Remarkable genetic diversity detected at river buffalo prolactin receptor (PRLR) gene and association studies with milk fatty acid composition

Prolactin is an anterior pituitary peptide hormone involved in many different endocrine activities and is essential for reproductive performance. This action is mediated by its receptor, the prolactin receptor, encoded by the PRLR gene. In this study, we sequenced and characterized the Mediterranean river buffalo PRLR gene (from exon 3 to 10), and we found remarkable genetic diversity. In particular, we found 24 intronic polymorphisms and 13 exonic SNPs, seven of which were non‐synonymous. Furthermore, the polymorphisms identified in the 3′‐UTR were investigated to establish their possible influence on microRNA binding sites. Considering all the amino acid changes and the observed allelic combinations, it is possible to deduce at least six different translations of the buffalo prolactin receptor and, consequently, the presence at the PRLR gene of at least six alleles. Furthermore, we identified a deletion of a CACTACC heptamer between nucleotides 1102 and 1103 of exon 10 (3′‐UTR), and we developed an allele‐specific PCR to identify the carriers of this genetic marker. Finally, the SNP g.11188A>G, detected in exon 10 and responsible for the amino acid replacement p.His328Arg, was genotyped in 308 Italian Mediterranean river buffaloes, and an association study with milk fat traits was carried out. The statistical analysis showed a tendency that approached significance for the AA genotype with higher contents of odd branched‐chain fatty acids. Thus, our results suggest that the PRLR gene is a good candidate for gene association studies with qualitative traits related to buffalo milk production.     

New data on the range,biology, and abundance of skilfish Erilepis zonifer (Anoplopomatidae)

Data on the occurrence, spatial-bathymetric distribution, and size composition of skilfish Erilepis zonifer are given on the basis of the materials collected at the long-line catches on the Emperor Ridge seamounts. This fish is a large representative of fam. Anoplopomatidae (maximal length 188 cm; weight 88.5 kg). From June to July 2009, the species was found on all five sampled underwater mountains (Nintoku, Jingu, Ojin, Koko, Northern Koko). The fish was found within the depth range 370–1040 m. The initial biomass of skilfish at the studied seamounts calculated by the Leslie method is approximately 203.5 tons. The structure of the range and possible ways of the dispersion of this species in the waters of the continental slope of the North-Pacific rim are discussed.     

New data on mollusks from the Miocene (Tarkhanian-Chokrakian) of northern Sinop Province,Turkey

An insufficiently known bivalve and gastropod assemblage from the Early-Middle Miocene (Tarkhanian-Chokrakian) of northern Sinop Province (Turkey), is analyzed. Environments of the assemblage are reconstructed for the Chokrakian as subtidal, with prevailing lime and sandy bottom and good aeration, and partially well vegetated. Impoverishment of the mollusk biocoenose in this part of the marine basin (only 18 bivalve and 22 gastropod species recorded) compared to other areas, including the closest regions, Bulgaria on the west and Georgia on the east, is emphasized. The relatively low diversity of the fauna is probably connected not only with insufficient collecting, but with special hydrological conditions. A special aspect of the fauna is highlighted by the presence of the bivalve Circomphalus foliaceolamellosus subplicatus (Orb.), which is rare in the Chokrakian.     

Palaeomicrocodium: A new view on its origin

Remains of Palaeomicrocodium from the Silurian and Devonian carbonate and clay deposits from the Timan-Northern Ural region, Salair, and Western Siberia are studied using various lithological and geochemical techniques. Characters suggesting their paleoecological and geochemical specialization are discussed. It is suggested that Palaeomicrocodium structures belong to ancient lichens or actinolichens. This hypothesis is based on a number of features of Palaeomicrocodium, including the presence of typical biologically fixed microelements of soil, such as Co, Cu, Zn, Ni, and Cd, sourced from the atmosphere; presence of kerogen carbonaceous matter in prismatic calcite monocrystals of Palaeomicrocodium; identification in their structure of probable hypha-like and rhizoid-like structures; morphological similarity to extant encrusting lichens. Like lichens, Palaeomicrocodium significantly contributed to chemical weathering of rocks by excreting various organic acids, which could effectively dissolve minerals and chelate metallic cations. As a result of the weathering induced by vital function of Palaeomicrocodium, rock-forming minerals exhibit surface corrosion.     

Trilobites Plicatolina lucida Lazarenko from the Upper Cambrian of the Kharaulakh Mountains (Northeastern Siberian Platform)

A collection of trilobites of the genus Plicatolina Shaw, 1951 from the upper Ogon’or Formation, Cambrian Section, Chekurovka Anticline (northeastern Siberian Platform, Kharaulakh Mountains), is studied. It is shown that all specimens of this collection belong to the same species, Plicatolina lucida Lazarenko, 1966, but represent different age stages. It is also shown that species of the genus Plicatolina (P. quadrata Pokrovskaya, 1966 and P. yakutica Pokrovskaya, 1966) described from the Upper Cambrian of the Siberian Platform are probably synonyms of P. lucida.     

Development of a Multiple Loci Variable Number of Tandem Repeats Analysis (MLVA) to Unravel the Intra-Pathovar Structure of Pseudomonas syringae pv. actinidiae Populations Worldwide

The bacterial canker of kiwifruit by Pseudomonas syringae pv. actinidiae is an emblematic example of a catastrophic disease of fruit crops. In 2008 a new, extremely virulent form of the pathogen emerged and rapidly devastated many Actinidia spp. orchards all over the world. In order to understand differences in populations within this pathovar and to elucidate their diffusion and movements on world scale, it is necessary to be able to quickly and on a routine basis compare new isolates with previous records. In this report a worldwide collection of 142 strains was analyzed by MLVA, chosen as investigative technique for its efficacy, reproducibility, simplicity and low cost. A panel of 13 Variable Number of Tandem Repeats (VNTR) loci was identified and used to describe the pathogen population. The MLVA clustering is highly congruent with the population structure as previously established by other molecular approaches including whole genome sequencing and correlates with geographic origin, time of isolation and virulence. For convenience, we divided the VNTR loci in two panels. Panel 1 assay, using six loci, recognizes 23 different haplotypes, clustered into ten complexes with highest congruence with previous classifications. Panel 2, with seven VNTR loci, provides discriminatory power. Using the total set of 13 VNTR loci, 58 haplotypes can be distinguished. The recent hypervirulent type shows very limited diversity and includes, beside the strains from Europe, New Zealand and Chile, a few strains from Shaanxi, China. A broad genetic variability is observed in China, but different types are also retrievable in Japan and Korea. The low virulent strains cluster together and are very different from the other MLVA genotypes. Data were used to generate a public database in MLVAbank. MLVA represents a very promising first-line assay for large-scale routine genotyping, prior to whole genome sequencing of only the most relevant samples.     

Lowland river reference condition: spatial and temporal patterns of the zoobenthos community in the Volga headwaters (2006–2010)

The Volga, the largest river in Europe, has experienced multiple stressors from human activities. Recently we showed that its upper course (about 500 km, from its source to Tver) still has large sections with low impact and a natural type-specific potamal flora and fauna. Our present research in the East European lowlands aim to define reference conditions for mid-sized to large lowland rivers in order to build a basis for future management and conservation. Three monitoring sites were selected based on the results from intensive sampling in 2005. In subsequent field campaigns between 2006 and 2010 regular surveys were carried out each year in summer and additional ones in spring. A taxon-rich macroinvertebrate fauna, including several rare potamal relict species, was recorded and the data was used to provide an overview of annual and interannual variation in community indices and metrics. The conditions described for the headwaters of the Volga River system can be used as a reference state for medium-sized and large lowland rivers in regions where reference sites of these types are lacking.     

Functional linear models for region-based association analysis

Regional association analysis is one of the most powerful tools for gene mapping because instead analysis of individual variants it simultaneously considers all variants in the region. Recent development of the models for regional association analysis involves functional data analysis approach. In the framework of this approach, genotypes of variants within region as well as their effects are described by continuous functions. Such approach allows us to use information about both linkage and linkage disequilibrium and reduce the influence of noise and/or observation errors. Here we define a functional linear mixed model to test association on independent and structured samples. We demonstrate how to test fixed and random effects of a set of genetic variants in the region on quantitative trait. Estimation of statistical properties of new methods shows that type I errors are in accordance with declared values and power is high especially for models with fixed effects of genotypes. We suppose that new functional regression linear models facilitate identification of rare genetic variants controlling complex human and animal traits. New methods are implemented in computer software FREGAT which is available for free download at http://mga.bionet.nsc.ru/soft/FREGAT/.