Biophysical methods for biochip analysis. Use of wide field digital fluorescent microscopy

This paper discusses an issue on the development of biophysical methods for biochip analysis. A scheme and construction of a biochip analyzer based on wide-field digital fluorescence microscopy are described. The analyzer is designed to register images of biological microchips labeled with fluorescent dyes. The device developed is useful for high-sensitive throughput recording analyses by biochips after interaction of immobilized probes with fluorescently labeled sample molecules as well as it provides the higher rate of the analysis compared to laser scanning devices. With this analyzer a scope where biological microchips can be applied becomes wider, the development of new protocols of the analyses is possible and standard analyses run faster with the use of biochips, the expenses for the analysis performance can be reduced.     

Is genetic structure of the southern pygmy mouse Baiomys musculus (Cricetidae) related to human-induced spatial landscape heterogeneity in a tropical dry forest?

Tropical dry forests are biologically important biomes sustaining a high rate of endemic species. However, these forests are highly threatened by human activities that negatively impact them on distinct levels, including the genetic diversity. Within the framework of landscape genetics (that seeks to evaluate the relation of characteristics of the environmental matrix with population genetics), we used ISSR markers to evaluate the relationship between the alteration of tropical dry forest by human-induced activities (conserved vs. disturbed) with the genetic structure of four breeding sites of the southern pygmy mouse Baiomys musculus. Averaging among the 105 loci used, the unbiased heterozygosis per population (0.247–0.305) was statistically similar among the four sites, as well as between conserved and disturbed conditions (2-way ANOVA F _(3,16)?=?1.47, P?=?0.1984). The genetic differentiation among the four breeding sites was high (F _ST?=?0.1122; 95?% CI 0.082–0.146) considering the geographical scale evaluated (ca. 4?km). Both, a factorial correspondence analysis and a model-based clustering analysis showed the existence of four genetic groups (one per breeding site). However, no association of genetic structure with disturbance conditions was revealed by these analyses. The absence of differences in mean genetic diversity and the lack of association of genetic structure with habitat transformation suggest that B. musculus has enough behavioral plasticity and enough genetic diversity to respond to environmental heterogeneity caused by human activities. We discussed conditions in which habitat transformation could indeed favor B. musculus.     

Mosaic patterns of transgene expression in plants

The review describes the phenomenon of mosaic transgene (gene) expression in plants. Parallels with the mosaic transgene (gene) expression in other organisms are presented. Parallels with the mosaic patterns of gene (transgene) expression in other organisms (Drosophila, transgenic animals, and others) are made.     

Diagnosis of mitochondrial disorders applying massive pyrosequencing

Mitochondrial disorders are a frequent cause of neurological disability affecting children and adults. Traditionally, molecular diagnosis of mitochondrial diseases was mostly accomplished by the use of Sanger sequencing and PCR–RFLP. However, there are particular drawbacks associated with the use of these methods. Recent multidisciplinary advances have led to new sequencing methods that may overcome these limitations. Our goal was to explore the use of a next generation sequencing platform in the molecular diagnosis of mitochondrial diseases reporting our findings in adult patients that present with a clinical-pathological diagnosis of a mitochondrial encephalomyopathy. Complete genomic sequences of mitochondrial DNA were obtained by 454 massive pyrosequencing from blood samples. The analysis of these sequences allowed us to identify two diagnostic pathogenic mutations and 74 homoplasmic polymorphisms, useful for obtaining high-resolution mitochondrial haplogroups. In summary, molecular diagnosis of mitochondrial disorders could be efficiently done from readily accessible samples, such as blood, with the use of a new sequencing platform.     

Changes of the state of rat kidneys under guerin carcinoma development and use of cytostatics

It was shown that development of the Guerin carcinoma and introduction of cisplatin led to the damage of the kidneys of rats that was confirmed by a relative increase of weight, proteinuria, change of gamma-glutamyl transpeptidase and lactate dehydrogenase activity in the urea and tissue homogenates of the kidneys, by a decrease of relative reabsorption and glomerular filtration. Introduction of nanoliposomal forms of the rhenium cluster compounds led to normalization of above mentioned diagnostic indexes and to reduction of the toxic cisplatin influence that was confirmed by biochemical and morphological investigations.     

Pseudomonas aeruginosa: characteristics of biofilm process

Definition of the biofilm process as one of the types of intercellular bacterial communications is presented. The modern data concerning the structure of the Pseudomonas aeruginosa biofilm matrix and genetic mechanisms necessary for its production are described. Active and passive rejections of biofilm bacteria, which are the basis of bacterial spreading to new surfaces, are discussed. The complexity and chain type of the reactions associated with biofilm formation are emphasized.     

Reconstruction of associative protein networks connected with processes of sodium exchange' regulation and sodium deposition in healthy volunteers by urine proteome analysis

The study was conducted during the experiment with 105-day isolation in experimental complex. In the present investigation we collected urine samples from 6 healthy volunteers. The physical activity, diurnal rhythm, temperature parameters and level of oxygen and carbon dioxide were controlled during the experiment. According to the program, food intake (electrolytes, water, calories, fat, carbohydrates, protein, vitamins, etc.) on each stage of experiment was normalized. All samples were analyzed using mass spectrometer of an ionic cyclotron resonance with transformation of Fure LTQ FT MS (Thermo) on the basis of the AMT-tags (accurate mass and time tags) approach. Among more than 20 000 we found out 690 proteotypical proteins and we identified about 600 urine proteins. For physiological interpretation of the proteome data we used computer systems ANDCell and ANDVisio. Clustering of proteins and application of these systems revealed proteins that are most closely associated with the regime of sodium intake, as well as build the network of their interactions.     

Synthesis and cardioprotective properties of apelin-12 and its structural analogs

The apelin-12 and a number of its analogs, resistant to degradation of proteases, were synthesized by Fmoc- method of SPPS. By-products of synthesis were examined. It was found that serine hydroxyl group was sulfating during the final deprotection of apelin-12 (I) and its analogs. Sulfate moiety of Arg-protecting group transfer into hydroxyl group of Ser. Amount of by-product depends on presence of water in cleavage mixture. Furthermore, the final deprotection of amide analogs of apelin-12 (III, IV) is closed with formation of by-product--4-hydroxybenzylamide, its amount range on 20-8% on reaction mixture accordance HPLC data and also depend on composition of cleavage mixture. Effects of the synthesized peptides on recovery of cardiac function after ischemia were examined in a model of isolated perfused rat heart. Infusions of any of the peptides (I-V) before ischemia resulted in a significant improvement of contractile and pump function recovery compared to the control. Cardioptotective efficacy of the peptides increased in the following rank (I) < (II) = (III) < (IV) = (V).     

Affine sorbent with typtophil-threonil-tirosine for binding immunoglobulin G: sorption characteristics and aspects of practical application

New chromatographic material based on tryptophil-threonil-tirosine was prepared. This sorbent effectively binds human, sheep, goat and cow immunoglobulins G. New sorbent shows high selectivity for removing immunoglobulins from blood plasma. Effective sorption capacity is 15-25 mg of immunoglobulin G per ml of matrix. Optimal method of covalent attachment ligand to polysaccharide matrix allows achieving high stability of the sorbents in terms of use and storage. This sorbent can be used in medicine and biotechnology.