Bayesian flux balance analysis applied to a skeletal muscle metabolic model

In this article, the steady state condition for the multi-compartment models for cellular metabolism is considered. The problem is to estimate the reaction and transport fluxes, as well as the concentrations in venous blood when the stoichiometry and bound constraints for the fluxes and the concentrations are given. The problem has been addressed previously by a number of authors, and optimization-based approaches as well as extreme pathway analysis have been proposed. These approaches are briefly discussed here. The main emphasis of this work is a Bayesian statistical approach to the flux balance analysis (FBA). We show how the bound constraints and optimality conditions such as maximizing the oxidative phosphorylation flux can be incorporated into the model in the Bayesian framework by proper construction of the prior densities. We propose an effective Markov chain Monte Carlo (MCMC) scheme to explore the posterior densities, and compare the results with those obtained via the previously studied linear programming (LP) approach. The proposed methodology, which is applied here to a two-compartment model for skeletal muscle metabolism, can be extended to more complex models.     

Functional characterization of fingers subdomain-specific monoclonal antibodies inhibiting the hepatitis C virus RNA-dependent RNA polymerase

The hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp), encoded by nonstructural protein 5B (NS5B), is absolutely essential for the viral replication. Here we describe the development, characterization, and functional properties of the panel of monoclonal antibodies (mAbs) and specifically describe the mechanism of action of two mAbs inhibiting the NS5B RdRp activity. These mAbs recognize and bind to distinct linear epitopes in the fingers subdomain of NS5B. The mAb 8B2 binds the N-terminal epitope of the NS5B and inhibits both primer-dependent and de novo RNA synthesis. mAb 8B2 selectively inhibits elongation of RNA chains and enhances the RNA template binding by NS5B. In contrast, mAb 7G8 binds the epitope that contains motif G conserved in viral RdRps and inhibits only primer-dependent RNA synthesis by specifically targeting the initiation of RNA synthesis, while not interfering with the binding of template RNA by NS5B. To reveal the importance of the residues of mAb 7G8 epitope for the initiation of RNA synthesis, we performed site-directed mutagenesis and extensively characterized the functionality of the HCV RdRp motif G. Comparison of the mutation effects in both in vitro primer-dependent RdRp assay and cellular transient replication assay suggested that mAb 7G8 epitope amino acid residues are involved in the interaction of template-primer or template with HCV RdRp. The data presented here allowed us to describe the functionality of the epitopes of mAbs 8B2 and 7G8 in the HCV RdRp activity and suggest that the epitopes recognized by these mAbs may be useful targets for antiviral drugs.     

The Effect of Personality on Daily Life Emotional Processes

Personality features are associated with individual differences in daily emotional life, such as negative and positive affectivity, affect variability and affect reactivity. The existing literature is somewhat mixed and inconclusive about the nature of these associations. The aim of this study was to shed light on what personality features represent in daily life by investigating the effect of the Five Factor traits on different daily emotional processes using an ecologically valid method. The Experience Sampling Method was used to collect repeated reports of daily affect and experiences from 104 healthy university students during one week of their normal lives. Personality traits of the Five Factor model were assessed using NEO Five Factor Inventory. Hierarchical linear modeling was used to analyze the effect of the personality traits on daily emotional processes. Neuroticism predicted higher negative and lower positive affect, higher affect variability, more negative subjective evaluations of daily incidents, and higher reactivity to stressors. Conscientiousness, by contrast, predicted lower average level, variability, and reactivity of negative affect. Agreeableness was associated with higher positive and lower negative affect, lower variability of sadness, and more positive subjective evaluations of daily incidents. Extraversion predicted higher positive affect and more positive subjective evaluations of daily activities. Openness had no effect on average level of affect, but predicted higher reactivity to daily stressors. The results show that the personality features independently predict different aspects of daily emotional processes. Neuroticism was associated with all of the processes. Identifying these processes can help us to better understand individual differences in daily emotional life.     

Risk induced by a native top predator reduces alien mink movements

1. Nonlethal predation effects may have stronger impacts on prey populations than direct predation impacts, and this should also apply to intraguild predation. The consequences of such interactions become especially important if invasive, and potentially destructive alien predators act as intraguild prey. 2. We studied the predation-risk impacts of a re-colonizing native top predator, Haliaeetus albicilla (white-tailed sea eagle), on the movements of Mustela vison (American mink), an alien predator in Europe. We radiocollared 20 mink in two study areas in the outer archipelago of the Baltic Sea, South-west Finland, during 2004 and 2005. In the archipelago, mink home ranges incorporate many islands, and mink are most predisposed to eagle predation while swimming between islands. Observed swimming distances of mink were compared to distances expected at random, and deviations from random swimming were explained by mink distance from nearest eagle nest, number of eagle observations near mink location, and mink home-range size. 3. Mink reduced their swimming distances with increasing sea eagle predation risk: for females, the reduction was 10% for an increase of 10 eagle observations, and 5% for each kilometre towards an eagle nest. Conclusions for males were restricted by their small sample size. 4. Our results suggest that female mink modify their behaviour according to eagle predation risk, which may reduce their population growth and have long-term cascading effects on lower trophic levels including bird, mammal and amphibian populations in the archipelago. Ecosystem restoration by bringing back the top predators may be one way of mitigating alien predator effects on native biota.     

Characterization and expression of the pepN gene encoding a general aminopeptidase from Lactobacillus helveticus

Abstract The putative ribosome binding sites preceding 32 of Lactobacillus delbrueckii subsp. lactis bacteriophage LL-H genes were compared. A highly conserved consensus sequence for the ribosome binding sites of LL-H genes was inferred, GAAAGGAG. This study included the characterization of the last nucleotides of the 3'-end of the 16S rRNA molecule from L. delbrueckii subsp. lactis and its comparison to the ribosome binding site consensus sequence.     

Joint Russian—Finnish study of radioactive contamination in the NW part of Lake Ladoga

In August 1992 a joint Russian-Finnish expedition was arranged to the NW part of Lake Ladoga to study radioactive contamination in the region. Special attention was paid to the area surrounding the Heinämaa Islands, where the wreck of the former mine carrier ship Kit had been lying about 30 years before it was moved to Novaya Zemlya in 1991. During this period the wreck had been used as a store for radioactive waste containing principally ⁹⁰Sr, ¹³⁷Cs and ^239,24OPu. Lake water, bottom sediment and some biological samples were collected for strontium, plutonium and gammaspectrometric analyses. In all the samples the radioactivity concentrations were very low, indicating radioactive contamination of about the same level as caused by global fallout in the 1960's and the Chernobyl fallout in the area. Only in two water samples taken close to the former site of the wreck slightly elevated ^239,240Pu concentrations were detected. The great water volume of Lake Ladoga and effective water exchange at the wreck site may explain the very low levels of radioactive wastes detected in the aquatic environment.     

Modelling non-uniform soil water uptake by a single plant root

The assumption of uniform water flow to the root or uniform water potential at the root surface was shown by Hainsworth and Aylmore (1986, 1989) to be erroneous. The present paper demonstrates how the non-uniform uptake of water by a single root can be modeled. Differential equations are numerically solved to describe simultaneous water movement in the plant and in the soil. In the plant, boundary conditions are the water potentials at the root surface (Ψ_s) and in the xylem at the root base (Ψ_b). A set of difference equations describe the flow of water radially through the cortex to the xylem and in the xylem axially upwards to the base. For calculating the water flow in the soil and the values of Ψ_s, i.e. the boundary conditions for flow in the root, the finite element method (FEM) is used, the boundary conditions being the flux of water into the plant root and the zero flow across the wall, bottom and surface of a hypothetical soil cylinder surrounding the root. ei]Section editor: B E Clothier     

DNA methylation is not involved in the structural alterations of Ornithine Decarboxylase or Total Chromatin of c-Ha-rasVal 12 Oncogene-Transformed NIH-3T3 Fibroblasts

The ornithine decarboxylase (odc) gene is an early response gene, whose increased expression and relaxed chromatin structure is closely coupled to neoplastic growth. In various tumour cells, the odc gene displays hypomethylation at the sequences CCGG. Hypomethylation of genes is believed to correlate with chromatin decondensation and gene expression. Since a given pattern of DNA methylation may not be preserved in neoplastic cells, we studied the methylation status of odc gene at the CCGG sequences in c-Ha-ras^{Val 12} oncogene-transformed NIH-3T3 fibroblasts during the growth cycle and relative to their normal counterparts. We found that the methylation state of the odc gene and its promoter and mid-coding and 3' regions remain unaltered during the cell cycle. We also found that in ras oncogene-transformed cells, which display a more decondensed nucleosomal organization of chromatin than the normal cells, the CCGG sequences in bulk DNA and at the odc gene were methylated to the same extent as in the nontransformed cells. These data suggest that DNA hypomethylation at the CCGG sequences is not a prerequisite for chromatin decondensation and cell transformation by the c-Ha-ras^{Val 12} oncogene.     

Cystic fibrosis in Finland: a molecular and genealogical study

Summary The incidence of cystic fibrosis (CF) in Finland is one tenth that in other Caucasian populations. To study the genetics of CF in Finland, we used a combined molecular and genealogical approach. Out of the 20 Finnish families with a living CF patient, 19 were typed for eight closely linked restriction fragment length polymorphisms (RFLP) at the MET, D7S8, and D7S23 loci. The birthplaces of the parents and grandparents were traced using population registries. Allele and haplotype frequencies in Finland are similar to those of other European and North American populations, but are modified by sampling: two regional CF gene clusters, evidently the results of a founder effect, were identified. Generally, the gene was evenly distributed over the population, carrier frequency being estimated at approximately 1.3%. We conclude that CF in Finland is caused by the common Caucasian mutation(s), and that the low frequency of the gene can be explained by a negative sampling effect and genetic drift.