Survival of pacific salmons in the North Pacific in winter-spring season

Influence of several factors (water temperature, food supply, predatory, size of juveniles) on pacific salmons survival during wintering is considered on the data collected from the upper pelagic layer in surveys conducted by Pacific Fisheries Research Center (TINRO) in the North-West Pacific. There is highly unlikely that the temperature influences on fish mortality directly. There is no obvious proof of negative influence of the low temperature on food base of salmons, as well. The lowering of forage zooplankton biomass in the Subarctic Front zone in February-March is insufficient for the salmons starvation taking into account that the total abundance of planktivorous nekton is also lowered in this area and generally in the Subarctic waters in winter-spring, so the food supply cannot be considered as a crucial factor of the salmons survival. Seasonal changes with lowering of feeding intensity, lipid accumulation, and somatic growth in winter known for pacific salmons aren’t forced by poor food base but are a feature of their species-specific life strategy with cyclic changes of metabolism. Predators are not abundant in the Subarctic zone in winter, so the predatory also cannot cause the high mortality of salmons. Relationship between the size of juveniles and their mortality in winter is considered in detail for the Okhotsk Sea stocks of pink salmon and there is concluded that the size of juveniles cannot be a predictor of their year-classes return for spawning. Thus, any single factor doesn’t determine winter mortality of pacific salmons but their survival is likely determined by a complex interaction of abiotic and biotic factors

Observation of the Dynamic Beta Effect at CESR with CLEO

Using the silicon strip detector of the CLEO experiment operating at the Cornell Electron-positron Storage Ring (CESR), we have observed that the horizontal size of the luminous region decreases in the presence of the beam-beam interaction from what is expected without the beam-beam interaction. The dependence on the bunch current agrees with the prediction of the dynamic beta effect. This is the first direct observation of the effect.Comment: 9 page uuencoded postscript file, postscritp file also available through http://w4.lns.cornell.edu/public/CLNS, submitted to Phys. Rev.

Sequence comparison of prefrontal cortical brain transcriptome from a tame and an aggressive silver fox (Vulpes vulpes)

<p>Abstract</p> <p>Background</p> <p>Two strains of the silver fox (<it>Vulpes vulpes</it>), with markedly different behavioral phenotypes, have been developed by long-term selection for behavior. Foxes from the tame strain exhibit friendly behavior towards humans, paralleling the sociability of canine puppies, whereas foxes from the aggressive strain are defensive and exhibit aggression to humans. To understand the genetic differences underlying these behavioral phenotypes fox-specific genomic resources are needed.</p> <p>Results</p> <p>cDNA from mRNA from pre-frontal cortex of a tame and an aggressive fox was sequenced using the Roche 454 FLX Titanium platform (> 2.5 million reads & 0.9 Gbase of tame fox sequence; >3.3 million reads & 1.2 Gbase of aggressive fox sequence). Over 80% of the fox reads were assembled into contigs. Mapping fox reads against the fox transcriptome assembly and the dog genome identified over 30,000 high confidence fox-specific SNPs. Fox transcripts for approximately 14,000 genes were identified using SwissProt and the dog RefSeq databases. An at least 2-fold expression difference between the two samples (p < 0.05) was observed for 335 genes, fewer than 3% of the total number of genes identified in the fox transcriptome.</p> <p>Conclusions</p> <p>Transcriptome sequencing significantly expanded genomic resources available for the fox, a species without a sequenced genome. In a very cost efficient manner this yielded a large number of fox-specific SNP markers for genetic studies and provided significant insights into the gene expression profile of the fox pre-frontal cortex; expression differences between the two fox samples; and a catalogue of potentially important gene-specific sequence variants. This result demonstrates the utility of this approach for developing genomic resources in species with limited genomic information.</p

Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

<p>Abstract</p> <p>Background</p> <p>Cucumber, <it>Cucumis sativus </it>L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line '9930' and the North American pickling type inbred line 'Gy14'. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber.</p> <p>Results</p> <p>A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The <it>in silico </it>PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newly-discovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available.</p> <p>Conclusions</p> <p>The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.</p

LONG-TERM AVERAGE BIOMASS AND DOMINANT FISH SPECIES IN THE BOTTOM BIOTOPES OF THE OKHOTSK SEA. PART 1. COMPOSITION AND QUANTITATIVE RATIO OF SPECIES ON SHELVES IN DIFFERENT AREAS OF THE SEA

Composition of the demersal fish community in the bottom biotopes of 14 biostatistical areas of the Okhotsk Sea is considered on the data of 9,189 standard trawl catches obtained in 95 expeditions conducted by Pacific Fish. Res. Center (TINRO) in 1977–2010. The most abundant fish species in each area are ranked by biomass. The total demersal fish biomass is estimated as 9583.0 . 103 t (2124.9 . 103 t without pollock and herring). The most numerous demersal species are: pacific cod Gadus macrocephalus, yellowfin sole Limanda aspera, pacific sand lance Ammodytes hexapterus, great sculpin Mycocephalus polyacanthocephalus, and saffron cod Eleginus gracilis