Theories of biological evolution from the viewpoint of the modern systemic biology

Theories of biological evolution advanced in the last 200 years are reviewed from the viewpoint of advances of modern genetics. The theory of gene networks as a key direction of systemic biology is a link connecting different evolutionary theories.     

DNA variation in the phenotypically-diverse brown alga Saccharina japonica

ABSTRACT: BACKGROUND: Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the "longipes" (LON) and "shallow-water" (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica. RESULTS: The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5'- and 3'- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5'- or 3'-) used for tree reconstruction. Consequently, the 5'-COI "barcoding" region (~ 650 bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events. CONCLUSION: Taking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered.     

Assessment of sensitivity of commercial test-systems for HBsAg immunodetection according to their ability to detect HBsAg-mutants of hepatitis B virus

Comparative study of widely distributed on Russian market commercial test-systems for HBsAg detection by enzyme immunoassay was performed. Panel of serum samples containing mutant forms of HBsAg was developed for the study. It showed that only 2 out of 7 studied test-systems are able to detect mutant forms of HBsAg with the same sensitivity as "wild-type" forms of HBsAg. Test-systems based only on monoclonal antibodies did not detect HBsAg with G145R substitution in concentration 5 ng/ml. The study confirms the relevance of problem of HBsAg-mutants detection for hepatitis B immunodiagnostics.     

The investigation of the composition of liquid radioactive waste

In investigation the process of composition sediment of liquid unorganic radioactive waste, that are forming in cistern-selectors at PNPI RAS, it was discovered apart from great quantity of ions of different metals and radionuclides considerable maintenance of organic material (to 30% and more from volume of sediment) unknown origin. A supposition was made about its microbiological origin. Investigation shows, that the main microorganisms, setting this sediment, are the bacterious of Pseudomonas kind, capable of effectively bind in process of grow the radionuclide 90Sr, that confirms the potential posibility of using this microorganisms for bioremediation of liquid low radioactive wastes (LRW).     

Spectroscopic and biological activity studies of the chromium-binding peptide EEEEGDD

While trivalent chromium has been shown at high doses to have pharmacological effects improving insulin resistance in rodent models of insulin resistance, the mechanism of action of chromium at a molecular level is not known. The chromium-binding and transport agent low-molecular-weight chromium-binding substance (LMWCr) has been proposed to be the biologically active form of chromium. LMWCr has recently been shown to be comprised of a heptapeptide of the sequence EEEEDGG. The binding of Cr³⁺ to this heptapeptide has been examined. Mass spectrometric and a variety of spectroscopic studies have shown that multiple chromic ions bind to the peptide in an octahedral fashion through carboxylate groups and potentially small anionic ligands such as oxide and hydroxide. A complex of Cr and the peptide when administered intravenously to mice is able to decrease area under the curve in intravenous glucose tolerance tests. It can also restore insulin-stimulated glucose uptake in myotubes rendered insulin resistant by treating them with a high-glucose media.     

High-throughput sequencing of the mitochondrial genomes from archived fish scales: an example of the endangered putative species flock of Sevan trout <Emphasis Type="Italic">Salmo ischchan</Emphasis>

Burrowing benthic animals belonging to the same functional group may produce species-specific effects on microbially mediated nitrogen (N) processes depending upon different ecological traits. We investigated the effects of two tube-dwelling organisms, amphipods (Corophium insidiosum) and chironomid larvae (Chironomus plumosus), on benthic N cycling in bioturbated estuarine sediments. Aims of this work were to analyze the interactions among burrowers and N-related microbial processes in two distinct sedimentary environments colonized by benthic animals with different ecological traits. We hypothesized higher rates of nitrification and higher coupled nitrification–denitrification in sediments with C. insidiosum due to continuous ventilation rates. We expected higher denitrification of water column nitrate in sediments with C. plumosus due to lower and intermittent ventilation activity and lower oxygen levels in burrows. To this purpose, we combined process–specific (nitrification and denitrification) with net N flux measurements in intact and reconstructed sediments. Sediments with C. insidiosum had higher rates of oxygen demand and of potential nitrification and higher concentration of pore water NH₄⁺ as compared to sediments with C. plumosus. Sediments with both species displayed comparable net N₂ fluxes, mostly sustained by respiration of water column NO₃^? in sediments with chironomid larvae and by NO₃^? produced within sediments in sediments with corophiid amphipods. Corophium insidiosum stimulated nitrification nearly 15-fold more as compared to C. plumosus. Overall, our results demonstrate that sediments with burrowing fauna may display similar rates of denitrification, but underlying mechanisms may deeply vary and be species-specific.     

Phylogeography and population history of the least weasel (Mustela nivalis) in the Palearctic based on multilocus analysis

The least weasel (Mustela nivalis) is one of the most widely distributed carnivorans. While previous studies have identified distinct western and eastern mitochondrial DNA (mtDNA) lineages of the species in the western Palearctic, their broader distributions across the Palearctic have remained unknown. To address the broad-scale phylogeographical structure, we expanded the sampling to populations in Eastern Europe, the Urals, the Russian Far East, and Japan, and analyzed the mtDNA control region and cytochrome b, the final intron of the zinc finger protein on Y chromosome (ZFY), and the autosomal agouti signaling protein gene (ASIP). The mtDNA data analysis exposed the previous western lineage (Clade I) but poorly supported assemblage extending across Palearctic, whereas the previous eastern lineage (Clade II) was reconfirmed and limited in the south western part of the Palearctic. The ZFY phylogeny showed a distinctive split that corresponding to the mtDNA lineage split, although less phylogeographical structure was seen in the ASIP variation. Our data concur with the previous inference of the Black Sea–Caspian Sea area having an ancestral character. The Urals region harbored high mitochondrial diversity, with an estimated coalescent time of around 100,000 years, suggesting this could have been a cryptic refugium. Based on the coalescent-based demographic reconstructions, the expansion of Clade I across the Palearctic was remarkably rapid, while Clade II was relatively stable for a longer time. It seems that Clade II has maintained a constant population size in the temperate region, and the expansive Clade I represents adaptation to the cold regions.     

Modification of DNA damage in rat hepatocytes following whole-body roentgen radiation using cysteamine and 8-bromocaffeine

Using the elastoviscosimetric method it was shown that the level of residual DNA double-strand breaks in rat hepatocytes depended on conditions of total-body X-irradiation: it increased in the presence of a sensitizer, 8-bromocaffeine and decreased in the presence of a protector, cysteamine. This correlation confirms a major role of fixed DNA double-strand breaks in the formation of a lethal effect in a cell.     

Natural montmorillonite clay as prebiotic catalyst

It is shown that complex intramolecular and intermolecular transformations of natural pinene terpenoids can proceed in the presence of natural montmorillonite clays with the preservation of optical activity. These facts support our assumption that natural clays could act as prebiotic catalysts and favor preservation of chirality in complex compounds formed from simple optically active molecules at early stages of life. The article is published in the original.