Forcing reversibility in the no strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons

Because of the base pairing rules in DNA, some mutations experienced by a portion of DNA during its evolution result in the same substitution, as we can only observe differences in coupled nucleotides. Then, in the absence of a bias between the two DNA strands, a model with at most 6 different parameters instead of 12 is sufficient to study the evolutionary relationship between homologous sequences derived from a common ancestor. On the other hand the same symmetry reduces the number of independent observations which can be made. Such a reduction can in some cases invalidate the calculation of the parameters. A compromise between biologically acceptable hypotheses and tractability is introduced and a five parameter reversible no-strand-bias condition (RNSB) is presented. The identifiability of the parameters under this model is shown by examples.Comment: 12 pages, 4 figures, corrected typo

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

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

ЧАСТНЫЕ СЛУЧАИ ОПРЕДЕЛЕНИЯ ПОЛОЖЕНИЯ ТРАНСПОРТНОГО СРЕДСТВА ПЕРЕД НАЧАЛОМ МАНЕВРА

The paper presents an algorithm for determining the position of the vehicle prior to maneuver using the two-axle vehicle standard steering mode and taking into account the structurally determined minimum turning radius. В статье представлен алгоритм определения положения транспортного средства до начала маневра по известной схеме классического поворота двухосного автомобиля и по заложенному конструкцией минимальному радиусу поворота.

ОПРЕДЕЛЕНИЕ УГЛА МЕЖДУ ПРОДОЛЬНЫМИ ОСЯМИ ТРАНСПОРТНЫХ СРЕДСТВ В МОМЕНТ СТОЛКНОВЕНИЯ МЕТОДОМ ГРАФИЧЕСКОГО МОДЕЛИРОВАНИЯ

An algorithm is proposed for determining the angle of relative position of vehicles at the moment of collision, using a graphic modeling method that involves building a damage model. В статье предложен алгоритм определения угла взаимного расположения транспортных средств в момент столкновения методом графического моделирования с построением модели повреждений.

ИСПОЛЬЗОВАНИЕ ГРАФИЧЕСКОГО РЕДАКТОРА СORELDRAW В ТРАНСПОРТНО-ТРАСОЛОГИЧЕСКОЙ ЭКСПЕРТИЗЕ

The author analyzes traces from the scene of a traffic accident using photos obtained from case materials, and transfers them to a dimensional drawing of the damaged vehicle with subsequent characterization of their shape, size and location with the help of graphics editors.Автор анализирует следы на месте ДТП, указанные на фото в материалах дела, переносит их на масштабный чертеж поврежденного автомобиля с последующим определением их формы, размеров и дислокации при помощи графических редакторов

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

Spectral analysis of the blood flow in the foot microvascular bed during thermal testing in patients with diabetes mellitus

Timely diagnostics of microcirculatory system abnormalities, which are the most severe diabetic complications, is one of the major problems facing modern health care. Functional abnormalities manifest themselves earlier than the structural ones, and therefore their assessment is the issue of primary importance. In this study Laser Doppler flowmetry, a noninvasive technique for the cutaneous blood flow monitoring, was utilized together with local temperature tests and wavelet analysis. The study of the blood flow in the microvascular bed of toes was carried out in the control group of 40 healthy subjects and in two groups of 17 type 1 and 23 type 2 diabetic patients. The local temperature tests demonstrated that the diabetic patients have impaired vasodilation in response to local heating. The tendency for impaired low frequency pulsations of the blood flow associated with endothelial and neurogenic activities in both diabetes groups was observed. Local thermal tests induced variations in perfusion and its spectral characteristics, which were different in the groups under study. In our opinion, the obtained preliminary results can be a basis for further research and provide a deeper understanding of pathological processes that drive microvascular abnormalities caused by diabetes mellitus