Genosystematics: from E. Chargaff and A. N. Belozersky up to date

A review of history of genosystematics (macromolecular systematics) from E. Chargaff and A. N. Belozersky up to date. The role of A.N. Belozersky and his collaborators in the development of this new branch of systematics is analyzed. Genosystematics was the source of valuable information clarifying some aspects of biological evolution. Its methods were successfully employed in microorganisms--(e.g., discovery of archaebacteria) and in eucaryote systematics (origin of plastids, falcification of "molecular clock" hypothesis, substantial changes in higher plants phylogenetics, etc.). However, attempts to employ some fragmentary and unreliable data obtained by genosystematics for modifying the existing phylogenetic schemes and systems of organisms failed. Nowadays genosystematics is like a newborn child suffering from children's diseases well-known to "classical" systematics. It is rather far from final conclusions describing the evolution of genotypes. Some of its recent achievments, e.g., elaboration of the concept of PhyloCode, allow to believe that this science is able to suggest revolutionary changes in Linnean systematics.     

From birth to christening

A brief history of comparative studies of nucleic acids for systematic purposes is given. These studies were initiated by a group of Moscow State University scientists headed by A. N. Belozersky. Based mostly on comparative DNA studies, some main dogmas of a new branch of systematics were gradually developed. In Russia, this new branch of systematics is called "genosystematics". Some of the main results obtained by genosystematics since its birth (1957) and up to its "christening" (1974) are described.     

On interrelation between genetic systematics and genomics

Review papers describing recent achievements of genomics usually do not pay attention to direct interrelation between genomics and genosystematics (DNA-systematics). Genomics on general is based in complete DNA sequencing of genomes. Initial aim of genosystematics was the same. Absence of historical perspective in review papers devoted to genomics decreases its value. In case it is done deliberately it becomes the problem of scientific ethics. It is postulated that genomics is a natural stage of genosystematics (DNA-systematics) development. Russian scientists were among the founders of these branches of biology.     

A view of an elemental naturalist at the DNA world (Base composition,sequences, methylation)

The pioneering data on base composition and pyrimidine sequences in DNA of pro-and eukaryotes are considered, and their significance for the origin of genosystematics is discussed. The modern views on specificity and functional role of enzymatic DNA methylation in eukaryotes are described. DNA methylation controls all genetic functions and is a mechanism of cellular differentiation and gene silencing. A model of regulation of DNA replication by methylation is suggested. Adenine DNA methylation in higher eukaryotes (higher plants) was first observed, and it was established that one and the same gene can be methylated at both cytosine and adenine moieties. Thus, there are at least two different and seemingly interdependent DNA methylation systems present in eukaryotic cells. The first eukaryotic adenine DNA-methyltransferase is isolated from wheat seedlings and described: the enzyme methylates DNA with formation of N⁶-methyladenine in the sequence TGATCA → TGm⁶ATCA. It is found that higher plants have endonucleases that are dependent on S-adenosyl-L-methionine (SAM) and sensitive to DNA methylation status. Therefore, as in bacteria, plants seem to have a restriction-modification (R-M) system. A system of conjugated up-and down-regulation of SAM-dependent endonucleases by SAM modulations is found in plants. Revelation of an essential role of DNA methylation in regulation of genetic processes is a fundament of materialization of epigenetics and epigenomics. Published in Russian in Biokhimiya, 2007, Vol. 72, No. 12, pp. 1583–1593.     

Plant Cell Wall Is a Stumbling Stone for Molecular Biologists

Cell wall is a key structure of the plant organism engaged in numerous functions, and plants spend enormous resources on cell wall formation. Cell wall components are the most widespread organic substances on the Earth. However important is assembling plant cell wall polysaccharides, this process has been insufficiently studied by the methods of molecular genetics; in particular, too little is known of the genes that code for the relevant enzymes (glycosyltransferases, GT). The review addresses the current situation by expounding on GT classification, describing the characteristics of enzymes that synthesize cell wall polysaccharides, and summing up the existing knowledge of already identified and putative cellulose and callose synthases and GT localized in the Golgi apparatus. The methodology for searching and characterizing new genes that participate in cell wall formation is under discussion.__________Translated from Fiziologiya Rastenii, Vol. 52, No. 3, 2005, pp. 443–462.Original Russian Text Copyright © 2005 by Gorshkova, Nikolovski, Finaev.     

Psephellus turcicus sp. nov. (Asteraceae), a new chasmophyte species from central Anatolia, Turkey

A new species, Psephellus turcicus A.Duran & Hamzaoğlu (Asteraceae) in sect. Psephelloidei (Boiss.) Wagenitz & Hellwig is described and illustrated from Anatolia, Turkey. The species grows on limestone crevices in Kazankaya Canyon (A5 Yozgat) in central Anatolia. A neo-endemic confined to Kazankaya Canyon, it is closely related to Psephellus psephelloides (Freny & Sint.) Wagenitz. Diagnostic morphological characters from closely similar taxa are discussed, and arranged in a key of Turkish similar Psephellus Cass. The ecology, biogeography and conservation status of the species are also presented. Achene surface morphology of P. turcicus and P. psephelloides are examined by SEM. The geographical distribution of the new species and other related species is mapped.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 495–500.     

Toxic Effect of Heavy Metals on Human Blood Neutrophils

Activity of the peroxidase-hydrogen peroxide system is proposed as a biological marker of ecological risk of heavy metal contamination of the environment. The effect of lead, copper, mercury, and cadmium ions on peroxidase system activity in human peripheral blood neutrophils was studied using cytochemical methods. A possible mechanism of suppression of peroxidase system activity by metal ions is discussed.__________Translated from Izvestiya Akademii Nauk, Seriya Biologicheskaya, No. 3, 2005, pp. 336–338.Original Russian Text Copyright © 2005 by Mushtakova, Fomina, Rogovin.     

Molecular mechanisms of hormonal activity. I. receptors. neuromediators. systems with second messengers

Hormone signal transfer along all of the cell compartments including nucleus is powered by signal transduction systems. Characteristics and importance of hormone receptors, principal components, functional mechanisms, and biological role of different systems with second messengers are described. Considerable examples of the importance of these systems for medicine are adduced. The drugs modifying these systems comprise more than 65% of contemporary medicines.Translated from Biokhimiya, Vol. 70, No. 1, 2005, pp. 33–50.Original Russian Text Copyright © 2005 by Kulinsky, Kolesnichenko.     

Human Milk Lactoferrin Hydrolyzes Ribonucleoside 5′-Triphosphates

Lactoferrin (LF), one of the most important and polyfunctional factors of nonspecific cell defense against bacteria, viruses, and cancer diseases, is the main iron-transferring protein of human biological fluids, blood, and milk. Electrophoretically homogeneous preparations of LF from human milk were obtained and studied. Using chromatography on Blue Sepharose, LF preparations were separated into several subfractions differing in their affinity for the sorbent, two of which exhibited nucleoside 5-triphosphate-hydrolyzing activity. Using different methods, including in-gel ATPase activity assay, it was demonstrated that hydrolysis of ATP and other nucleotides is an intrinsic property of LF and that LF is the major ATPase of human milk. It is shown that the ATP-hydrolyzing center is located at the C-terminal domain of the LF molecule and that interaction between ATP and this center increases the oligonucleotide-hydrolyzing activity of the DNA-binding domain of this protein.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 3, 2005, pp. 513–520.Original Russian Text Copyright © 2005 by Babina, Semenov, Buneva, Nevinsky.     

Stock enhancement of the edible jellyfish (<Emphasis Type="Italic">Rhopilema esculentum</Emphasis> Kishinouye) in Liaodong Bay,China: a review

Among the edible species, jellyfish Rhopilema esculentum, is one of the most abundant and important fishery species in China. The jellyfish fishery is characterized by considerable fluctuations in catch and a very short fishing season. In this article, we first review the research results on the biology of R. esculentum, which previously were published in Chinese, as related to the jellyfish enhancement and fishery. Next, we review results from enhancement experiments conducted from 1984 to 2004, with the aims of stabilizing and increasing catch. During 2005 and 2006, stock enhancement of R. esculentum was carried out on a large scale for the first time in Liaodong Bay, China, where 414 million juvenile jellyfish (umbrella diameter > 1 cm) were released. We present results of these enhancements, including the survey methods, catch prediction, enhancement assessment, and fishery management. In 2005 and 2006, the recapture rate of released jellyfish was 3.0 and 3.2%, respectively. The fishermen earned ￥ 159 million during the 2 years. The ratio of the input (cost of culturing juvenile jellyfish) to the output (value of the sales) was about 1:18. The high commercial value of R. esculentum enhancement in Liaodong Bay makes this a very successful enterprise. Guest editors: K. A. Pitt & J. E. Purcell Jellyfish Blooms: Causes, Consequences, and Recent Advances     

Role of Genetic Processes in Modification Variability. Prophecy of B.L. Astaurov

In his pioneering work on mutation tetraptera in Drosophila melanogaster, B.L. Astaurov discovered spontaneous modifications based on variability in gene expression. This new approach to the phenomenon of modifications should be considered as the first stimulus to development of the general theory of variability. Contemporary classification of variability based predominantly on phenomenology encounters many contradictions. The same specific molecular mechanisms may be responsible, for example, for both hereditary and nonhereditary variability depending on the taxonomic status. Some mechanisms responsible for both mutations and modifications or for mutations, recombination, and ontogenetic variability have been considered from this viewpoint. It may well be more productive to consider different types of variability with respect to the main genetic processes: replication and expression of genetic material.__________Translated from Ontogenez, Vol. 36, No. 4, 2005, pp. 274–279.Original Russian Text Copyright © 2005 by Inge-Vechtomov.     

Shape identification of electrocardiographic ST segment based on radial basis function neural network

The types of myocardial ischemia can be revealed by electrocardiographic (ECG) ST segment. Effective measurement and electrocardiographic analysis of ST as well as calculation of displacement and shape change of ST segment can help doctors diagnose coronary heart disease and myocardial ischemia, especially for asymptomatic myocardial ischemia. Therefore, it is a very important subject in clinical practice to measure and classify the ECG ST segment. In this paper, we introduce a computerized automatic identification method of the electrocardiographic ST segment shape with radial basis function neural network based on adaptive fuzzy system, which has a better effect than other methods. It helps to analyze the reason of the ST segment change and confirm the position of myocardial ischemia, and is useful for doctor diagnosis. Translated from Acta Biophysica Sinica, 2005, 21(6): 443–448 [译自: 生物物理学报]     

Grain Protein Content in Wheat: Genetics of the Character and Some Predictions for Its Improvement in Common Wheat

The results of studies on genetic control of the grain protein content in common wheat and the attempts of its improvement using traditional breeding approaches and methods of experimental mutagenesis and introgressive hybridization are presented. The evolution of the views on the genetic structure of the character is considered. Possible explanations are given to the fact that the attempts to significantly improve the character in question in common wheat cultivars have failed in spite of long-term genetic and selection studies. Possible lines of further investigation of genetic control of grain protein content and its increase in common wheat are discussed.__________Translated from Genetika, Vol. 41, No. 8, 2005, pp. 1013–1026.Original Russian Text Copyright © 2005 by Zlatska.     

Forecasting the start of <Emphasis Type="Italic">Quercus</Emphasis> pollen season using several methods – the evaluation of their efficiency

Forecasting the time when the atmospheric pollen season of allergenic plants begins is particularly important for doctors and their patients. The aim of this paper is to determine whether it is possible to forecast the start of the oak (Quercus) pollen season in Rzeszów, Poland. In the elaboration of the most effective model, various forecasting techniques were tested: growth degree days (GDD°C); meteorological factors; bioclimatic factors; and indicator taxon. The aerobiological monitoring was carried out in 1997–2005 and 2007 in Rzeszów (SE Poland). In the presented investigation, three methods defining the start of the Quercus pollen season were selected on the basis of accumulated sums of pollen or the constant occurrence of pollen grains in air. Despite the application of different combinations of GDD°C methods and threshold temperatures, the correlation coefficients between the expected and obtained values were low. In some cases, however, they proved highly effective for the test years (2005, 2007) with the accuracy of a few days. For GDD°C methods, the best threshold temperatures range between 5 and 6°C. Models based on bioclimatic indices and meteorological variables were not satisfactory. On the basic of the 10 years of results, the method of indicator species were good for forecast the start of oak pollen season. Birch was the best indicator taxa.     

How many freshwater diatoms are pH specialists? A response to Pither & Aarssen (2005)

Pither & Aarssen (2005) propose a null model approach to assess the proportion of niche specialist taxa along ecological gradients. They apply this methodology to a large data set of lacustrine diatom assemblages and conclude that a majority of the taxa are generalists on a pH gradient. This conflicts with previous work, which shows that many diatom taxa have a statistically significant relationship with pH. We demonstrate the methods used by Pither & Aarssen (2005) have a high Type II error for rare taxa, and that this problem is compounded by the non-uniform sampling of the pH gradient which effectively precludes acid-lake specialist diatoms from being recognized as such. We re-analyse the data used by Pither & Aarssen (2005) and show that most of the diatoms have a statistically significant relationship with pH, and we thus refute their conclusions that few diatom species are specialists.     

Synthesis of Analogues of Natural Coumarins and Coumarinolignans

3-Aryl-4H-coumarins with the 1,3-benzodioxol, 1,4-benzodioxane, and 1,5-benzodioxepane moieties were synthesized by modified methods.__________Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 3, 2005, pp. 326–330.Original Russian Text Copyright © 2005 by Ismailova.     

Simple method for fractionation of <Emphasis Type="Italic">Parmelia sulcata</Emphasis> lichen thalli

Three fractions were isolated from Parmelia sulcata lichen thalli: mycobiont-enriched fraction, highly purified preparation of Trebouxia sp. alga, and a photobiont-enriched fraction, in which the fungal component and symbiotic relations between the bionts were retained. The ratio between the fungal and algal components in all fractions was estimated from the photosynthesis/respiration and chlorophyll/dry weight ratios. Simple methods for lichen thallus fractionation are suggested to study symbiotic relationships of bionts.Translated from Fiziologiya Rastenii, Vol. 52, No. 2, 2005, pp. 306–310.Original Russian Text Copyright © 2005 by Maslov, Pavlova.This revised version was published online in April 2005 with a corrected cover date.     

Response of Pinus sylvestris L. to recent climatic events in the French Mediterranean region

Exceptional climatic events from 2003 to 2005 (scorching heat and drought) affected the whole of the vegetation in the French Mediterranean region and in particular the Scots pine (Pinus sylvestris L.), one of the most important forest tree species in this area. To understand its response to these extreme conditions, we investigated its radial growth, branch length growth, architectural development and reproduction for the period 1995–2005, and linked these variables to climatic parameters. We used four plots situated in southeastern France and presenting different levels of site quality and potential forest productivity. The results show that: (1) the climatic episode 2003–2005 was highly detrimental to the growth (bole and branches), crown development, and cone production but favored the production of male flowers; (2) these variables depend on climatic factors of both the current and previous years; (3) the 2003 scorching heat impact was strong but was mainly apparent from 2004; it was part of a 6-year-long unfavorable cycle beginning in 2000, characterized by high minimum and maximum temperatures and very dry springs; (4) in spite of a significant effect of site quality, the Scots pine’s response to extreme climatic conditions was homogeneous in the French Mediterranean area; and (5) the stress induced by poor site conditions generally resulted in the same consequences for tree growth, architecture, and reproduction as in unfavorable climatic conditions.     

Ester Derivatives of Nucleoside Inhibitors of Reverse Transcriptase: 1. Molecular Transport Systems for 3′-Azido-3′-Deoxythymidine and 2′,3′-Didehydro-3′-Deoxythymidine

The methods of synthesis of the derivatives of nucleoside analogues esterified with various aliphatic, aromatic, and heteroaromatic acids and the construction from them of molecular transport systems that involve lipids, carbohydrates, peptides, and amino acids are discussed. The characteristics of the biological activity of a number of such systems are described.__________Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 4, 2005, pp. 339–356.Original Russian Text Copyright © 2005 by Berezovskaya, Chudinov.     

Participation of Interferon-Alpha in Regulation of Apoptosis

According to current data, endocrine system is closely related to immune system and interferons play an important role in this relationship. Interferons can inhibit cell proliferation or control apoptosis. Interferon-alpha (IA) produces a stimulatory effect on DNA sites controlling, via JAK/STAT-pathway, production of anti-apoptotic proteins of the Bcl-2 family. Besides, a very important property of IA is its ability to arrest the cell in the G1-G0 phase, which is what determines static effect of IA on growth of many tumors. Later, in these cells, either apoptosis can develop or they can survive. This depends on many factors including physiological state of the tissue and cell, its differentiation, stage of cellular cycle, etc.__________Translated from Zhurnal Evolyutsionnoi Biokhimii i Fiziologii, Vol. 41, No. 2, 2005, pp. 101–106.Original Russian Text Copyright © 2005 by Bazhanova.