Comparative analysis of vertebrate EIF2AK2 (PKR) genes and assignment of the equine gene to ECA15q24-q25 and the bovine gene to BTA11q12-q15

The structures of the canine, rabbit, bovine and equine EIF2AK2 genes were determined. Each of these genes has a 5\u27 non-coding exon as well as 15 coding exons. All of the canine, bovine and equine EIF2AK2 introns have consensus donor and acceptor splice sites. In the equine EIF2AK2 gene, a unique single nucleotide polymorphism that encoded a Tyr329Cys substitution was detected. Regulatory elements predicted in the promoter region were conserved in ungulates, primates, rodents, Afrotheria (elephant) and Insectifora (shrew). Western clawed frog and fugu EIF2AK2 gene sequences were detected in the USCS Genome Browser and compared to those of other vertebrate EIF2AK2 genes. A comparison of EIF2AK2 protein domains in vertebrates indicates that the kinase catalytic domains were evolutionarily more conserved than the nucleic acid-binding motifs. Nucleotide substitution rates were uniform among the vertebrate sequences with the exception of the zebrafish and goldfish EIF2AK2 genes, which showed substitution rates about 20% higher than those of other vertebrates. FISH was used to physically assign the horse and cattle genes to chromosome locations, ECA15q24-q25 and BTA11q12-15, respectively. Comparative mapping data confirmed conservation of synteny between ungulates, humans and rodents

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety

Background. Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. Principal Findings. We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitisspecific large scale duplication event concerning at least 10 chromosomes (duplication not reported before). Conclusions. Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape

Reactive oxygen species in pathogenesis of atherosclerosis.

Co-author affiliations: - Sechenov Institute of Evolutionary Physiology and Biochemistry RAS, Saint Petersburg, Russia - Research Institute of Hygiene, Occupational Pathology and Human Ecology, Saint Petersburg, Russia - Koltzov Institute of Developmental Biology RAS, Moscow, Russia - Institute of Cell Biophysics RAS, Pushchino, Russia - Institute of General Pathology and Pathophysiology RAMS, Moscow, RussiaThe volume of publications on the role of reactive oxygen species (ROS) in biological processes has been increasing exponentially over the last decades. ROS in large amounts clearly have detrimental effects on cell physiology, whereas low concentrations of ROS are permanently produced in cells and play a role as signaling molecules. An imbalance in ROS production and defense mechanisms can lead to pathological vascular remodeling, atherosclerosis being among them. The aim of this review is to examine different sources of ROS from the point of view of their participation in pathogenesis of atherosclerosis and related cardiovascular risk. Among the possible sources of ROS discussed here are mitochondria, NADPH-oxidases, xanthine oxidase, peroxidases, NO-synthases, cytochrome P450, cyclooxygenases, lipoxygenases, and hemoglobin of red blood cells. A great challenge for future research is to establish interrelations, feedback and feed-forward regulation mechanisms of various sources of ROS in development of atherosclerosis and other vascular pathologies

Blood flow oscillations as a signature of microvascular abnormalities

Laser Doppler flowmetry (LDF) was utilized for blood ow measurements. Wavelet analysis was used to identify spectral characteristics of the LDF signal in patients with rheumatic diseases and diabetes mellitus. Baseline measurements were applied for both pathological groups. Blood flow oscillations analyses were performed by means of the wavelet transform. Higher baseline perfusion was observed in both pathological groups in comparison to controls. Differences in the spectral properties between the groups studied were revealed. The results obtained demonstrated that spectral properties of the LDF signal collected in basal conditions may be the signature of microvasculature functional state

Characterization of the equine 2\u27-5\u27 oligoadenylate synthetase 1 (OAS1) and ribonuclease L (RNASEL) innate immunity genes

BACKGROUND: The mammalian OAS/RNASEL pathway plays an important role in antiviral host defense. A premature stop-codon within the murine Oas1b gene results in the increased susceptibility of mice to a number of flaviviruses, including West Nile virus (WNV). Mutations in either the OAS1 or RNASEL genes may also modulate the outcome of WNV-induced disease or other viral infections in horses. Polymorphisms in the human OAS gene cluster have been previously utilized for case-control analysis of virus-induced disease in humans. No polymorphisms have yet been identified in either the equine OAS1 or RNASEL genes for use in similar case-control studies. RESULTS: Genomic sequence for equine OAS1 was obtained from a contig assembly generated from a shotgun subclone library of CHORI-241 BAC 100I10. Specific amplification of regions of the OAS1 gene from 13 horses of various breeds identified 33 single nucleotide polymorphisms (SNP) and two microsatellites. RNASEL cDNA sequences were determined for 8 mammals and utilized in a phylogenetic analysis. The chromosomal location of the RNASEL gene was assigned by FISH to ECA5p17-p16 using two selected CHORI-241 BAC clones. The horse genomic RNASEL sequence was assembled. Specific amplification of regions of the RNASEL gene from 13 horses identified 31 SNPs. CONCLUSION: In this report, two dinucleotide microsatellites and 64 single nucleotide polymorphisms within the equine OAS1 and RNASEL genes were identified. These polymorphisms are the first to be reported for these genes and will facilitate future case-control studies of horse susceptibility to infectious diseases

Characterization of the equine 2'-5' oligoadenylate synthetase 1 (OAS1) and ribonuclease L (RNASEL) innate immunity genes

Background The mammalian OAS/RNASEL pathway plays an important role in antiviral host defense. A premature stop-codon within the murine Oas1b gene results in the increased susceptibility of mice to a number of flaviviruses, including West Nile virus (WNV). Mutations in either the OAS1 or RNASEL genes may also modulate the outcome of WNV-induced disease or other viral infections in horses. Polymorphisms in the human OAS gene cluster have been previously utilized for case-control analysis of virus-induced disease in humans. No polymorphisms have yet been identified in either the equine OAS1 or RNASEL genes for use in similar case-control studies. Results Genomic sequence for equine OAS1 was obtained from a contig assembly generated from a shotgun subclone library of CHORI-241 BAC 100I10. Specific amplification of regions of the OAS1 gene from 13 horses of various breeds identified 33 single nucleotide polymorphisms (SNP) and two microsatellites. RNASEL cDNA sequences were determined for 8 mammals and utilized in a phylogenetic analysis. The chromosomal location of the RNASEL gene was assigned by FISH to ECA5p17-p16 using two selected CHORI-241 BAC clones. The horse genomic RNASEL sequence was assembled. Specific amplification of regions of the RNASEL gene from 13 horses identified 31 SNPs. Conclusion In this report, two dinucleotide microsatellites and 64 single nucleotide polymorphisms within the equine OAS1 and RNASEL genes were identified. These polymorphisms are the first to be reported for these genes and will facilitate future case-control studies of horse susceptibility to infectious diseases

Effect of short peptides on seed germination and morphometric parameters of flax seedlings

The use of peptide preparations is one of the current trends in modern agriculture. These preparations can be used to increase the efficiency of sowing treatment of agricultural crops seeds. The article presents the results of a laboratory experiment aimed at studying the effect of a complex of short peptides AC-3 (glutamic acid, aspartic acid, leucine) on seed germination and morphometric parameters of flax seedlings (Linum usitatissimum L.) - Tverskoy variety. The maximum germination energy (68, 68 and 74%, 50% at the control) and seed germination values (95, 95 and 100%, 75% at the control) were obtained in variants with seed treatment with a complex of short peptides at concentrations of 1*10-12, 1*10-13, and 1*10-15 g/l, respectively. According to the totality of the maximum values of seed quality indicators and morphometric characteristics of flax seedlings, the Tverskoy variety (the length of roots and sprouts, the yield of raw and dry biomass of seedlings), the optimal concentration of a complex of short peptides for pre-sowing seed treatment is 1*10-15 g/l

Laser doppler spectrum decomposition applied in diagnostics of microcirculatory disturbances

Laser Doppler flowmetry (LDF) is widely used to study blood microcirculation in the skin. However, during tradition signal processing based on the integral estimations of the power spectrum of detector photocurrent, the significant part of the information about the skin blood ow is lost. In this study, we propose to analyse the distribution of the blood perfusion over the Doppler shift frequencies, which correlate with the RBC velocity. This approach provides localisation of the blood ow oscillations in different subranges of the Doppler shift. The method applied together with the wavelet analysis has been tested in healthy volunteers and patients with psoriasis on the unaffected surface of the skin. It was revealed, that the significant difference in the amplitude of myogenic oscillations is allocated in the region of the low frequency Doppler shift (1-200 Hz). This frequency region can be associated with the signal from slow components of the skin microcirculation, that can point out on a different state of the lymphatic system of the skin in psoriasis

Peculiarities of local blood microcirculation in patients with psoriasis

Local hemodynamic parameters were studied by means of laser Doppler flowmetry in 15 patients with psoriasis in the stationary stage, who have plaques on the inner surface of the forearm. LDF signals recorded at the site of psoriatic lesions of the tissue as well as in the intact tissue at a distance of 1-2 cm from the affected area were analysed. LDF signals were postprocessed by continuous wavelet transform using the Morlet wavelet