The bovine lactation genome: insights into the evolution of mammalian milk

One of the major genomics challenges is to better understand how correct gene expression is orchestrated. Recent studies have shown how spatial chromatin organization is critical in the regulation of gene expression. Here, we developed a suite of computer programs to identify chromatin conformation signatures with 5C technology http://Dostielab.biochem.mcgill.ca. We identified dynamic HoxA cluster chromatin conformation signatures associated with cellular differentiation. Genome-wide chromatin conformation signature identification might uniquely identify disease-associated states and represent an entirely novel class of human disease biomarkers.     

Stimulation of r- vs. K-selected microorganisms by elevated atmospheric CO2 depends on soil aggregate size

Increased root exudation under elevated atmospheric CO₂ and the contrasting environments in soil macro- and microaggregates could affect microbial growth strategies. We investigated the effect of elevated CO₂ on the contribution of fast- ( r -strategists) and slow-growing ( K -strategists) microorganisms in soil macro- and microaggregates. We fractionated the bulk soil from the ambient and elevated (for 5 years) CO₂ treatments of FACE-Hohenheim (Stuttgart) into large macro- (>2 mm), small macro- (0.25–2.00 mm), and microaggregates (<0.25 mm) using 'optimal moist' sieving. Microbial biomass (C_mic), the maximum specific growth rate (μ), growing microbial biomass (GMB) and lag-period ( t _lag) were estimated by the kinetics of CO₂ emission from bulk soil and aggregates amended with glucose and nutrients. Although C_org and C_mic were unaffected by elevated CO₂, μ values were significantly higher under elevated than ambient CO₂ for bulk soil, small macroaggregates, and microaggregates. Substrate-induced respiratory response increased with decreasing aggregate size under both CO₂ treatments. Based on changes in μ, GMB and lag period, we conclude that elevated atmospheric CO₂ stimulated the r- selected microorganisms, especially in soil microaggregates. Such an increase in r -selected microorganisms indicates acceleration of available C mineralization in soil, which may counterbalance the additional C input by roots in soils in a future elevated atmospheric CO₂ environment.     

Microsatellite genetic variation of Asian populations of Dolly Varden char

Genetic variation at eight microsatellite loci was examined in 21 populations of Dolly Varden charrs, Salvelinus malma, representing five geographical regions (Kamchatka Peninsula, Sea of Okhotsk coast, Sea of Japan coast, Sakhalin Island, and Kuril islands). Hierarchical analysis of molecular variance showed that 11% (58% in terms of R-statistics) of the variation was distributed among of northern subspecies of Dolly Varden, Salvelinus malma malma and southern Asian Dolly Varden, S. m. krascheninnikovi while similar values were attributed to the among-regional level within northern Dolly Varden 9% (7%) and southern Asian Dolly Varden 11% (14%). Permutation-based tests indicated a mutational component to genetic differentiation based on allelic size variance and suggested that divergence of the two subspecies had occurred at least 3,000 generations ago. On large spatial scales (within the Asian range of the species), populations clustered according to their geographical location. On smaller scales (within regions and subregions) correlation between genetic and geographic distances was not significant. Northern Dolly Varden has higher allelic diversity and more private alleles than southern subspecies, this probably indicating differences in demographic history.     

Proinflammatory Cytokines Induce Hyaluronan Synthesis and Monocyte Adhesion in Human Endothelial Cells through Hyaluronan Synthase 2 (HAS2) and the Nuclear Factor-κB (NF-κB) Pathway

Chronic inflammation is now accepted to have a critical role in the onset of several diseases as well as in vascular pathology, where macrophage transformation into foam cells contributes in atherosclerotic plaque formation. Endothelial cells (EC) have a critical function in recruitment of immune cells, and proinflammatory cytokines drive the specific expression of several adhesion proteins. During inflammatory responses several cells produce hyaluronan matrices that promote monocyte/macrophage adhesion through interactions with the hyaluronan receptor CD44 present on inflammatory cell surfaces. In this study, we used human umbilical chord vein endothelial cells (HUVECs) as a model to study the mechanism that regulates hyaluronan synthesis after treatment with proinflammatory cytokines. We found that interleukin 1β and tumor necrosis factors α and β, but not transforming growth factors α and β, strongly induced HA synthesis by NF-κB pathway. This signaling pathway mediated hyaluronan synthase 2 (HAS2) mRNA expression without altering other glycosaminoglycan metabolism. Moreover, we verified that U937 monocyte adhesion on stimulated HUVECs depends strongly on hyaluronan, and transfection with short interference RNA of HAS2 abrogates hyaluronan synthesis revealing the critical role of HAS2 in this process.     

Dental Variation in Sibling Species <Emphasis Type="Italic">Microtus arvalis</Emphasis> and <Emphasis Type="Italic">M. rossiaemeridionalis</Emphasis> (Arvicolinae,Rodentia): Between-Species Comparisons and Geography of Morphotype Dental Patterns

The data on dental variability in natural populations of sibling species of common voles (“arvalis” group, genus Microtus) from European and Asian parts of the species’ ranges are summarized using a morphotype-based approach to analysis of dentition. Frequency distributions of the first lower (m1) and the third upper (M3) molar morphotypes are analyzed in about 65 samples of M. rossiaemeridionalis and M. arvalis represented by arvalis and obscurus karyotypic forms. Because of extreme similarity of morphotype dental patterns in the taxa studied, it is impossible to use molar morphotype frequencies for species identification. However, a morphotype-based approach to analysis of dental variability does allow analysis of inter-species comparisons from an evolutionary standpoint. Three patterns of dental complexity are established in the taxa studied: simple, basic (the most typical within the ranges of both species), and complex. In M. rossiaemeridionalis and in M. arvalis obscurus only the basic pattern of dentition occurs. In M. arvalis arvalis, both simple and basic dental patterns are found. Analysis of association of morphotype dental patterns with geographical and environmental variables reveals an increase in the number of complex molars with longitude and latitude: in M. arvalis the pattern of molar complication is more strongly related to longitude, and in M. rossiaemeridionalis—to latitude. Significant decrease in incidence of simple molars with climate continentality and increasing aridity is found in M. arvalis. The simple pattern of dentition is found in M. arvalis arvalis in Spain, along the Atlantic coast of France and on islands thereabout, in northeastern Germany and Kirov region in European Russia. Hypotheses to explain the distribution of populations with different dental patterns within the range of M. arvalis sensu stricto are discussed.     

Ecologically safe method for improved feather wastes biodegradation

Twenty thermophilic actinomycetes were selected that were able to degrade feather wastes in high degree (87–91%). Increased proteolytic and lipolytic activity and exopolysaccharide production of the strains growing on feathers suggested their important role in the complex process of feathers biodegradation. Highest soluble protein content was determined in the fermented broths of the strains 3H, 8H, 4C, M4, and 27A. Based on data obtained, a mixed culture of three selected thermoactinomycete strains – 3H, 8H and M4, has been designed that considerably improved the feathers digestion process. The addition of feathers from 0.7 to 3% and pH values from 7.5 to 8.5 provided highest soluble protein content in the fermented broth of the mixed culture. It was shown that the hydrolysate obtained after 72 h growth of the mixed culture on feathers is rich in soluble proteins and amino acids including essential ones like lysine, threonine, leucine, isoleucine and valine, and rare ones like threonine, proline and serine. Therefore, the obtained value-added protein hydrolysate could be used for preparation of fertilizers or soil amendments, as well as protein source in animal feeding. To our knowledge, this is first report of using mixed culture of thermoactinomycete strains for improved feathers biodegradation. The proposed ecologically safe method is simple and economically viable thus applicable on industrial scale.     

Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis

Non-coding RNAs of complex tertiary structure are involved in numerous aspects of the replication and processing of genetic information in many organisms; however, an understanding of the complex relationship between their structural dynamics and function is only slowly emerging. The Neurospora Varkud Satellite (VS) ribozyme provides a model system to address this relationship. First, it adopts a tertiary structure assembled from common elements, a kissing loop and two three-way junctions. Second, catalytic activity of the ribozyme is essential for replication of VS RNA in vivo and can be readily assayed in vitro. Here we exploit single molecule FRET to show that the VS ribozyme exhibits previously unobserved dynamic and heterogeneous hierarchical folding into an active structure. Readily reversible kissing loop formation combined with slow cleavage of the upstream substrate helix suggests a model whereby the structural dynamics of the VS ribozyme favor cleavage of the substrate downstream of the ribozyme core instead. This preference is expected to facilitate processing of the multimeric RNA replication intermediate into circular VS RNA, which is the predominant form observed in vivo.