Comparison of different methods of census of juvenile salmonids (Salmonidae) in the small river Mikocheva (Western Kamchatka)

Seinings of the lowland bed of a typical small river of Western Kamchatka demonstrated that of several methods for the census of juveniles of salmonids (Salmonidae) the most accurate result in comparison with complete removal is obtained by three-fold seining with calculation of abundance by the Zippin method. In comparison with a seine, a drive-in trap and electrofishing possess a lower average catching efficiency and a higher selectivity. The average density of fish estimated by the results of seining at the investigated stretch was 0.55–0.57 specimens/m².     

Trophic-based diversification in benthivorous charrs (Salvelinus) dwelling littoral zones of Northern lakes

Charrs of the genus Salvelinus form distinct trophic morphs living in sympatry in numerous postglacial lakes. Here we demonstrate that charrs can diversify into amphipod foraging specialists and sedentary macrobenthos consumers in the shallow-water ecosystems. This pattern was revealed in three out of six lakes under exploration supported by differences in stomach content, trophic-transmitted parasite, and stable isotope ratio analyzes. The body shape and growth rate comparison indicates that this kind of trophic-based diversification emerges at a juvenile stage and is maintained throughout the whole life. The restriction in gene flow found between the morphs allows to propose the possibility for the hereditable-based specialization to evolve. We found that those diversification phenomena are possible only in the lakes situated in vicinity of the ocean coastline, while no evidence of this split was found for inland mountain lakes. We suggest that the trophic-based diversification in the littoral ecosystems is accounted for the heterogeneity in the ecological conditions and food resources’ distribution linked to coastal wind action. This phenomenon was previously reported for the charr in Lake Fjellfrosvatn, Scandinavia, so it seems to be some universal yet poorly described kind of disruptive selection pressure for northern latitude fishes.

     

Alkaline protease production by an actinomycete MA1-1 isolated from marine sediments

Alkaliphilic actinomycetes isolated from sediment samples of the Izmir Gulf, Turkey were studied for the production of protease activity. Strain MA1-1 was selected as a good alkaline protease producer as measured by the clear zone diameter by the hydrolysis of skim-milk and casein. The alkaline protease production from the marine alkaliphilic actinomycete MA1-1 was studied by using different carbon and nitrogen sources in medium containing glycerol, peptone, KCl, MgSO₄, K₂HPO₄, and trace elements at 30°C for 72 h. Among the different carbon and nitrogen sources, fructose, starch, maltose, D(+) glucose, yeast extract, malt extract, beef extract and peptone provided higher production of protease. Starch was also found to be effective for growth and enzyme production with highest specific activity at 699 U mg^?1. Purification was achieved by adsorption on Diaion HP 20 which resulted in a recovery rate of 68% with a specific activity of 7618 U mg^?1 protein and 40-fold purification. The optimum pH and temperature of the partially purified protease were determined as pH 9.0 and 50°C, but high activity was also observed at pH 8.0–13.0 and 35–50°C. The inhibition profile exhibited by phenylmethylsulphonyl fluoride (PMSF) showed that this enzyme belongs to the serine-protease group.     

Analysis of essential oil of Coridothymus capitatus (L.) and its antibacterial and antifungal activity

The water-distilled essential oil the leaves of Coridothymus capitatus were analyzed by GC/MS and also analyzed by direct thermal desorption GC/MS. Comparison was made between two analyses techniques. The essential oil consisted mainly of monoterpenes 98.9%, while oxygenated hydrocarbons were identified as 55.6 % and non-oxygenated hydrocarbons as 43.6%. As major components were found carvacrol (35.6%), p-cymene (21.0%), thymol (18.6%), gamma-terpinene (12.3%), alpha-terpinene (3.2%), beta-myrcene (3.0%) and alpha-thujene (1.3%) by hydrodistillation and by the GC/MS method. The direct thermal desorption GC/MS analysis also showed the same major components, namely carvacrol (51.6%), thymol (21.7%), p-cymene (9.7%) gamma-terpinene (8.2%), alpha-terpinene (1.64%). The essential oil of C. capitatus showed strong activity against S. aureus, P. vulgaris, P. aeruginosa, E. coli, K. pneumonia, B.     

Evaluation of the androgenic competence of 66 wild Turkish Vaccaria hispanica (Mill.) Rauschert genotypes through microspore culture

One of the most remarkable natural plants is Vaccaria hispanica (Mill.) Rauschert, which has a high economic, medicinal and industrial potential due to its valuable compounds. However, it is mostly an underused plant worldwide. To implement doubled haploid technology in plant breeding programs and exploit its potential, first knowing the particulars of the species is necessary. This study was aimed to explore the androgenic potential of different wild Turkish V. hispanica genotypes collected from different Turkish regions, as a starting point to identify bottlenecks to solve in future studies. As to induction of microspore embryogenesis, nearly all of them responded, with efficiencies reaching 300 embryos/100 buds in some cases. However, we also found three main bottlenecks. First, the presence of foam-producing saponins in flowers prevented an efficient isolation of microspores. Second, embryos showed a reduced ability to germinate. Third, a dense network of hairy roots prevented the formation of a true, fully functional root system. Together, these drawbacks led to the production of very few DH plants. The presence of rhizogenic endophytes may be the cause of most of these problems, which opens the door for possible solutions.

     

Equilibrium fluctuations in myoglobin and lysozyme

The angular dependencies of inelastic intensities of Rayleigh scattering of Moessbauer radiation were measured for myoglobin and lysozyme (in the hydration range h = 0.05-0.7). The data were fitted within the framework of model, when two types of intraglobular motions were taken into account: individual motions of small side-chain groups and cooperative motions of segments. The best agreement with the experiment at h > 0.05 was obtained when individual motions of small groups together with the cooperative motions of alpha-helices and beta-sheets for lysozyme, and alpha-helices for myoglobin were considered. At further hydration (h = 0.45), mean-square displacements (x2) of both types of motions strongly increase with the increase in hydration degree, while the motions with a large correlation radius (not less than macromolecule radius) remain nearly the same as for h = 0.05. The results of the study of the radial distribution function deduced by Fourier-transform from the diffuse x-ray measurements together with RSMR data allow one to conclude that the water during protein hydration competes with the intramolecular hydrogen bonds, loosens the protein and increases the internal dynamics. Concurrently, water arranges the ordering of macromolecule, which takes the native structure at h = 0.4-0.7. The analysis of auto and cross-correlation functions of bending fluctuations of alpha-helices in the large domain of lysozyme performed by molecular dynamics allows one to come to the final conclusion that it is the difference in the structural organization of myoglobin and lysozyme and not the presence of SS-bonds in lysozyme macromolecule that is responsible for different structural fluctuations in these proteins.     

The secretion antigen SA5K has a role in the adaptation of Mycobacterium bovis bacillus Calmette-Guérin to intracellular stress and hypoxia

The Mycobacterium tuberculosis TB8.4 (Rv1174c) gene encodes a secreted protein of 8.4 kDa (TB8.4) which has been suggested to be involved in reactivation of dormant mycobacteria. We have previously reported that inactivation of an identical gene (sa5k) in Mycobacterium bovis BCG causes impaired ability of the mutant strain (BCGsa5k::aph) to grow inside human macrophages. This study aimed to investigate the role of TB8.4 in the reactivation of aged cultures of BCG as well as the role of the sa5k gene in the resistance of BCG to intracellular stress conditions and adaptation to hypoxia. Although when added to aged cultures of BCG, TB8.4 caused a statistically significant increase in the number of colony-forming units, a similar effect was obtained in cultures incubated with BSA, suggesting a non-specific growth stimulation by TB8.4. Compared to parental BCG, the BCGsa5k::aph strain showed an increased susceptibility to reactive oxygen and nitrogen intermediates and to acid stress and an impaired ability to adapt to reduced O2 concentrations, when tested in the oxygen-limited Wayne culture system. These results suggest that the product of the sa5k gene (SA5K protein) has a role in both resistance of BCG to intracellular stress and in its adaptation to hypoxia.     

A study of protein structure changes during hydration by diffuse X-ray scattering: II. Fourier transform analysis of diffuse X-ray scattering data

Radial distribution functions were deduced by Fourier transform analysis of the angular dependences of diffuse X-ray scattering intensities for the following proteins with different hydration degrees: water-soluble α-protein myoglobin, water-soluble (α + β) protein lysozyme, and transmembrane proteins from the photosynthetic reaction centers of purple bacteria Rhodobacter sphaeroides and Blastochlorii (Rhodopseudomonas) viridis. The results of Fourier transform analysis of X-ray scattering intensities give quantitative characteristics of the mechanism underlying the influence of water on the formation of biological macromolecules. On the one hand, water loosens the network of hydrogen bonds, which results in a considerable conformational mobility in the molecules of lysozyme and myoglobin and the reaction centers. On the other hand, water stabilizes and orders the protein globule. A strict correlation was found between the shift of the “first” maximum of the radial distribution function, loosening of the intraglobular hydrogen bonds, increase in the intramolecular mobility, and appearance of pronounced functional activity in macromolecules. The pattern of behavior of the first maximum in the transmembrane proteins of the reaction center was similar to that observed for the water-soluble proteins. However, the first maximum reached the limiting value of 2.9 Å at a considerably lower hydration degree compared with the water-soluble proteins. A quick transition of the protein complex of the reaction center to its native state is due to the fact that the dehydrated conformation of this complex is very close to the native conformation. Comparison of the radial distribution function for water, water-soluble proteins, and transmembrane proteins suggests a quantitative conclusion that water is the least densely packed and ordered system, the water-soluble proteins are more densely packed than water, and the transmembrane proteins are the most densely packed and ordered system.     

Disruption of the ESX-5 system of Mycobacterium tuberculosis causes loss of PPE protein secretion, reduction of cell wall integrity and strong attenuation

The chromosome of Mycobacterium tuberculosis encodes five type VII secretion systems (ESX-1-ESX-5). While the role of the ESX-1 and ESX-3 systems in M. tuberculosis has been elucidated, predictions for the function of the ESX-5 system came from data obtained in Mycobacterium marinum, where it transports PPE and PE_PGRS proteins and modulates innate immune responses. To define the role of the ESX-5 system in M. tuberculosis, in this study, we have constructed five M. tuberculosis H37Rv ESX-5 knockout/deletion mutants, inactivating eccA(5), eccD(5), rv1794 and esxM genes or the ppe25-pe19 region. Whereas the Mtbrv1794ko displayed no obvious phenotype, the other four mutants showed defects in secretion of the ESX-5-encoded EsxN and PPE41, a representative member of the large PPE protein family. Strikingly, the MtbeccD(5) ko mutant also showed enhanced sensitivity to detergents and hydrophilic antibiotics. When the virulence of the five mutants was evaluated, the MtbeccD(5) ko and MtbΔppe25-pe19 mutants were found attenuated both in macrophages and in the severe combined immune-deficient mouse infection model. Altogether these findings indicate an essential role of ESX-5 for transport of PPE proteins, cell wall integrity and full virulence of M. tuberculosis, thereby opening interesting new perspectives for the study of this human pathogen.     

Population consequences of mass coming of pink salmon Oncorhynchus gorbuscha to the Northeastern Coast of Kamchatka in 2009

During mass spawning of pink salmon Oncorhynchus gorbuscha in two rivers of central Karaginskii Bay (Kamchatka), the average coverage of the spawning hillock did not vary much (0.6?C0.7 m²) even though the abundance of the spawning adults varied greatly. When the abundance of spawning females was less than 1.4 ind. per m² of spawning ground, the spawning hillocks did not interlock. When the abundance of spawning females varied from 1.7 to 1.8 ind./m², the spawning hillocks interlocked, and approximately 20?C25% of them were re-excavated. When the abundance of spawning females was higher than 2.0 ind./m², all the early-deposited spawning hillocks were re-excavated. The re-excavation of the spawning hillocks increased the population mortality also by the mass pre-spawning death of the breeders and spawning outside the spawning grounds. Meanwhile, fish-kill of the eggs in the spawning hillocks was not observed, and the mortality of embryos and larvae did not depend on the spawning intensity. The ratio of live and dead embryos in the spawning hillocks before their hatching was approximately 60%, varying from 44 up to 92% in regard to the environment of the spawning ground (autumn low water, freezing, and siltation). Significant correlation was found between the survivability and grain-size composition of the spawning hillocks when the impact of small-size fraction was a limiting factor.