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

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

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

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

Fibre-optic probe for fluorescence diagnostics with blood influence compensation

To minimise the influence of blood content on the fluorescence measurements in vivo, a fibre optical probe combining fluorescence and diffuse reflectance measurements was developed. For the inverse solution of the blood content recovery, a set of neural networks trained by the Monte Carlo generated learning set was used. An approach of fluorescence measurements triggered by simultaneous real-time measurements of blood content in living tissue during moderate changes in contact pressure of the optic probe is proposed. The method allows one to decrease the necessary pressure on the probe as well as increase the repeatability of the measurements. The developed approach was verified in a series of experiments on volunteers with fluorescence excitation at 365 nm and 450 nm. The proposed technology is of particular interest in the development of new fluorescence-based optical biopsy systems

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

Wearable laser Doppler sensors for evaluating the nutritive and shunt blood flow

This study is devoted to the trials of wearable diagnostic system that implements the laser Doppler flowmetry technique to analyse the blood microcirculation. We do preliminary test with involvement of limited group of healthy volunteers of different age and in patients with type 2 diabetes. During the series of measurements, the microcirculation parameters was measured for 10 minutes in the palmar surfaces of the big toes and in the inner sides of the upper thirds of the shins. A statistically significant differences was found in bypass index, nutritive and shunt blood ow in shins between older group of volunteers and patients' group as well as in shunt blood flow in fingers between younger and older groups of volunteers