固氮酶铬铁蛋白的晶体生长

在合适的结晶条件下 ,从含Cr无氨培养基中生长的固氮菌 (AzotobactervinelandiiLipmann)突变种UW3 中纯化出的CrFe蛋白可从溶液中析出深棕色斜四棱柱晶体 ,晶体最大的两条对角线长度分别可达 0 .2 5mm和 0 .12mm。PEG 80 0 0、MgCl2 、NaCl、Tris和Hepes缓冲液的浓度及结晶方法等对该蛋白的出晶率、晶核数目、晶体大小和质量都有明显影响。CrFe蛋白结晶所需的上述化合物的最适浓度与在Mn中生长的固氮菌突变种UW3 的MnFe蛋白和缺失nifZ固氮菌突变种的ΔnifZMoFe蛋白结晶所需的最适浓度有所不同。结果表明 ,该蛋白晶体可能为CrFe蛋白的晶体     

Multivariate exploratory tools for microarray data analysis

The ultimate success of microarray technology in basic and applied biological sciences depends critically on the development of statistical methods for gene expression data analysis. The most widely used tests for differential expression of genes are essentially univariate. Such tests disregard the multidimensional structure of microarray data. Multivariate methods are needed to utilize the information hidden in gene interactions and hence to provide more powerful and biologically meaningful methods for finding subsets of differentially expressed genes. The objective of this paper is to develop methods of multidimensional search for biologically significant genes, considering expression signals as mutually dependent random variables. To attain these ends, we consider the utility of a pertinent distance between random vectors and its empirical counterpart constructed from gene expression data. The distance furnishes exploratory procedures aimed at finding a target subset of differentially expressed genes. To determine the size of the target subset, we resort to successive elimination of smaller subsets resulting from each step of a random search algorithm based on maximization of the proposed distance. Different stopping rules associated with this procedure are evaluated. The usefulness of the proposed approach is illustrated with an application to the analysis of two sets of gene expression data.     

The modulation of phagocyte oxygen metabolism by recombinant cytokines and a complex of natural cytokines

The data on the modulating function of cytokines on the oxygen-producing function of peritoneal exudate cells of rats are presented. As priming agents, recombinant cytokines IL1 beta and TFR beta 1, as well as the natural complex of cytokines, were used. The priming action of cytokines was studied by changing in the production of active forms of oxygen by peritoneal exudate cells of rats, stimulated with opsonized zymosan, by the method of luminol-dependent chemiluminescence. The study revealed that IL1 beta and the natural complex of cytokines primed peritoneal exudate cells for the production of active forms of oxygen. The maximum value of the prestimulation index was 1.9 +/- 0.1 and 2.95 +/- 0.27 respectively. The preincubation of peritoneal exudate cells of rats with TFR beta 1 led to the pronounced inhibition of the intensity of the chemiluminescent response of cells. The prestimulation index did not exceed 1.06 +/- 0.1. Moreover, as revealed with the use of the probe Fura-2/AM, in the process the prestimulation of phagocytes with the natural complex of cytokines the intracellular concentration of calcium increased from 0.86 +/- 0.15 to 1.86 +/- 0.2 microM/ml. The mechanism of the prestimulation of peritoneal exudate cells of rats cytokines seems to be calcium-dependent.     

A comparison of the effects of laser and light-emitting diodes on superoxide dismutase activity and nitric oxide production in rat wound fluid

The action of laser and light-emitting diode radiation in the visible region on the content of reactive nitrogen species and activity of superoxide dismutase in rat wound fluid was studied, and efficiency of action of coherent laser and incoherent light emitting diode radiations in the red region of the spectrum on the parameters under study was compared. A model of incised aseptic wounds in rats proposed by L.I. Slutskiy was used. A He-Ne laser (632 nm) and a Y-332B light emitting diode served as radiation sources. It was shown that (1) exposure of wounds to the visible light of both laser and light-emitting diodes causes dose-dependent changes in superoxide dismutase activity and production of nitrites and (2) the radiation coherence does not play any significant role in the changes of superoxide dismutase activity or nitrogen oxide formation by wound fluid phagocytes.     

Multivariate search for differentially expressed gene combinations

Background

To identify differentially expressed genes, it is standard practice to test a two-sample hypothesis for each gene with a proper adjustment for multiple testing. Such tests are essentially univariate and disregard the multidimensional structure of microarray data. A more general two-sample hypothesis is formulated in terms of the joint distribution of any sub-vector of expression signals.

Results

By building on an earlier proposed multivariate test statistic, we propose a new algorithm for identifying differentially expressed gene combinations. The algorithm includes an improved random search procedure designed to generate candidate gene combinations of a given size. Cross-validation is used to provide replication stability of the search procedure. A permutation two-sample test is used for significance testing. We design a multiple testing procedure to control the family-wise error rate (FWER) when selecting significant combinations of genes that result from a successive selection procedure. A target set of genes is composed of all significant combinations selected via random search.

Conclusions

A new algorithm has been developed to identify differentially expressed gene combinations. The performance of the proposed search-and-testing procedure has been evaluated by computer simulations and analysis of replicated Affymetrix gene array data on age-related changes in gene expression in the inner ear of CBA mice.

     

Variable selection and pattern recognition with gene expression data generated by the microarray technology

Lack of adequate statistical methods for the analysis of microarray data remains the most critical deterrent to uncovering the true potential of these promising techniques in basic and translational biological studies. The popular practice of drawing important biological conclusions from just one replicate (slide) should be discouraged. In this paper, we discuss some modern trends in statistical analysis of microarray data with a special focus on statistical classification (pattern recognition) and variable selection. In addressing these issues we consider the utility of some distances between random vectors and their nonparametric estimates obtained from gene expression data. Performance of the proposed distances is tested by computer simulations and analysis of gene expression data on two different types of human leukemia. In experimental settings, the error rate is estimated by cross-validation, while a control sample is generated in computer simulation experiments aimed at testing the proposed gene selection procedures and associated classification rules.     

On Choosing Control Objects in Experimental Gerontological Research

Recently, a large number of papers have appeared that describe the successful use of various biologically active compounds (short peptides, mitochondrial antioxidants, antidiabetic biguanides, mimetics of dietary restriction, autophagy modulators, etc.) as geroprotectors. However, in our opinion, in most cases, the positive results of such studies are determined by a “successful” selection of control objects. Animals with certain abnormalities are often used for this purpose, so that any favorable effect on the corresponding pathological processes leads to an increase in their lifespan. In addition, control animals can be normal (i.e., wildtype) but placed under certain extreme conditions that can be overcome just by using certain biologically active compounds. Thus, in this case, the treatment of pathologies rather than the effect on fundamental processes of aging is observed. There is a point of view that the results of Clive McCay’s well-known experiments, which have significantly prolonged the life of rats by limiting caloric intake, were determined by the facts that, firstly, the control animals fed ad libitum (which is absolutely untypical for animals in the wild) and, secondly, Fisher-344 rats, which were used in these experiments, are short-lived. The above considerations, apparently, also apply to the gerontological experiments on cultured cells. In particular, we sometimes hear remarks from our colleagues regarding the model of “stationary phase aging” of cell cultures, which is used in our laboratory, due to the fact that most of the experiments are performed on transformed rather than normal cells. However, this approach seems to us quite justified, because the phenomenon of “stationary phase”/chronological aging is common to a wide variety of cells, including bacteria, yeasts, cyanobacteria, mycoplasmas, as well as animal and plant cells. Cells with an unlimited mitotic potential do not change either from experiment to experiment or during long-term cultivation both with and without subcultivation (within the framework of the stationary phase aging model), which cannot be said of the normal diploid fibroblasts, whose telomeres are shortened with each division. In the period from seeding to entering the stationary phase of growth, the cells divide up to ten times! We believe that, to search for effective geroprotectors that affect the fundamental mechanisms of aging, it is necessary to perform studies on “maximally healthy” animals or on “maximally stable” model systems.     

A comparative study of the effects of laser and LED radiation on lipid peroxidation in rat wound fluid

The effect of laser (632 nm) and LED (630 nm) on lipid peroxidation in rat wound fluid (exudate) was studied with the aim of comparing the efficiency of coherent and incoherent light on the processes that take place during wound healing. The study was performed using the model of cut aseptic wounds proposed by L.I. Slutskii. It was shown that irradiation of wounds with light of both laser and LED caused a decrease in the concentration of lipid peroxidation products in wound fluid as compared with the control group. An increase in the antioxidative activity of wound fluid was observed. It was concluded that irradiation with light of both laser and LED decreases the level of oxidative stress in wound fluid and that radiation coherence does not play a significant role.     

Molecular and cellular mechanisms of the low intensity laser radiation effect

The main aspects of the free radical conception of the molecular and cellular mechanisms of the stimulating action of low-intensity radiation in the red region of the spectrum were considered. These are: (1) Primary acceptors of incident radiation are endogenous porphyrins, which may act as photosensitizers giving initiator-radicals for secondary free radical reactions. (2) Target cells for light irradiation during quantum therapy may be blood leukocytes, fibroblasts, keratinocytes, endotheliocytes, etc. (3) The initiation of the secondary free radical reactions due to lipid peroxidation of cell membranes (in particular, of leukocytes) brings about an increase in ion permeability including that for calcium. The increase in intracellular calcium concentration leads to phagocytes priming, i.e., to increased production of reactive oxygen species (ROS) under subsequent stimulation of the cell. (4) Photosensitized generation of ROS in the cytoplasm of some cells induces a free-radical activation of synthesis of proteins, the most significant in the light of the present concept being the de novo synthesis of inducible NO-synthase, superoxide dismutase, and various cytokines. The experimental evidence for the basic statements of the conception of free radical mechanisms for the stimulating action of low-intensity laser and noncoherent radiations is presented. A relation between the primary mechanisms of the stimulating action of light and the secondary effects that determine the sanative effect of quantum therapy in the process of wound healing (bactericidity, cell proliferation, and improved microcirculation) was established. Moreover, it was shown that nitrosyl complexes of heme proteins, such as hemoglobin and cytochrome c, are the primary chromophores of laser radiation. Upon irradiation, they can easily dissociate to produce free nitric oxide. In turn, released nitric oxide may be responsible for blood vessel relaxation and activation of mitochondrial respiration. This phenomenon is just observed during phototherapy by means of low-intensity laser radiation.