Diversity of the rDNA ITS haplotypes of the nematodes Haemonchus contortus (Trichostrongyloidea, Rhabditida) of the same host

Specimens sampled in Central Mongolia have been examined for the intraspecific polymorphism of the nucleotide sequences of ribosomal DNA internal transcribed spacers (ITS1 + 5.8S + ITS2) of the parasitic nematode Haemonchus contortus. A considerable diversity of haplotypes differing in the nucleotide composition of this DNA region has been observed. The phylogenetic relationships between the haplotypes detected in Central Mongolia and the corresponding sequences from other parts of the nematode distribution area (deposited with the NCBI GenBank) have been analyzed. Significantly different sequences have been found along with the haplotypes already observed in H. contortus or differing from them by one-two nucleotides.     

137Cs vertical migration in boggy soils in the long term after the Chernobyl accident

137Cs vertical migration in boggy soils has been studied 15 years after the Chernobyl accident. The rate of vertical migration of the radionuclide is shown to be dependent on the peculiarities of formation of peatbogs, their moistening regime and soil properties. 137Cs migration in a high-land peatbog is characterized by higher intensity then in lowland or transitional peatbogs. Differences in 137Cs vertical migration are to a large extent caused by the contents in soil of exhangeable and mobile radionuclide forms. The derived experimental data that describe 137Cs distribution over the profiles of peaty soils of different type are used for parameterization of two-component convective-diffusion model. Ecological and effective half-life periods of 137Cs content reduction in the soil root layer have been calculated. A long-term prediction is given of the dynamics of the radionuclide content in the root layer of peaty soils.     

A model-based optimization framework for the inference on gene regulatory networks from DNA array data

MOTIVATION: Identification of the regulatory structures in genetic networks and the formulation of mechanistic models in the form of wiring diagrams is one of the significant objectives of expression profiling using DNA microarray technologies and it requires the development and application of identification frameworks. RESULTS: We have developed a novel optimization framework for identifying regulation in a genetic network using the S-system modeling formalism. We show that balance equations on both mRNA and protein species led to a formulation suitable for analyzing DNA-microarray data whereby protein concentrations have been eliminated and only mRNA relative concentrations are retained. Using this formulation, we examined if it is possible to infer a set of possible genetic regulatory networks consistent with observed mRNA expression patterns. Two origins of changes in mRNA expression patterns were considered. One derives from changes in the biophysical properties of the system that alter the molecular-interaction kinetics and/or message stability. The second is due to gene knock-outs. We reduced the identification problem to an optimization problem (of the so-called mixed-integer non-linear programming class) and we developed an algorithmic procedure for solving this optimization problem. Using simulated data generated by our mathematical model, we show that our method can actually find the regulatory network from which the data were generated. We also show that the number of possible alternate genetic regulatory networks depends on the size of the dataset (i.e. number of experiments), but this dependence is different for each of the two types of problems considered, and that a unique solution requires fewer datasets than previously estimated in the literature. This is the first method that also allows the identification of every possible regulatory network that could explain the data, when the number of experiments does not allow identification of unique regulatory structure.     

Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations

Translation is a central cellular process in every organism and understanding translation from the systems (genome-wide) perspective is very important for medical and biochemical engineering applications. Moreover, recent advances in cell-wide monitoring tools for both mRNA and protein levels have necessitated the development of such a model to identify parameters and conditions that influence the mapping between mRNA and protein expression. Experimental studies show a lack of correspondence between mRNA and protein expression profiles. In this study, we describe a mechanistic genome-wide model for translation that provides mapping between changes in mRNA levels and changes in protein levels. We use our model to study the system in detail and identify the key parameters that affect this mapping. Our results show that the correlation between mRNA and protein levels is a function of both the kinetic parameters and concentration of ribosomes at the reference state. In particular, changes in concentration of free and total ribosomes in response to a perturbation; changes in initiation and elongation kinetics due to competition for aminoacyl tRNAs; changes in termination kinetics; average changes in mRNA levels in response to the perturbation; and changes in protein stability are all important determinants of the mapping between mRNA and protein expression.     

A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering

When mentioning prokaryotic metabolic engineering, most people will immediately think of Jay Bailey. Jay's contribution to this fast-growing field is evident and familiar to many. Therefore, instead of a detailed technical review, we attempt in this article to summarize his contribution and dissect reasons for his success in this area from a standpoint of one of his former students (VH) and of a colleague in the field (JCL). This short review is by no means complete and provides only a partial view of Jay's contribution to the metabolic engineering of prokaryotes.     

Muscle electrolyte measurements during and after hypokinesia in determining muscle electrolyte depletion during hypokinesia in the rat

Hypokinesia (diminished movement) induces muscle mineral depletion. However, the mechanism of muscle mineral depletion during hypokinesia (HK) remains unknown. Measuring electrolyte retention and electrolyte values in muscle, plasma, and urine during and after HK, the aim of this study was to discover if HK could depress mineral retention and lead to muscle mineral depletion. Studies were done on 204 13-wk-old male Wistar rats (370–390 g) during 10 d pre-HK period, 98 d HK period, and 15 d post-HK period. Rats were equally divided into two groups: vivarium control rats (VCR) and hypokinetic rats (HKR). All hypokinetic rats were kept for 98 d in small individual cages, which restricted their movements in all directions without hindering food and water intakes. All control rats were housed for 98 d in individual cages under vivarium control conditions. Both groups of rats were pair-fed. During the HK period skeletal muscle sodium (Na), potassium (K), magnesium (Mg), calcium (Ca), and water content and electrolyte retention decreased significantly (p < 0.05), while urinary and plasma electrolyte levels increased significantly (p < 0.05) in HKR compared with their pre-HK values and their respective VCR. During the initial days of the post-HK period, mineral retention increased significantly (p < 0.05), plasma and urinary electrolyte level decreased significantly (p < 0.05), while muscle electrolyte and water content remained significantly (p < 0.05) depressed in HKR compared with VCR. Muscle mineral and water content, electrolyte retention, plasma, and urinary electrolyte values did not change in VCR compared with their pre-HK values. It was concluded that during HK decreased muscle mineral content may suggest muscle mineral depletion, while increased urinary electrolyte loss and muscle mineral depletion may demonstrate reduced mineral retention. Reduced electrolyte excretion and depressed muscle mineral content during post-HK may indicate skeletal muscle mineral depletion during HK. Dissociation between electrolyte retention and muscle mineral depletion may demonstrate the presence of decreased electrolyte retention as the mechanism of muscle electrolyte depletion during prolonged HK.     

Comparative characteristic of serpin--alpha-1 proteinase inhibitor in human and mice serum

Serpin alpha-1-proteinase inhibitor have been studied in human subjects and in mice of different lines as acute phase reactant and during tumor development. In humans, there was no difference of serpin activity between men and women. Increased activity was noted in men with acute trauma (acute phase reaction). Comparatively to male, in female mice of different lines decreased activity of serum alpha-1-proteinase inhibitor, was shown. There was no increase of alpha-1-proteinase inhibitor activity during inflammation induced by zymosan administration in mice. alpha-1-proteinase inhibitor belongs to acute phase reactants in humans but not in mice; for mice alpha-2-macroglobulin is a more typical acute phase reactant as compared to alpha-1-proteinase inhibitor. Murine tumor development (hepatoma HA-1, lymphosarcoma LS, Lewis lung adenocarcinoma) was followed by a decreased activity of serum alpha-1-proteinase inhibitor both in successfully treated and untreated groups. According to data of literature, similar dated were obtained in humans with tumors. It was suggested that changes of expressiln of alpha-1-proteinase inhibitor by tumors and its secretion were involved in decreased activity of alpha-1-proteinase inhibitor.