Identification of the human homolog of the imprinted mouse Air non-coding RNA

Genomic imprinting is widely conserved amongst placental mammals. Imprinted expression of IGF2R, however, differs between mice and humans. In mice, Igf2r imprinted expression is seen in all fetal and adult tissues. In humans, adult tissues lack IGF2R imprinted expression, but it is found in fetal tissues and Wilms' tumors where it is polymorphic and only seen in a small proportion of tested samples. Mouse Igf2r imprinted expression is controlled by the Air (Airn) ncRNA whose promoter lies in an intronic maternally-methylated CpG island. The human IGF2R gene carries a homologous intronic maternally-methylated CpG island of unknown function. Here, we use transfection and transgenic studies to show that the human IGF2R intronic CpG island is a ncRNA promoter. We also identify the same ncRNA at the endogenous human locus in 16–40% of Wilms' tumors. Thus, the human IGF2R gene shows evolutionary conservation of key features that control imprinted expression in the mouse.     

Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation

Cyclin-dependent kinase 2 (CDK2) is the most thoroughly studied of the cyclin-dependent kinases that regulate essential cellular processes, including the cell cycle, and it has become a model for studies of regulatory mechanisms at the molecular level. This contribution identifies flexible and rigid regions of CDK2 based on temperature B-factors acquired from both X-ray data and molecular dynamics simulations. In addition, the biological relevance of the identified flexible regions and their motions is explored using information from the essential dynamics analysis related to conformational changes of CDK2 and knowledge of its biological function(s). The conserved regions of CMGC protein kinases' primary sequences are located in the most rigid regions identified in our analyses, with the sole exception of the absolutely conserved G13 in the tip of the glycine-rich loop. The conserved rigid regions are important for nucleotide binding, catalysis, and substrate recognition. In contrast, the most flexible regions correlate with those where large conformational changes occur during CDK2 regulation processes. The rigid regions flank and form a rigid skeleton for the flexible regions, which appear to provide the plasticity required for CDK2 regulation. Unlike the rigid regions (which as mentioned are highly conserved) no evidence of evolutionary conservation was found for the flexible regions.     

Comparative study of mouse and human feeder cells for human embryonic stem cells

Various types of feeder cells have been adopted for the culture of human embryonic stem cells (hESCs) to improve their attachment and provide them with stemness-supporting factors. However, feeder cells differ in their capacity to support the growth of undifferentiated hESCs. Here, we compared the expression and secretion of four well-established regulators of hESC pluripotency and/or differentiation among five lines of human foreskin fibroblasts and primary mouse embryonic fibroblasts throughout a standard hESC culture procedure. We found that human and mouse feeder cells secreted comparable levels of TGF beta 1. However, mouse feeder cells secreted larger quantities of activin A than human feeder cells. Conversely, FGF-2, which was produced by human feeder cells, could not be detected in culture media from mouse feeder cells. The quantity of BMP-4 was at about the level of detectability in media from all feeder cell types, although BMP-4 dimers were present in all feeder cells. Production of TGF beta 1, activin A, and FGF-2 varied considerably among the human-derived feeder cell lines. Low- and high-producing human feeder cells as well as mouse feeder cells were evaluated for their ability to support the undifferentiated growth of hESCs. We found that a significantly lower proportion of hESCs maintained on human feeder cell types expressed SSEA3, an undifferentiated cell marker. Moreover, SSEA3 expression and thus the pluripotent hESC compartment could be partially rescued by addition of activin A. Cumulatively, these results suggest that the ability of a feeder layer to promote the undifferentiated growth of hESCs is attributable to its characteristic growth factor production.     

Development of a sensitive and controlled real-time RT-PCR assay for viral haemorrhagic septicaemia virus (VHSV) in marine salmonid aquaculture

A survey was undertaken to determine the potential distribution of viral haemorrhagic septicaemia virus (VHSV) in marine cage-based salmonid farms in Scotland. A rapid, accurate and sensitive quantitative real-time RT-PCR (qRT-PCR) assay was developed, targeting a conserved region of the nucleoprotein (N) gene of the virus. The qRT-PCR assay was shown to be more sensitive than the conventional VHSV RT-PCR. A validation protocol included several different virus isolates as the target and confirmed that the assay could detect all European VHSV genotypes (I, II and III). Both endogenous and exogenous controls were designed to control for integrity of template and distinguish between true VHSV positives and contamination with the positive control material. In total, the universal European VHSV qRT-PCR assay with exogenous positive control was applied to screen 2040 individual Atlantic salmon Salmo salar and 150 individual rainbow trout Oncorhynchus mykiss. No evidence of the presence of VHSV in association with either salmonid species in Scottish marine farms was detected. However, both marine Atlantic salmon and rainbow trout are still considered possible carriers of VHSV, which remains a potential threat to freshwater farming. Therefore, a continued surveillance of these species in marine environment is recommended.     

LDLs induce fibroblast spreading independently of the LDL receptor via activation of the p38 MAPK pathway

Because adventitial fibroblasts play an important role in the repair of blood vessels, we assessed whether elevation in LDL concentrations would affect fibroblast function and whether this depended on activation of intracellular signaling pathways. We show here that in primary human fibroblasts, LDLs induced transient activation of the p38 mitogen-activated protein kinase (MAPK) pathway, but not the c-Jun N-terminal kinase MAPK pathway. This activation did not require the recruitment of the LDL receptor (LDLR), because LDLs efficiently stimulated the p38 MAPK pathway in human and mouse fibroblasts lacking functional LDLR, and because receptor-associated protein, an LDLR family antagonist, did not block the LDL-induced p38 activation. LDL particles also induced lamellipodia formation and cell spreading. These effects were blocked by SB203580, a specific p38 inhibitor. Our data demonstrate that LDLs can regulate the shape of fibroblasts in a p38 MAPK-dependent manner, a mechanism that may participate in wound healing or vessel remodeling as in atherosclerosis.     

Mitochondrial membrane fluidity, potential, and calcium transients in the myocardium from acute diabetic rats

In this study, we report for the first time concurrent measurements of membrane potential and dynamics and respiratory chain activities in rat heart mitochondria, as well as calcium transients in the hearts of rats in an early phase of streptozotocin diabetes, not yet accompanied with diabetes-induced complications. Quantitative relationships among these variables were assessed. The mitochondria from diabetic rats exhibited decreased fluorescence anisotropy values of diphenylhexatriene. This indicates that hydrophobic core of the membranes was more fluid compared with controls (p<0.05). We discuss the changes in fluidity as having been associated with augmented energy transduction through the diabetic membranes. Reduced ratio of JC-1 fluorescence (aggregates to monomers) in the mitochondria from diabetic hearts reflected descendent transmembrane potential. A significant negative association between membrane fluidity and potential in the diabetic group was found (p<0.05; r=0.67). Further, we observed an increase in calcium transient amplitude (CTA) in the diabetic cardiomyocytes (p=0.048). We conclude that some of the calcium-induced regulatory events that dictate fuel selection and capacity for ATP production in diabetic heart occur at the membrane level. Our findings offer new insight into acute diabetes-induced changes in cardiac mitochondria.     

Improvement of very high gravity ethanol fermentation by media supplementation using Saccharomyces cerevisiae

The final ethanol concentration achieved was increased by 17% (to 103 g ethanol/l) when excess assimilable nitrogen was added to the batch very high gravity (VHG) ethanolic fermentations by Saccharomyces cerevisiae. The supplementation of the media with 12 g yeast extract l–1, 0.3 g cell walls l–1, 3 g glycine l–1 and 20 g soya flour l–1 led to halving reduction of the fermentation time to 28 h. The ethanol productivity was enhanced by more than 50% (to achieved value 3.3 g l–1 h–1).     

Comparison of Y-STR polymorphisms in three different Slovak population groups

Eleven Y-chromosomal microsatellite loci included in the Powerplex Y multiplex kit were analyzed in different Slovak population samples: Habans (n = 39), Romanies (n = 100) and Slovak Caucasian (n = 148) individuals, respectively, from different regions of Slovakia. The analysis of molecular variance between populations indicated that 89.27% of the haplotypic variations were found within populations and only 10.72% between populations (Fst = 0.1027; p = 0.0000). The haplotype diversities were ranging from 0.9258 to 0.9978, and indicated a high potential for differentiating between male individuals. The study reports differences in allele frequencies between the Romanies, Habans and Slovak Caucasian men. Selected loci showed that both the Romany and Haban population belonged to endogamous and relatively small founder population groups, which developed in relatively reproductive isolated groups surrounded by the Slovak Caucasian population.