The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways

Plasmids are mobile genetic elements that play a key role in the evolution of bacteria by mediating genome plasticity and lateral transfer of useful genetic information. Although originally considered to be exclusively circular, linear plasmids have also been identified in certain bacterial phyla, notably the actinomycetes. In some cases, linear plasmids engage with chromosomes in an intricate evolutionary interplay, facilitating the emergence of new genome configurations by transfer and recombination or plasmid integration. Genome sequencing of Streptomyces clavuligerus ATCC 27064, a Gram-positive soil bacterium known for its production of a diverse array of biotechnologically important secondary metabolites, revealed a giant linear plasmid of 1.8 Mb in length. This megaplasmid (pSCL4) is one of the largest plasmids ever identified and the largest linear plasmid to be sequenced. It contains more than 20% of the putative protein-coding genes of the species, but none of these is predicted to be essential for primary metabolism. Instead, the plasmid is densely packed with an exceptionally large number of gene clusters for the potential production of secondary metabolites, including a large number of putative antibiotics, such as staurosporine, moenomycin, β-lactams, and enediynes. Interestingly, cross-regulation occurs between chromosomal and plasmid-encoded genes. Several factors suggest that the megaplasmid came into existence through recombination of a smaller plasmid with the arms of the main chromosome. Phylogenetic analysis indicates that heavy traffic of genetic information between Streptomyces plasmids and chromosomes may facilitate the rapid evolution of secondary metabolite repertoires in these bacteria

The Progeny of Arabidopsis thaliana Plants Exposed to Salt Exhibit Changes in DNA Methylation, Histone Modifications and Gene Expression

Plants are able to acclimate to new growth conditions on a relatively short time-scale. Recently, we showed that the progeny of plants exposed to various abiotic stresses exhibited changes in genome stability, methylation patterns and stress tolerance. Here, we performed a more detailed analysis of methylation patterns in the progeny of Arabidopsis thaliana (Arabidopsis) plants exposed to 25 and 75 mM sodium chloride. We found that the majority of gene promoters exhibiting changes in methylation were hypermethylated, and this group was overrepresented by regulators of the chromatin structure. The analysis of DNA methylation at gene bodies showed that hypermethylation in the progeny of stressed plants was primarily due to changes in the 5′ and 3′ ends as well as in exons rather than introns. All but one hypermethylated gene tested had lower gene expression. The analysis of histone modifications in the promoters and coding sequences showed that hypermethylation and lower gene expression correlated with the enrichment of H3K9me2 and depletion of H3K9ac histones. Thus, our work demonstrated a high degree of correlation between changes in DNA methylation, histone modifications and gene expression in the progeny of salt-stressed plants

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.Peer reviewe

Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood

Peer reviewe

колективна монографія

Кримінальний процесуальний кодекс 2012 року: ідеологія та практика правозастосування: колективна монографія / за заг. ред. Ю. П. Аленіна ; відпов. за вип. І. В. Гловюк. - Одеса : Видавничий дім «Гельветика», 2018. - 1148 с

Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.

In the version of this article initially published, there was a mistake in the calculation of the nucleotide mutation rate per site per generation: 1 × 10−9 mutations per site per generation was used, whereas 9.5 × 10−9 was correct. This error affects the interpretation of population-size changes over time and their possible correspondence with known geological events, as shown in the original Fig. 4 and supporting discussion in the text, as well as details in the Supplementary Note. Neither the data themselves nor any other results are affected. Figure 4 has been revised accordingly. Images of the original and corrected figure panels are shown in the correction notice

Improving a Methodology of Theoretical Determination of the Frame and Directing Forсes in Modern Diesel Trains

The method for determining the directing force was improved, taking into consideration the effect of transverse creep forces and the angle of the directing force inclination to the vertical axis.It was established that when determining the directing force, it is necessary to check the gap between the wheel flange and the rail head which is difficult to realize without computer simulation.When determining the frame force on the axle of the wheel set, a comprehensive approach was adopted taking into account geometric irregularities of the track path, both in vertical and horizontal planes; longitudinal and transverse creep forces at the point of the wheel-rail contact and influence of adjacent wheel sets of the diesel train car.Dependences of the frame and directing forces on speed of the carriage movement and the value of amplitude of the horizontal irregularity of the rail track were obtained. It was established that when moving in the straight section of the track, an increase in speed from 0 m/s to 50 m/s results in a rise in the value of the frame force: up to 8.3 kN for the first wheel set and 19.37 kN for the second wheel set and the directing force up to 31.38 kN for the first wheel set and up to 46.83 kN for the second wheel set. The increase in amplitude of the horizontal irregularity of the track, which is one of the primary causes of occurrence of forced oscillations of the carriage section above the springs also leads to an increase in numerical values of the forces of interaction of the rolling stock with the rail track. All this can bring about an increased power influence of the wheel set on the track and a negative impact on the basic criteria of traffic safety.Influence of the carriage movement speed on the value of transverse creep forces was studied. It has been established that with an increase in the carriage speed from 0 m/s to 50 m/s, these forces grow from 0 to 15.75 kN for the 1st wheel set and from 0 to 29.22 kN for the 2nd wheel set. This indicates impermissibility of neglecting the transverse creep forces when determining the directing force.Comparison of numerical values of the directing force determined by different methodologies was performed. It has been established that the methodology used in conducting forensic examination of railroad accidents may result in underestimation of fulfillment of the derailing condition. At the same time, calculations according to the formula improved in this study give an opportunity to obtain the results most approximate to the real operation conditions.Comparison of the experimental and theoretical calculated values of the frame force acting on the first wheel set of the diesel train car was made and their practical coincidence was shown. Discrepancy of the compared values of the frame force was within 7.2

Studying the Railroad Track Geometry Deterioration as a Result of an Uneven Subsidence of the Ballast Layer

A method for calculating impairment of the track geometry under influence of dynamic loads in the course of passing the track unevenness by the rolling stock was developed. The method takes into consideration interrelated short-term processes of dynamic interaction and long-term processes of subsidence of the ballast layer in a mutual influence on each other. Mathematical model of dynamic interaction of the track in the form of a planar three-layer continual beam system with a two-mass discrete system corresponding to the rolling stock is the basis of the first part of the method. This model makes it possible to simulate dynamic loads from individual sleepers to the ballast when the rolling stock passes geometric unevennesses and the track elasticity unevennesses.The second part of the method is based on the phenomenological mathematical model of accumulation of residual deformations formed using the results of laboratory studies of subsidence of individual sleepers in the ballast layer. Peculiarity of this model consists in taking into consideration not only uniform accumulation of residual subsidence from the passed tonnage but also presence of a plastic component of subsidence which depends on the maximum stresses in the history of ballast loading by each sleeper.A new theoretical mechanism of development of the track unevenness was proposed. It takes into consideration not only residual subsidences of the ballast layer but also appearance of gaps under sleepers resulting in a local change of the track elasticity. This mechanism enables taking into consideration the ambiguous influence of subsidences with occurrence of gaps under the sleepers. Subsidence causes an increase in dynamic loads on the track and the ballast layer on the one hand and onset of the gap causes a decrease in the track rigidity and corresponding reduction of dynamic loads on the other hand.Practical application of the developed method was demonstrated on an example of quantitative estimation of long-term uneven subsidences of the ballast layer when changing the sleeper diagra

Genome-Wide Exon-Capture Approach Identifies Genetic Variants of Norway Spruce Genes Associated With Susceptibility to Heterobasidion parviporum Infection

Root and butt rot caused by members of the Heterobasidion annosum species complex is the most economically important disease of conifer trees in boreal forests. Wood decay in the infected trees dramatically decreases their value and causes considerable losses to forest owners. Trees vary in their susceptibility to Heterobasidion infection, but the genetic determinants underlying the variation in the susceptibility are not well-understood. We performed the identification of Norway spruce genes associated with the resistance to Heterobasidion parviporum infection using genome-wide exon-capture approach. Sixty-four clonal Norway spruce lines were phenotyped, and their responses to H. parviporum inoculation were determined by lesion length measurements. Afterwards, the spruce lines were genotyped by targeted resequencing and identification of genetic variants (SNPs). Genome-wide association analysis identified 10 SNPs located within 8 genes as significantly associated with the larger necrotic lesions in response to H. parviporum inoculation. The genetic variants identified in our analysis are potential marker candidates for future screening programs aiming at the differentiation of disease-susceptible and resistant trees.Peer reviewe

Examining the Current of Drilling Mud in a Power Section of the Screw Down­hole Motor

By using the module Flow Simulation from the programming environment SolidWorks, we obtained parametric fields of turbulent flow of drilling mud in the subject of research – a power section of the screw down-hole motor (SDM). The subject of research is the characteristics of turbulence of the drilling mud flow. An analysis of the obtained model parametric fields of turbulent flow of drilling mud in the power section of SDM shows two distinctive regions that differ by the characteristics of turbulence in the drilling mud current. These sections are localized in the neighborhood of contact points "rotor-stator", and along the distance between these points. In the first section, the developed flow turbulence almost disappears; the dissipation of flow energy significantly decreases. In the second section, there is a developed turbulence of drilling mud, which causes increased dissipation of flow energy and a possible damage to the stator by a solid phase of drilling mud. Vorticity of drilling mud in this region reaches the maximum values of 1,875.7 s-1. Turbulent time scale in the second region reaches the minimum values of 0.001 s, and the metrical scale of pulsations is comparatively small – from 0.011 to 5.666 m, indicating the presence of small-scale turbulent vortices and the elevated dissipation of flow energy. Thus, the second section is the most vulnerable to a damage to the stator by a solid phase of drilling mud.An endoscopic examination of the surface of the SDM stator, which we conducted, revealed damage to its working surface, specifically deep scratches, guide scratches, cavities. Localization of damage is from the middle and to the tail part of the power section at a distance of 2.53−4.78 m from the beginning of the power section of SDM.The models obtained are recommended for using in hydraulic calculations of SDM, for choosing a rational mode of its operatio