS, CS, and HS PGs in human cornea and showed that organ culture is associated with a change in distribution of stromal PGs.     

Ribonuclease P (RNase P) RNA is converted to a Cd(2+)-ribozyme by a single Rp-phosphorothioate modification in the precursor tRNA at the RNase P cleavage site

To study the cleavage mechanism of bacterial Nase P RNA, we have synthesized precursor tRNA substrates carrying a single Rp- or Sp-phosphorothioate modification at the RNase P cleavage site. Both the Sp- and the Rp-diastereomer reduced the rate of processing by Escherichia coli RNase P RNA at least 1000-fold under conditions where the chemical step is rate-limiting. The Rp-modification had no effect and the Sp-modification had a moderate effect on precursor tRNA ground state binding to RNase P RNA. Processing of the Rp-diastereomeric substrate was largely restored in the presence of the "thiophilic" Cd2+ as the only divalent metal ion, demonstrating direct metal ion coordination to the (pro)-Rp substituent at the cleavage site and arguing against a specific role for Mg(2+)-ions at the pro-Sp oxygen. For the Rp-diastereomeric substrate, Hill plot analysis revealed a cooperative dependence upon [Cd2+] of nH = 1.8, consistent with a two-metal ion mechanism. In the presence of the Sp-modification, neither Mn2+ nor Cd2+ was able to restore detectable cleavage at the canonical site. Instead, the ribozyme promotes cleavage at the neighboring unmodified phosphodiester with low efficiency. Dramatic inhibition of the chemical step by both the Rp- and Sp-phosphorothioate modification is unprecedented among known ribozymes and points to unique features of transition state geometry in the RNase P RNA-catalyzed reaction.     

Loss of heterozygosity in tuberous sclerosis hamartomas

We have previously described in tuberous sclerosis (TSC) hamartomas the phenomenon of loss of heterozygosity (LOH) for DNA markers in the region of both the TSC2 gene on chromosome 16p13.3 and the TSC1 gene on 9q34. We now describe the spectrum of LOH in 51 TSC hamartomas from 34 cases of TSC. DNA was extracted from leucocytes or normal paraffin embedded tissue, and from frozen paraffin embedded hamartoma tissue from the same patient. The samples were analysed for 11 markers spanning the TSC1 locus and nine markers spanning the TSC2 locus. Twenty-one of 51 hamartomas showed LOH (41%). There was significantly more LOH on 16p13.3, with 16 hamartomas showing LOH around TSC2, and five in the vicinity of TSC1. No hamartoma showed LOH for markers around both loci. All the areas of LOH on chromosome 9 were large, but the smallest region of overlap lay between the markers D9S149 and D9S114, providing independent evidence for the localisation of the TSC1 gene. These data show that LOH is a common finding in a wide range of hamartomas, affecting the same TSC locus in different lesions from the same patient but not affecting both loci. These data support the hypothesis that both the TSC genes act as tumour suppressors and that the manifestations of TSC in patients with germline TSC mutations rise from "second hit" somatic mutations inactivating the remaining normal copy of the TSC gene.     

Thermal Boundary Resistance in GaN Films Measured by Time Domain Thermoreflectance with Robust Monte Carlo Uncertainty Estimation

In this work, we investigate the thermal boundary resistance and thermal conductivity of GaN layers grown on Si with 100 nm AlN transition layers using time domain thermoreflectance (TDTR). The GaN layers ranged from 0.31 to 1.27 μm. Due to the challenges in determining the thermal boundary resistance of the buried interfaces found in this architecture, a new data reduction scheme for TDTR that utilizes a Monte Carlo fitting method is introduced and found to dramatically reduce the uncertainty in certain model parameters. The results show that the GaN thermal conductivity does not change significantly with layer thickness, whereas the resistance of the AlN layer decreases slightly with GaN thickness.     

Australia's housing choices: Retrospect and prospect

This article identifies issues around the Auckland Region's strategy for urban intensification and discusses the ensuing policy implications. Medium density housing forms an important element of the strategy for growth management. Implications for its success are primarily drawn from research into a major housing development in Waitakere City. It is argued that for ideological, political and technical reasons the strategy could be easily undermined. The article also suggests that something of a paradigm shift is underway in urban planning.     

Mathematical similarities in engineering network analysis

This paper examines the proposition that structural trusses and pipe networks for water supply are closely related in a mathematical sense. It shows that in terms of representation, physical quantities, constitutive equations, analysis problem formulations and methods of analysis they both belong to the same class of nonlinear potentiated networks, the truss being a special linear case for problems of analysis. The analysis of nonlinear potentiated networks may therefore be efficiently performed by linearization of the relevant nonlinear quantities and the iterative use of well-known truss analysis methods. The commonality established between structural trusses and water supply systems has potential for exploitation in respect of other network-related problems of optimum design, reliability evaluation and design for resilience.     

Biodegradability of lubricant base stocks and fully formulated products

Increasing awareness of the environmental impact of consumer and industrial products has produced a demand for lubricants that biodegrade. There is a number of biodegradation tests that can be used on lubricants, although not all are always appropriate, as this paper explains. The CEC test is among the best known and is in use for both conventional and synthetic oils. There will, in future, be a greater movement to biodegradable oils in Europe, perhaps extending to all oils.     

A constrained binary knapsack approximation for shortest path network interdiction

A modified shortest path network interdiction model is approximated in this work by a constrained binary knapsack which uses aggregated arc maximum flow as the objective function coefficient. In the modified shortest path network interdiction problem, an attacker selects a path of highest non-detection probability on a network with multiple origins and multiple available targets. A defender allocates a limited number of resources within the geographic region of the network to reduce the maximum network non-detection probability between all origin-target pairs by reducing arc non-detection probabilities and where path non-detection probability is modeled as a product of all arc non-detection probabilities on that path. Traditional decomposition methods to solve the shortest path network interdiction problem are sensitive to problem size and network/regional complexity. The goal of this paper is to develop a method for approximating the regional allocation of defense resources that maintains accuracy while reducing both computational effort and the sensitivity of computation time to network/regional properties. Statistical and spatial analysis methods are utilized to verify approximation performance of the knapsack method in two real-world networks.     

Probability-based validation of protein identifications using a modified SEQUEST algorithm

Database-searching algorithms compatible with shotgun proteomics match a peptide tandem mass spectrum to a predicted mass spectrum for an amino acid sequence within a database. SEQUEST is one of the most common software algorithms used for the analysis of peptide tandem mass spectra by using a cross-correlation (XCorr) scoring routine to match tandem mass spectra to model spectra derived from peptide sequences. To assess a match, SEQUEST uses the difference between the first- and second-ranked sequences (ACn). This value is dependent on the database size, search parameters, and sequence homologies. In this report, we demonstrate the use of a scoring routine (SEQUEST-NORM) that normalizes XCorr values to be independent of peptide size and the database used to perform the search. This new scoring routine is used to objectively calculate the percent confidence of protein identifications and posttranslational modifications based solely on the XCorr value.