Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction

Background Chlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria. Results We report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system. Conclusions This combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity

High rates of genome rearrangements and pathogenicity of Shigella spp.

Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands

РАЗРАБОТКА И ВНЕДРЕНИЕ КОМПЬЮТЕРНЫХ СРЕДСТВ ОБУЧЕНИЯ В УЧЕБНЫЙ ПРОЦЕСС ФИЗИЧЕСКОГО ВОСПИТАНИЯ В ВУЗЕ

The article deals with the innovative activity of the physical education and sport departmentin the computer technology application in the educational process of physical education.Internet provides an overview of educational materials on physical training for universitystudents. Relevance of the study is confirmed with the strategic direction of the project«MESI - smart-University». The article purpose is to identify opportunities for e-learning in physical education, summarize the experience of using computer resources in physicaleducation and get an idea of the electronic content on physical culture for students. The results of the study may be useful for the organization of open, distance, electronic learningin physical culture, as well as the creation of electronic teaching materials and courses inthe discipline, in particular e-learning course «Physical training» for students of economics.Встатьераскрытаинновационнаядеятельностькафедрыфизическоговоспитания и спорта в области применения компьютерных технологий в учебном процессе физического воспитания. Содержится Интернет-обзор учебных материалов по физическойкультуредлястудентоввузов. Актуальностьисследованияподтверждается стратегическим направлением развития проекта «МЭСИ - smart-университет». Цельработы- выявитьвозможностиэлектронногообучениявобластифизического воспитания, обобщить опыт применения компьютерных средств в физкультурном образовании, получить представление об электронном контенте по физической культуре для студентов вузов. Результаты исследования могут быть полезны при организации открытого, дистанционного, электронного обучения по физической культуре, а также при создании электронных учебно-методических материалов и курсов по дисциплине, в частности электронного курса «Физическая культура» для студентов экономических специальностей

Essential functions of the 32 kDa subunit of yeast replication protein A

Replication protein A (RPA) is a heterotrimeric (70, 32 and 14 kDa subunits), single-stranded DNA-binding protein required for cellular DNA metabolism. All subunits of RPA are essential for life, but the specific functions of the 32 and 14 kDa subunits remains unknown. The 32 kDa subunit (RPA2) has multiple domains, but only the central DNA-binding domain (called DBD D) is essential for life in Saccharomyces cerevisiae. To define the essential function(s) of RPA2 in S. cerevisiae, a series of site-directed mutant forms of DBD D were generated. These mutant constructs were then characterized in vitro and in vivo. The mutations had minimal effects on the overall structure and activity of the RPA complex. However, several mutants were shown to disrupt crosslinking of RPA2 to DNA and to dramatically lower the DNA-binding affinity of a RPA2-containing subcomplex. When introduced into S. cerevisiae, all DBD D mutants were viable and supported normal growth rates and DNA replication. These findings indicate that RPA2–DNA interactions are not essential for viability and growth in S. cerevisiae. We conclude that DNA-binding activity of RPA2 is dispensable in yeast and that the essential function of DBD D is intra- and/or inter-protein interactions

Erot spatiaalisissa ja ajallisissa reaktionormeissa kevään ja syksyn fenologisille tapahtumille

For species to stay temporally tuned to their environment, they use cues such as the accumulation of degree-days. The relationships between the timing of a phenological event in a population and its environmental cue can be described by a population-level reaction norm. Variation in reaction norms along environmental gradients may either intensify the envi- ronmental effects on timing (cogradient variation) or attenu- ate the effects (countergradient variation). To resolve spatial and seasonal variation in species’ response, we use a unique dataset of 91 taxa and 178 phenological events observed across a network of 472 monitoring sites, spread across the nations of the former Soviet Union. We show that compared to local rates of advancement of phenological events with the advancement of temperature-related cues (i.e., variation within site over years), spatial variation in reaction normsPeer reviewe

Localization of xeroderma pigmentosum group A protein and replication protein A on damaged DNA in nucleotide excision repair

The interaction of xeroderma pigmentosum group A protein (XPA) and replication protein A (RPA) with damaged DNA in nucleotide excision repair (NER) was studied using model dsDNA and bubble-DNA structure with 5-{3-[6-(carboxyamido-fluoresceinyl)amidocapromoyl]allyl}-dUMP lesions in one strand and containing photoreactive 5-iodo-dUMP residues in defined positions. Interactions of XPA and RPA with damaged and undamaged DNA strands were investigated by DNA–protein photocrosslinking and gel shift analysis. XPA showed two maximums of crosslinking intensities located on the 5′-side from a lesion. RPA mainly localized on undamaged strand of damaged DNA duplex and damaged bubble-DNA structure. These results presented for the first time the direct evidence for the localization of XPA in the 5′-side of the lesion and suggested the key role of XPA orientation in conjunction with RPA binding to undamaged strand for the positioning of the NER preincision complex. The findings supported the mechanism of loading of the heterodimer consisting of excision repair cross-complementing group 1 and xeroderma pigmentosum group F proteins by XPA on the 5′-side from the lesion before damaged strand incision. Importantly, the proper orientation of XPA and RPA in the stage of preincision was achieved in the absence of TFIIH and XPG

Phenological shifts of abiotic events, producers and consumers across a continent

Ongoing climate change can shift organism phenology in ways that vary depending on species, habitats and climate factors studied. To probe for large-scale patterns in associated phenological change, we use 70,709 observations from six decades of systematic monitoring across the former Union of Soviet Socialist Republics. Among 110 phenological events related to plants, birds, insects, amphibians and fungi, we find a mosaic of change, defying simple predictions of earlier springs, later autumns and stronger changes at higher latitudes and elevations. Site mean temperature emerged as a strong predictor of local phenology, but the magnitude and direction of change varied with trophic level and the relative timing of an event. Beyond temperature-associated variation, we uncover high variation among both sites and years, with some sites being characterized by disproportionately long seasons and others by short ones. Our findings emphasize concerns regarding ecosystem integrity and highlight the difficulty of predicting climate change outcomes. The authors use systematic monitoring across the former USSR to investigate phenological changes across taxa. The long-term mean temperature of a site emerged as a strong predictor of phenological change, with further imprints of trophic level, event timing, site, year and biotic interactions.Peer reviewe

Chronicles of nature calendar, a long-term and large-scale multitaxon database on phenology

We present an extensive, large-scale, long-term and multitaxon database on phenological and climatic variation, involving 506,186 observation dates acquired in 471 localities in Russian Federation, Ukraine, Uzbekistan, Belarus and Kyrgyzstan. The data cover the period 1890-2018, with 96% of the data being from 1960 onwards. The database is rich in plants, birds and climatic events, but also includes insects, amphibians, reptiles and fungi. The database includes multiple events per species, such as the onset days of leaf unfolding and leaf fall for plants, and the days for first spring and last autumn occurrences for birds. The data were acquired using standardized methods by permanent staff of national parks and nature reserves (87% of the data) and members of a phenological observation network (13% of the data). The database is valuable for exploring how species respond in their phenology to climate change. Large-scale analyses of spatial variation in phenological response can help to better predict the consequences of species and community responses to climate change.Peer reviewe

Du Šekspyro įvaizdžiai Anthony Burgesso romane „Niekas neprilygsta saulei“ ir Jurijaus Dombrovskio apsakymuose

The purpose of the article is to compare images of Shakespeare in the novel “Nothing like the Sun. A Story of Shakespeare’s Love Life” (1964) by the English writer Anthony Burgess and in the stories “The Dark Lady”, “The Second Quality Bed” and “The Royal Rescript” (1969) by the Russian writer Jurij Dombrovskij. Distinctions of the images are explained, first of all, by the different literary tradition and poetics of realism and modernism accordingly. Similarities speak of the commonality of the tendencies in the European historical and literary process of the 20th century, and also of the creative biography of writers, their aversion of totalitarianism and aspiration to create an image of a free person. The fundamental complexity is to create the image of the historic figure in general and Shakespeare in particular. It is as though shrouded by the foggy veil through which we can rather see the features of Burgess and Dombrovskij themselves than of the Stratford playwright that remains a riddle for readers.Šio straipsnio tikslas – palyginti Šekspyro įvaizdžius anglų autoriaus Anthony Burgesso romane „Niekas neprilygsta saulei. Šekspyro meilės gyvenimo istorija“ (1964) ir rusų rašytojo Jurijaus Dombrovskio apsakymuose „Tamsioji dama“, „Antroji geroji lova“ ir „Karališkas atsakas“ (1969). Įvaizdžių skirtumai pirmiausia aiškinami skirtingomis literatūrinėmis tradicijomis ir realizmo bei modernizmo poetikos bruožais. Panašumai atskleidžia XX a. Europos istorinių ir literatūrinių procesų bendruosius bruožus bei abiejų autorių kūrybinių biografijų panašumus, jų bjaurėjimąsi totalitarizmu ir siekį sukurti laisvo asmens įvaizdį. Užduoties sudėtingumas glūdi istorinio asmens įvaizdžio, o ypač Šekspyro įvaizdžio, kūrime. Jis tarsi pridengtas miglos skraiste, per kurią veikiau įžvelgiame pačių Burgesso ir Dombrovskio portretus, o ne dramaturgo iš Stratfordo – taip ir liekančio skaitytojui neįminta mįsle

Antimutagenic activity of probiotic drugs on the example of Drosophila

Probiotic preparations were obtained on the basis of cryopreserved forms of pure cultures of L. plantarum and B. subtilis using freeze drying. The antimutagenic activity of the obtained probiotic preparations was investigated in relation to 1%, 0.1% and 0.01% concentrations of cobalt sulfate using the example of dominant lethal mutations of Drosophila. A positive antimutagenic effect of probiotic preparations was shown in relation to 0.1% and 0.01% concentrations of CoSO4 with an exposure duration of at least 3 days