Mouse proteome analysis

A general overview of the protein sequence set for the mouse transcriptome produced during the FANTOM2 sequencing project is presented here. We applied different algorithms to characterize protein sequences derived from a nonredundant representative protein set (RPS) and a variant protein set (VPS) of the mouse transcriptome. The functional characterization and assignment of Gene Ontology terms was done by analysis of the proteome using InterPro. The Superfamily database analyses gave a detailed structural classification according to SCOP and provide additional evidence for the functional characterization of the proteome data. The MDS database analysis revealed new domains which are not presented in existing protein domain databases. Thus the transcriptome gives us a unique source of data for the detection of new functional groups. The data obtained for the RPS and VPS sets facilitated the comparison of different patterns of protein expression. A comparison of other existing mouse and human protein sequence sets (e.g., the International Protein Index) demonstrates the common patterns in mammalian proteornes. The analysis of the membrane organization within the transcriptome of multiple eukaryotes provides valuable statistics about the distribution of secretory and transmembrane proteins

A model to investigate hepatic extraction of oxygen during anaesthesia in the dog

Measurement of hepatic oxygen extraction was performed on six healthy Greyhound dogs over a two hour period. The Greyhounds were anaesthetised and a right subcostal surgical incision performed. Ultrasonic flow transducers were used to measure flow rate in the hepatic artery and the portal vein. The blood oxygen tensions in arterial blood and in the portal and hepatic veins were also measured. Hepatic oxygen extraction remained stable throughout the study, despite a steady decline in arterial blood pressure. The methodology described in this study provides a direct measure of oxygen uptake by the liver in the dog and could readily be used to investigate hepatic uptake of drugs. (C) 2003 Elsevier Ltd. All rights reserved.

Biaxial failure model for fiber reinforced concrete

Steel fiber reinforced concrete (SFRC) is widely applied in the construction industry. Numerical elastoplastic analysis of the macroscopic behavior is complex. This typically involves a piecewise linear failure curve including corner singularities. This paper presents a single smooth biaxial failure curve for SFRC based on a semianalytical approximation. Convexity of the proposed model is guaranteed so that numerical problems are avoided. The model has sufficient flexibility to closely match experimental results. The failure curve is also suitable for modeling plain concrete under biaxial loading. Since this model is capable of simulating the failure states in all stress regimes with a single envelope, the elastoplastic formulation is very concise and simple. The finite element implementation is developed to demonstrate the conciseness and the effectiveness of the model. The computed results display good agreement with published experimental data.

Model-based analysis of anaerobic acetate uptake by a mixed culture of polyphosphate-accumulating and glycogen-accumulating organisms

An increasing number of studies shows that the glycogen-accumulating organisms (GAOs) can survive and may indeed proliferate under the alternating anaerobic/aerobic conditions found in EBPR systems, thus forming a strong competitor of the polyphosphate-accumulating organisms (PAOs). Understanding their behaviors in a mixed PAO and GAO culture under various operational conditions is essential for developing operating strategies that disadvantage the growth of this group of unwanted organisms. A model-based data analysis method is developed in this paper for the study of the anaerobic PAO and GAO activities in a mixed PAO and GAO culture. The method primarily makes use of the hydrogen ion production rate and the carbon dioxide transfer rate resulting from the acetate uptake processes by PAOs and GAOs, measured with a recently developed titration and off-gas analysis (TOGA) sensor. The method is demonstrated using the data from a laboratory-scale sequencing batch reactor (SBR) operated under alternating anaerobic and aerobic conditions. The data analysis using the proposed method strongly indicates a coexistence of PAOs and GAOs in the system, which was independently confirmed by fluorescent in situ hybridization (FISH) measurement. The model-based analysis also allowed the identification of the respective acetate uptake rates by PAOs and GAOs, along with a number of kinetic and stoichiometric parameters involved in the PAO and GAO models. The excellent fit between the model predictions and the experimental data not involved in parameter identification shows that the parameter values found are reliable and accurate. It also demonstrates that the current anaerobic PAO and GAO models are able to accurately characterize the PAO/GAO mixed culture obtained in this study. This is of major importance as no pure culture of either PAOs or GAOs has been reported to date, and hence the current PAO and GAO models were developed for the interpretation of experimental results of mixed cultures. The proposed method is readily applicable for detailed investigations of the competition between PAOs and GAOs in enriched cultures. However, the fermentation of organic substrates carried out by ordinary heterotrophs needs to be accounted for when the method is applied to the study of PAO and GAO competition in full-scale sludges. (C) 2003 Wiley Periodicals, Inc.

Metabolic model for glycogen-accumulating organisms in anaerobic/aerobic activated sludge systems

Glycogen-accumulating organisms (GAO) have the potential to directly compete with polyphosphate-accumulating organisms (PAO) in EBPR systems as both are able to take up VFA anaerobically and grow on the intracellular storage products aerobically. Under anaerobic conditions GAO hydrolyse glycogen to gain energy and reducing equivalents to take up VFA and to synthesise polyhydroxyalkanoate (PHA). In the subsequent aerobic stage, PHA is being oxidised to gain energy for glycogen replenishment (from PHA) and for cell growth. This article describes a complete anaerobic and aerobic model for GAO based on the understanding of their metabolic pathways. The anaerobic model has been developed and reported previously, while the aerobic metabolic model was developed in this study. It is based on the assumption that acetyl-CoA and propionyl-CoA go through the catabolic and anabolic processes independently. Experimental validation shows that the integrated model can predict the anaerobic and aerobic results very well. It was found in this study that at pH 7 the maximum acetate uptake rate of GAO was slower than that reported for PAO in the anaerobic stage. On the other hand, the net biomass production per C-mol acetate added is about 9% higher for GAO than for PAO. This would indicate that PAO and GAO each have certain competitive advantages during different parts of the anaerobic/aerobic process cycle. (C) 2002 Wiley Periodicals, Inc.

Model studies on the role of citrate, malate and pectin esterification on the enzymatic degradation of Al- and Ca-pectate gels: possible implications for Al-tolerance

Aluminium (At) tolerance in plants may be conferred by reduced binding of Al in the cell wall through low root cation exchange capacity (CEC) or by organic acid exudation. Root CEC is related to the degree of esterification (DE) of pectin in the cell wall, and pectin hydrolysis plays a role in cell expansion. Therefore, it was hypothesised that Al-tolerant plants with a low root CEC maintain pectin hydrolysis in the presence of Al, allowing cell expansion to continue. Irrespective of the DE, binding of Al to pectin reduced the enzymatic hydrolysis of Al-pectin gels by polygalacturonase (E.C. 3.2.1.15). Pectin gels with calcium (Ca) were slightly hydrolysed by polygalacturonase. It was concluded, therefore, that Al tolerance conferred by low root CEC is not mediated by the ability to maintain pectin hydrolysis. Citrate and malate, but not acetate, effectively dissolved Al-pectate gel and led to hydrolysis of the dissolved pectin by polygalacturonase. The organic acids did not dissolve Ca-pectate, nor did they increase pectin hydrolysis by polygalacturonase. It was concluded that exudation of some organic acids can remove Al bound to pectin and this could alleviate toxicity, constituting a tolerance mechanism. (C) 2003 Editions scientitiques et medicales Elsevier SAS. All rights reserved.

Displaying the future: Techno-nationalism and the rise of the consumer in postwar Japan

This paper explains how, in the aftermath of World War II, a type of techno-nationalism emerged that linked being Japanese to science and technology and the increased consumption of electrical appliances. By closely examining official exhibitions, we can see how the state and private sector strongly encouraged this techno-scientific dreaming. Dazzling displays highlighted how the peaceful atom would help lead the nation to achieve high economic growth. At the same time, through the judicious purchase of labor saving appliances, consumers could reconcile the need to spend with the need to save.

Alterations of neocortical pyramidal cell phenotype in the Ts65Dn mouse model of Down syndrome: Effects of environmental enrichment

Mental retardation in individuals with Down syndrome (DS) is thought to result from anomalous development and function of the brain; however, the underlying neuropathological processes have yet to be determined. Early implementation of special care programs result in limited, and temporary, cognitive improvements in DS individuals. In the present study, we investigated the possible neural correlates of these limited improvements. More specifically, we studied cortical pyramidal cells in the frontal cortex of Ts65Dn mice, a partial trisomy of murine chromosome 16 (MMU16) model characterized by cognitive deficits, hyperactivity, behavioral disruption and reduced attention levels similar to those observed in DS, and their control littermates. Animals were raised either in a standard or in an enriched environment. Environmental enrichment had a marked effect on pyramidal cell structure in control animals. Pyramidal cells in environmentally enriched control animals were significantly more branched and more spinous than non-enriched controls. However, environmental enrichment had little effect on pyramidal cell structure in Ts65Dn mice. As each dendritic spine receives at least one excitatory input, differences in the number of spines found in the dendritic arbors of pyramidal cells in the two groups reflect differences in the number of excitatory inputs they receive and, consequently, complexity in cortical circuitry. The present results suggest that behavioral deficits demonstrated in the Ts65Dn model could be attributed to abnormal circuit development.

Structural characterization of respiratory syncytial virus fusion inhibitor escape mutants: homology model of the F protein and a syncytium formation assay

Respiratory syncytial virus (RSV) is a ubiquitous human pathogen and the leading cause of lower respiratory tract infections in infants. Infection of cells and subsequent formation of syncytia occur through membrane fusion mediated by the RSV fusion protein (RSV-F). A novel in vitro assay of recombinant RSV-F function has been devised and used to characterize a number of escape mutants for three known inhibitors of RSV-F that have been isolated. Homology modeling of the RSV-F structure has been carried out on the basis of a chimera derived from the crystal structures of the RSV-F core and a fragment from the orthologous fusion protein from Newcastle disease virus (NDV). The structure correlates well with the appearance of RSV-F in electron micrographs, and the residues identified as contributing to specific binding sites for several monoclonal antibodies are arranged in appropriate solvent-accessible clusters. The positions of the characterized resistance mutants in the model structure identify two promising regions for the design of fusion inhibitors. (C) 2003 Elsevier Science (USA). All rights reserved.

On the evaluation of some differential formulations for the pom-pom constitutive model

In recent years, progress has been made in modelling long chain branched polymers by the introduction of the so-called pompom model. Initially developed by McLeish and Larson (1998), the model has undergone several improvements or alterations, leading to the development of new formulations. Some of these formulations however suffer from certain mathematical defects. The purpose of the present paper is to review some of the formulations of the pom-pom constitutive model, and to investigate their possible mathematical defects. Next, an alternative formulation is proposed, which does not appear to exhibit mathematical defects, and we explore its modelling performance by comparing the predictions with experiments in non-trivial rheometric flows of an LDPE melt. The selected rheometric flows are the double step strain, as well as the large amplitude oscillatory shear experiments. For LAOS experiments, the comparison involves the use of Fourier-transform analysis.

Evaluating a model of parental influence on youth physical activity

Objective: To test a conceptual model linking parental physical activity orientations, parental support for physical activity, and children's self-efficacy perceptions with physical activity participation. Participants and Setting: The sample consisted of 380 students in grades 7 through 12 (mean age, 14.0 +/- 1.6 years) and their parents. Data collection took place during the fall of 1996. Main Outcome Measures: Parents completed a questionnaire assessing their physical activity habits, enjoyment of physical activity, beliefs regarding the importance of physical activity, and supportive behaviors for their child's physical activity. Students completed a 46-item inventory assessing physical activity during the previous 7 days and a 5-item physical activity self-efficacy scale. The model was tested via observed variable path analysis using structural equation modeling techniques (AMOS 4.0). Results: An initial model, in which parent physical activity orientations predicted child physical activity via parental support and child self-efficacy, did not provide an acceptable fit to the data. Inclusion of a direct path from parental support to child physical activity and deletion of a nonsignificant path from parental physical activity to child physical activity significantly improved model fit. Standardized path coefficients for the revised model ranged from 0.17 to 0.24, and all were significant at the p < 0.0001 level. Conclusions: Parental support was an important correlate of youth physical activity, acting directly or indirectly through its influence on self-efficacy. Physical activity interventions targeted at youth should include and evaluate the efficacy of individual-level and community-level strategies to increase parents' capacity to provide instrumental and motivational support for their children's physical activity.

Phase equilibria and surface tension of pure fluids using a molecular layer structure theory (MLST) model

This paper presents a new model based on thermodynamic and molecular interaction between molecules to describe the vapour-liquid phase equilibria and surface tension of pure component. The model assumes that the bulk fluid can be characterised as set of parallel layers. Because of this molecular structure, we coin the model as the molecular layer structure theory (MLST). Each layer has two energetic components. One is the interaction energy of one molecule of that layer with all surrounding layers. The other component is the intra-layer Helmholtz free energy, which accounts for the internal energy and the entropy of that layer. The equilibrium between two separating phases is derived from the minimum of the grand potential, and the surface tension is calculated as the excess of the Helmholtz energy of the system. We test this model with a number of components, argon, krypton, ethane, n-butane, iso-butane, ethylene and sulphur hexafluoride, and the results are very satisfactory. (C) 2002 Elsevier Science B.V. All rights reserved.