[Phylogeography and Mitochondrial Polymorphism of Asian Coho Salmon].

Multiple Pleistocene glaciations significantly affected the gene pool of many species inhabiting the Northern part of the Pacific Rim, an area with a rich glacial history. This paper is devoted to the study of intraspecific polymorphism of the coho salmon and the routes of its settlement throughout the Asian part of its range. Such problems are traditionally solved by comparing parts of the mitochondrial genome. Here, two fragments of mtDNA, the control region (D-loop) and the cytochrome b gene (cytb), were investigated. It was shown that the settlement of the Asian Pacific coast by the coho salmon was preceded by a chain of successive migration events from the refugium located on the North American continent to the South of the ice sheet covering the area of modern Canada and southern Alaska. The low level of genetic polymorphism in Asian coho populations seems to be a result of a pronounced founder effect, rather than being characteristic of the species as a whole.

[Genetic diversity of charrs of the Commander Islands based on the analysis of mitochondrial DNA].

Nucleotide sequences of the mitochondrial DNA cytochrome b (CytB) gene fragment and the control region (D-loop) of Dolly Varden (Salvelinus malma) from the Commander Islands and the Kol River of the Kamchatka Peninsula were examined. A high level of genetic variability of island populations comparable to that of the mainland population of western Kamchatka was demonstrated. The belonging of the Commander Islands chars to the genetic lineage of northern Dolly Varden Salvelinus malma malma was confirmed.

[Genetic variation at the pantophysin (PanI) locus in North-East Arctic cod Gadus morhua L. (Gadiformes: Gadidae) population in the Barents Sea and adjacent waters].

We investigated polymorphisms in the pantophysin gene (Pan I locus) in a population of North-East Arctic cod, Gadus morhua L., throughout its foraging area in the Barents Sea and adjacent waters. Correlations between the frequencies of Pan I alleles and habitat conditions, such as depth and temperature, were explored. This study was based on a large number of specimens (2210 individuals) of different age and wide geographic sampling coverage. The frequency of the Pan I(A) allele, a known genetic marker of coastal cod, varied from zero to 0.47. Allele frequencies correlated with depth at the sampling location but not with bottom water temperatures. We observed variations in Pan I(A) frequencies among different age cohorts from the same area. The most prominent shift in Pan I polymorphism was detected at the early stages of the fish life cycle, between pelagic juveniles and benthic cod. We found that the Pan I(A) allele frequency in pelagic yearling cod was essentially same throughout the studied areas in the Barents Sea. In turn, juveniles settling at the northern and deep water locations showed a significant decrease in the allele frequency. In contrast, the frequency of the Pan I(A) allele remained constant in juveniles settling in shallow waters when compared to the pelagic stage. These results confirm the selective nature of the cod Pan I locus and indicate that selection process acting on individuals with different genotypes at the Pan I locus leads to the formation of a stable spatial distribution of allele frequencies observed in adult cod.

[Advanced approaches to studying the population diversity of marine fishes: new opportunities for fisheries control and management].

Recent conceptual and technological advances now enable fisheries geneticists to detect and monitor the dynamics and distribution of marine fish populations more effectively than ever before. Information on the extent of genetically-based divergence among populations, so-called "population diversity", is crucial in the quest to manage exploited living resources sustainably since it endows evolutionary potential in the face of environmental change. The generally limited dialogue between scientists, fisheries managers and policy makers, however, continues to constrain integration of population genetic data into tangible policy applications. Largely drawing on the approach and outputs from a European research project, FishPopTrace, we provide an example how the uncovering of marine fish population diversity enables players from genetics, forensics, management and the policy realm to generate a framework tackling key policy-led questions relating to illegal fishing and traceability. We focus on the use of single-nucleotide polymorphisms (SNPs) in European populations of cod, herring, hake and common sole, and explore how forensics together with a range of analytical approaches, and combined with improved communication of research results to stakeholders, can be used to secure sufficiently robust, tractable and targeted data for effective engagement between science and policy. The essentially binary nature of SNPs, together with generally elevated signals of population discrimination by SNPs under selection, allowed assignment of fish to populations from more areas and with higher certainty than previously possible, reaching standards suitable for use in a court of law. We argue that the use of such tools in enforcement and deterrence, together with the greater integration of population genetic principles and methods into fisheries management, provide tractable elements in the arsenal of tools to achieve sustainable exploitation and conservation of depleted marine fish stocks.

[Population structure of beaked redfish (Sebastes mentella Travin, 1951) in the Irminger Sea and adjacent waters inferred from microsatellite data].

Samples of beaked redfish from the Irminger Sea and adjacent waters were examined for polymorphism at ten microsatellite loci. The strategy of the material collection enabled investigation of geographic, bathymetric, and temporal variation of this species. The results did not support the evidence on spatial differentiation and temporal stability of the species distribution, favoring the idea that the water area examined was inhabited by a single pelagic population of beaked redfish.

Hypolimnion behavior of technetium in freshwater at various stages of eutrophication.

The article presents a study of various mechanisms of hypolimnion technetium behavior which occur at different stages of waterbodies eutrophication. Eutrophication stage was found to be positively correlated with the rate of 99Tc removal from water phase. The study identified a complex biogeochemical mechanism of technetium behavior. Planktonic phototrophic community plays a pivotal role in such a mechanism by ensuring fast oxygen consumption in hypolimnion. This creates favorable conditions for the active development of anaerobic bottom bacteria of sulfur and iron cycles given nutrients inflow. Sulfates and nitrates were discovered to have inhibitory effect on 99Tc biosorption by bottom sediments due to oxidizing conditions. Apart from the shift of redox potential of the medium to reducing values, the 99Tc removal and partial immobilization are also promoted by the presence of inorganic mineral phases of reduced sulfur and iron. These phases form a reducing barrier in the silt, thus preventing the oxidation and migration of technetium. We suggest the ways of stimulating in situ waterbody remediation by means of various additives, which will allow irreversible immobilization of technetium in silt once several growth periods have passed.

[Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (Oncorhynchus nerka) from Eastern and Western Kamchatka].

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.

[Seasonal and interannual variations of sockeye salmon (Oncorhynchus nerka) microsatellite DNA in two Kamchatka lake-river systems].

Seasonal and interannual variations in the sockeye salmon populations from two lake-river systems of the East and West Kamchatka were studied. Stability of allele and genotypic frequencies of six microsatellite DNA loci in the adjacent generations and spawning populations of the sockeye salmon of the Bol'shaya River was confirmed experimentally. The pairwise intersample differentiation (F(st)) of the local sockeye salmon populations from the southwestern Kamchatka coast (Ozernaya and Bol'shaya Rivers)was almost 7 times higher than the corresponding values for the spawning populations of the Bol'shaya River sockeye salmon of the adjacent years; 15 times, for the adjacent Bol'shaya River sockeye salmon generations; and four times, for the seasonal races within the Kamchatka River.

[Red king crab (Paralithodes camtschaticus) in the Barents Sea: a comparative study of introduced and native populations].

Red king crab (Paralithodes camtschaticus) was introduced into the Barents Sea in the 1960-1970s. Its present habitation area spans on the coastal zone from Hammerfest (Northern Norway) to the Barents Sea Funnel in the north-east of the Kola Peninsula. We studied the polymorphism of a mitochondrial gene encoding cytochrome oxidase (COI) and five nuclear microsatellite loci in four samples from the Barents Sea and two donor populations from the Western Kamchatka and Primorye. No decrease in the genetic diversity of the introduced populations was detected. Microsatellite assay demonstrated that the sample from Varrangerfjord was distinct from the rest five populations. However, no significant differences between the rest samples were found. Possible reasons underlying this phenomenon are discussed.

[Comparative genome analysis in pea Pisum sativum L. varieties and lines with chromosomal and molecular markers].

C banding, Ag-NOR staining, FISH with pTa71 (45S rDNA) and pTa794 (5S rDNA), and RAPD-PCR analysis were used to study the genome and chromosome polymorphism in four varieties (Frisson, Sparkle, Rondo, and Finale) and two genetic lines (Sprint-2 and SGE) of pea Pisum sativum L. A comparison of the C-banding patterns did not reveal any polymorphism within the varieties. The most significant between-variety differences were observed for the size of C bands on satellite chromosomes 4 and 7. All grain pea varieties (Frisson, Sparkle, and Rondo) had a large C band in the satellite of chromosome 4 and a medium C band in the region adjacent to the satellite thread on chromosome 7. C bands were almost of the same size in the genetic lines and vegetable variety Finale. In all accessions, 45S rDNA mapped to the secondary constriction regions of chromosomes 1, 3, and 5. The signal from chromosome 5 in the lines was more intense than in the varieties. Ag-NOR staining showed that the transcriptional activity of the 45S rRNA genes on chromosome 7 was higher than on chromosome 4 in all accessions. No more than four Ag-NOR-positive nucleoli were observed in interphase nuclei. Statistical analysis of the total area of Ag-NOR-stained nucleoli did not detect any significant difference between the accessions examined. RAPD-PCR analysis revealed high between-variety and low within-variety genomic polymorphism. Chromosomal and molecular markers proved to be promising for genome identification in pea varieties and lines.

[Comparative study of the population structure and population assignment of sockeye salmon Oncorhynchus nerka from West Kamchatka based on RAPD-PCR and microsatellite polymorphism].

Using two types of molecular markers, a comparative analysis of the population structure of sockeye salmon from West Kamchatka as well as population assignment of each individual fish were carried out. The values of a RAPD-PCR-based population assignment test (94-100%) were somewhat higher than those based on microsatellite data (74-84%). However, these results seem quite satisfactory because of high polymorphism of the microsatellite loci examined. The UPGMA dendrograms of genetic similarity of three largest spawning populations, constructed using each of the methods, were highly reliable, which was demonstrated by high bootstrap indices (100% in the case of RAPD-PCR; 84 and 100%, in the case of microsatellite analysis), though the resultant trees differed from one another. The different topology of the trees, in our view, is explained by the fact that the employed methods explored different parts of the genome; hence, the obtained results, albeit valid, may not correlate. Thus, to enhance reliability of the results, several methods of analysis should be used concurrently.

Translation enhancing properties of the 5'-leader of potato virus X genomic RNA.

The double-stranded DNA copy corresponding to the 5'-nontranslated alpha beta-leader of potato virus X (PVX) genomic RNA (positions -3 to-85 according to AUG initiator) was chemically synthesized and fused to the transcription plasmids containing three different reporter genes: neomycinphosphotransferase type II (NPT II) gene, Bacillus thuringiensis coleopteran-specific toxic protein gene and beta-glucuronidase (GUS) gene. Expression of the reporter genes in vitro and in plant protoplasts (in the case of GUS gene) reveals that the alpha beta-leader of PVX RNA acts as a translation enhancer despite the presence of the upstream vector-derived sequence and irrespective of the length of the spacer sequence preceding the reporter genes.

Expression of RNA transcripts of potato virus X full-length and subgenomic cDNAs.

Translation of synthetic potato virus X (PVX) RNAs was examined in Krebs II ascite cell extracts and rabbit reticulocyte lysates. Either full-length or subgenomic RNAs produced by in vitro transcription of cDNAs cloned in the T7 promoter vectors were used. Full-length PVX RNA-transcript directed the synthesis of a large polypeptide which was indistinguishable from the translation product (165 kDa) of authentic viral genomic RNA on SDS-PAGE. Translation of the full-length and 3'-truncated RNA species was stimulated by addition of m7GpppG to the T7 transcription system. Subgenomic cDNA transcripts corresponding to the 3'-proximal part of PVX RNA were efficiently translated into the PVX coat protein and 2 as yet unidentified small hydrophobic proteins.

A novel open reading frame in tobacco mosaic virus genome coding for a putative small, positively charged protein.

From sequence comparisons between the tobramovirus genomes an open reading frame (ORF-X) potentially encoding a small, positively charged protein (33- to 45-amino-acids long) was found to overlap the immediate 3' and 5' sides of the transport protein gene and coat protein gene, respectively. In vitro translation of the monocistronic artificial transcripts generated with T7 RNA polymerase yielded a protein of M(r) 4000 (p4) and an unexpected trypsin-sensitive complex of M(r) 54,000 that was resistant to reduction with 2-mercaptoethanol but could be dissociated by 8 M urea. Assembly of this complex was inhibited completely by site-directed mutagenesis within a conserved, positively charged 5-amino-acid long segment of the ORF-X protein. After centrifugation in low salt buffer the 54-kDa complex remained mostly associated with ribosomes. Apparently this complex represents a specific aggregate of the p4 product of ORF-X with a protein of approximate M(r) 50,000 that is a component of the translation apparatus.

Poly(A) addition site mapping and polyadenylation signal analysis in a plant circovirus replication-related gene.

The transcripts of a genomic component of coconut foliar decay virus (CFDV), a plant circovirus with a single-stranded DNA genome, were characterized by sequencing the 3' termini of the respective cDNA clones. It was shown that transcription of the putative replication-related gene terminated at one major site (six bases downstream of the termination codon) in electroporated barley mesophyll protoplasts and that the resulting transcripts were polyadenylated. A deletion downstream of the AATAAA sequence including the poly(A) addition site did not inhibit polyadenylation signal activity but altered the distance between the polyadenylation signal and the polyadenylation site. However, deletion of the sequences upstream of the AATAAA stretch resulted in inhibition of the polyadenylation in this region. These observations and the finding of a silent CFDV AATAAA sequence downstream of the active poly(A) signal confirm the role of the upstream elements in processing of RNA transcripts in plants.

Genome characterization and taxonomy of Plantago asiatica mosaic potexvirus.

The complete nucleotide sequence of Plantago asiatica mosaic virus (P1AMV) genomic RNA has been determined. The 6128 nucleotide sequence contains five open reading frames (ORFs) coding for proteins of M(r) 156K (ORF1), 25K (ORF2), 12K (ORF3), 13K (ORF4) and 22K (ORF5). The sequences of these P1AMV proteins exhibit strong homology to the proteins of the other potexviruses. Phylogenetic trees based on the multiple sequence alignments of three conserved domains in ORF1 product and capsid protein reveal a close relationship of P1AMV to papaya mosaic virus and clover yellow mosaic virus. The P1AMV genomic RNA and a major subgenomic RNA (sgRNA) of 0.9 kb have been detected in infected leaves by Northern blot hybridization. The latter sgRNA is the messenger for virus capsid protein and its 5' terminus has been located 23 nucleotides upstream of the initiator codon of the coat protein gene. The P1AMV virion RNA and RNA transcript resembling the 0.9 kb sgRNA have been translated in vitro giving rise to a single major 170K product and a major 22K product, respectively.

Expression strategy of the potato virus X triple gene block.

The mode of expression of the overlapping genes of the triple block positioned internally in potato virus X (PVX) RNA was examined. The results of In vitro translation of synthetic RNA transcripts and natural PVX-specific methylmercuric hydroxide-denatured dsRNAs suggest that the 25K protein is expressed as a single translation product of the 2.1 kb subgenomic (sg) RNA and that both the 12K and 8K proteins are expressed from the same 1.4 kb sgRNA.