Seven clusters in genomic triplet distributions

Motivation: In several recent papers new algorithms were proposed for detecting coding regions without requiring learning dataset of already known genes. In this paper we studied cluster structure of several genomes in the space of codon usage. This allowed to interpret some of the results obtained in other studies and propose a simpler method, which is, nevertheless, fully functional. Results: Several complete genomic sequences were analyzed, using visualization of tables of triplet counts in a sliding window. The distribution of 64-dimensional vectors of triplet frequencies displays a well-detectable cluster structure. The structure was found to consist of seven clusters, corresponding to protein-coding information in three possible phases in one of the two complementary strands and in the non-coding regions. Awareness of the existence of this structure allows development of methods for the segmentation of sequences into regions with the same coding phase and non-coding regions. This method may be completely unsupervised or use some external information. Since the method does not need extraction of ORFs, it can be applied even for unassembled genomes. Accuracy calculated on the base-pair level (both sensitivity and specificity) exceeds 90%. This is not worse as compared to such methods as HMM, however, has the advantage to be much simpler and clear

Citrate and isocitrate in plant metabolism

The relevance of citrate and isocitrate metabolism in plants is discussed in connection with the different pathways for their conversions. The routes for citrate and isocitrate conversions are incorporated into the system of cross-linked metabolic processes and may provide carbon skeletons for nitrogen assimilation and reducing equivalents for biosynthetic reactions, support the functioning of the glyoxylate cycle and play an important role in the TCA and energy metabolism as a whole. The possibility of the coupling of citrate and isocitrate metabolism with various electron transport systems is discussed from the point of view of the efficiency of the balancing cellular NAD P H Ž . Ž . rNAD P and ATP q rADP ratios. The role of citrate and isocitrate and their derivations as potent effectors of some enzymes is considered. Special attention is paid to the enzymes associated with citrate and isocitrate metabolism and to the mechanisms which regulate their activity. The possibilities of the coordination of the main processes of energy and biosynthetic metabolism at the level of citrate and isocitrate distribution are discussed.The authors are grateful to Dr., Professor, Academician of the Russian Academy of Sciences, V.P. ŽSkulachev Moscow State University, Institute of. Molecular Biology for carefully and critically reading the manuscript and stimulating discussions. We also thank Dr. Teresa M. Santos for her help during the preparation of the manuscript. The work of Prof. Tatyana N. Popova in Madeira University was supported by the grant no. 9r96r1r0618 of the Portuguese Foundation for Support of the Scientific Community JNICT and the Madeiran Scientific and Ž . Technological Centre CITMA . Ž .info:eu-repo/semantics/publishedVersio

SMART technologies as the innovative way of development and the answer to challenges of modern time

One of the promising tasks in education lies in reforming it into the knowledge economy, integrating and creating a market oriented towards results of intellectual activity. On the other hand, globalization process requires transition of the educational environment to the format of information, communication and digital space. Primarily these areas are set as the nodal tasks, which directs authors of this article to the comparative analysis of educational system making it possible to identify general and particular, positive or negative consequences and characteristics of digitalization in the higher education system. In accordance with current trends and processes of globalization and informatization, the authors are considering the prospects for interaction and mutual influence of Smart technologies used in building a future educational model in the higher education area. Technological innovations today are called upon not only to qualitatively change methods, forms and technologies in the education content, but rather to train personnel capable of operating in the new information and telecommunication community. Therefore, studying the influence and the capabilities of modern digital technologies that meet needs of society, on the one hand, and, on the other hand, contribute to formation of professional competencies in students, which requires major alterations in the learning process, changes in its state towards flexibility, adaptation, personalization, continuity, multidimensionality and systematicity, becomes of specific relevance for authors of this article

Metabolic Remodeling during Long-Lasting Cultivation of the Endomyces magnusii Yeast on Oxidative and Fermentative Substrates

In this study, we evaluated the metabolic profile of the aerobic microorganism of Endomyces magnusii with a complete respiration chain and well-developed mitochondria system during long-lasting cultivation. The yeast was grown in batches using glycerol and glucose as the sole carbon source for a week. The profile included the cellular biological and chemical parameters, which determined the redox status of the yeast cells. We studied the activities of the antioxidant systems (catalases and superoxide dismutases), glutathione system enzymes (glutathione peroxidase and reductase), aconitase, as well as the main enzymes maintaining NADPH levels in the cells (glucose-6-phosphate dehydrogenase and NADP+-isocitrate dehydrogenase) during aging of Endomyces magnusii on two kinds of substrates. We also investigated the dynamics of change in oxidized and reduced glutathione, conjugated dienes, and reactive oxidative species in the cells at different growth stages, including the deep stationary stages. Our results revealed a similar trend in the changes in the activity of all the enzymes tested, which increased 2–4-fold upon aging. The yeast cytosol had a very high reduced glutathione content, 22 times than that of Saccharomyces cerevisiae, and remained unchanged during growth, whereas there was a 7.5-fold increase in the reduced glutathione-to-oxidized glutathione ratio. The much higher level of reactive oxidative species was observed in the cells in the late and deep stationary phases, especially in the cells using glycerol. Cell aging of the culture grown on glycerol, which promotes active oxidative phosphorylation in the mitochondria, facilitated the functioning of powerful antioxidant systems (catalases, superoxide dismutases, and glutathione system enzymes) induced by reactive oxidative species. Moreover, it stimulated NADPH synthesis, regulating the cytosolic reduced glutathione level, which in turn determines the redox potential of the yeast cell during the early aging process

Metabolic Remodeling during Long-Lasting Cultivation of the Endomyces magnusii Yeast on Oxidative and Fermentative Substrates

In this study, we evaluated the metabolic profile of the aerobic microorganism of Endomyces magnusii with a complete respiration chain and well-developed mitochondria system during long-lasting cultivation. The yeast was grown in batches using glycerol and glucose as the sole carbon source for a week. The profile included the cellular biological and chemical parameters, which determined the redox status of the yeast cells. We studied the activities of the antioxidant systems (catalases and superoxide dismutases), glutathione system enzymes (glutathione peroxidase and reductase), aconitase, as well as the main enzymes maintaining NADPH levels in the cells (glucose-6-phosphate dehydrogenase and NADP+-isocitrate dehydrogenase) during aging of Endomyces magnusii on two kinds of substrates. We also investigated the dynamics of change in oxidized and reduced glutathione, conjugated dienes, and reactive oxidative species in the cells at different growth stages, including the deep stationary stages. Our results revealed a similar trend in the changes in the activity of all the enzymes tested, which increased 2–4-fold upon aging. The yeast cytosol had a very high reduced glutathione content, 22 times than that of Saccharomyces cerevisiae, and remained unchanged during growth, whereas there was a 7.5-fold increase in the reduced glutathione-to-oxidized glutathione ratio. The much higher level of reactive oxidative species was observed in the cells in the late and deep stationary phases, especially in the cells using glycerol. Cell aging of the culture grown on glycerol, which promotes active oxidative phosphorylation in the mitochondria, facilitated the functioning of powerful antioxidant systems (catalases, superoxide dismutases, and glutathione system enzymes) induced by reactive oxidative species. Moreover, it stimulated NADPH synthesis, regulating the cytosolic reduced glutathione level, which in turn determines the redox potential of the yeast cell during the early aging process

Identification of aluminum resistant genotypes among Madeiran regional wheats

Forty-eight genotypes representing wheat diversity from the Island of Madeira were screened for resistance to aluminum (Al) in nutrient solution. Seeds of wheat used in the experiments were obtained from local farmers. The soil pH and content of ionic Al of plots cultivated with wheat were analyzed. The pH of topsoils varied between 3.83 and 6.59. The amount of ionic Al in soil samples varied between 0.38 and 1.36 cmol Al3 + per kg of soil and was positively correlated with the altitude of a plot. Eriochrome cyanine staining was used to evaluate the effect of Al ions on the root elongation. Seventy-two hour exposure of 3-day-old seedlings to 100 and 200 mM Al in nutrient solution revealed a high number of Al resistant genotypes among wheat germplasm. After withdrawal of Al stress, survival and root regrowth was observed in 28 and 23 genotypes screened at 100 and 200 mM Al in nutrient solution, respectively. Enhanced resistance to Al among Madeiran genotypes was associated with the amount of ionic Al in the soils. Complexity and various patterns of responses of tested cultivars to Al stress may suggest that Madeiran germplasm could be a valuable source of genes controlling Al resistance for conventional breeding programs and for studies of molecular bases of mechanisms of Al resistance.Portuguese Foundation for the Science and Technology (FCT, Fundac¸o para a Cieˆncia e Tecnologia) has sponsored this work, through the Centre of Biological and Geological Sciences (C.C.B.G.) and the project POCTI/no. 33005/AGR/1999. The authors are also grateful to the Madeiran Centre of Science and Technology (CITMA) for financial support. Acknowledgements are due to Mr. Roge´rio Correia and Juan Silva for the technical assistance in conducting the laboratory and fieldwork and to Dr. Andrzej Aniol for valuable advice during preparation of this manuscript.info:eu-repo/semantics/publishedVersio