Lys98 Substitution in Human AP Endonuclease 1 Affects the Kinetic Mechanism of Enzyme Action in Base Excision and Nucleotide Incision Repair Pathways

Human apurinic/apyrimidinic endonuclease 1 (APE1) is a key enzyme in the base excision repair (BER) and nucleotide incision repair (NIR) pathways. We recently analyzed the conformational dynamics and kinetic mechanism of wild-type (wt) protein, in a stopped-flow fluorescence study. In this study, we investigated the mutant enzyme APE1K98A using the same approach. Lys98 was known to hydrogen bond to the carboxyl group of Asp70, a residue implicated in binding the divalent metal ion. Our data suggested that the conformational selection and induced fit occur during the enzyme action. We expanded upon the evidence that APE1 can pre-exist in two conformations. The isomerization of an enzyme-product complex in the BER process and the additional isomerization stage of enzyme-substrate complex in the NIR process were established for APE1K98A. These stages had not been registered for the wtAPE1. We found that the K98A substitution resulted in a 12-fold reduction of catalytic constant of 5′-phosphodiester bond hydrolysis in (3-hydroxytetrahydrofuran-2-yl)methyl phosphate (F, tetrahydrofuran) containing substrate, and in 200-fold reduction in 5,6-dihydrouridine (DHU) containing substrate. Thus, the K98A substitution influenced NIR more than BER. We demonstrated that the K98A mutation influenced the formation of primary unspecific enzyme-substrate complex in a complicated manner, depending on the Mg2+ concentration and pH. This mutation obstructed the induced fit of enzyme in the complex with undamaged DNA and F-containing DNA and appreciably decreased the stability of primary complex upon interaction of enzyme with DNA, containing the natural apurinic/apyrimidinic (AP) site. Furthermore, it significantly delayed the activation of the less active form of enzyme during NIR and slowed down the conformational conversion of the complex of enzyme with the cleavage product of DHU-substrate. Our data revealed that APE1 uses the same active site to catalyze the cleavage of DHU- and AP-substrates

Biodegradation Potential of SteccherinumOchraceum: Growth on Different Wood Types and Preliminary Evaluation of Enzymatic Activities

White-rot fungi isa source of a great variety of oxidative and hydrolytic enzymes suitable for biotechnological applications, e.g. in pulp and paper, textile and food industries, bioethanol production, degradation of recalcitrant environmental pollutants,and others. Steccherinumochraceum is a xylotrophicwhite-rot basidiomycetethat can be found in variousclimatic zones on different woody substrates (mostly well decayed). For this research, seventeenstrains of S. ochraceumwere collected in different regions of Russia from various wood substrates (aspen, alder, oak, hazel, birch and willow). Phylogeneticanalyseswere performedbasedon the nucleotide sequences of ITS1, ITS2, 5.8S rRNA, 28S rRNA, β-tubulin and tef1.Oxidaseandcellulaseactivitieswereassessedbyplate-tests with ABTS and CMC. Forevaluation of biodegradation potential,solid state fermentation on alder and pine sawdust wasperformed. Weightanddensitylossaswellas the C:Nratioweremeasuredafter 90 days of cultivation.All S. ochraceum strains exhibited high oxidative activity towards ABTS, indicating secretion of oxidative enzymes (i.e. laccases and class II peroxidases). Cellulase activity was medium or low for most strains and in some strains – absent. Allstrainswereabletodegradealderandpinesawdust. There was no correlation between the enzymatic activity, biodegradation potential and geographic origin of S. ochraceum strains. However, S. ochraceum strains isolated from the same wood substrates exhibited similar characteristics in most cases. Strain LE-BIN 3398 was the most effective for degrading both alder and pine sawdust and could be regarded as a promising source of oxidative enzymes for biotechnology. Keywords: basidiomycetes, biodegradation, solid state fermentation, oxidase activity, Steccherinumochraceu

Evaluation of rate of pathological changes in parenchymal organs for embryo of caspian seal <i>Phoca caspica</i> in modern conditions of the ecosystem in the Caspian Sea

Pathological changes of the caspian seal fetus caused by negative processes in the mother’s organism under influence of disease and harmful environments are investigated. For that, parenchymal organs of the fetus are examined by histological methods. Active replacement of the fetus’ tissues by conjunctive tissue is detected in all organs, the most profound abnormalities are registered in the kidney and live

Determination of the physico-mechanical properties of the protective oxide scale by nano-indentation

Nano-indentation test was used to determine the hardness and the Young’s modulus of the thermally grown oxide formed during the high temperature (1100°C) isothermal oxidation of single crystal Ni-based superalloy. Multiple nano-indentation tests at different loads were performed on the polished cross-section and on the surface of oxide scale. The measured values of Young's modulus were E IT = 320 GPa, and E IT = 256 GPa using the cross-section indentation and the indentation normal to the surface of oxide scale correspondently. The effect of applied load on the measured values was observed. The measured values of Young's modulus were used to determine the values of the work of adhesion of metal/oxide interface

Forms of International Cooperation in Environmental Education: the Experience of Saint Petersburg State University

The authors analyse different forms of environmental education projects and programmes implemented in the Baltic Sea region. The first one is "The Baltic University" programme taught in English. The "Baltic University" is a network of more than 200 universities from 14 counties of the Baltic Sea region. This education programme offers an opportunity for students to enroll on bachelor and master degree programmes related to environmental and social problems of the Baltic Sea region. The Polar and Marine Sciences, POMOR master programme, represents the second form of international environmental education. Russian and German researchers from six universities and four research centres have developed the programme. The target group of the programme are Russian and international students, studying together during the whole duration of the programme. It is the first internationally accredited MA programme taught in English. International accreditation proves the compliance of the programme with international education standards. The same cooperation model is used in a new international master programme - Cold Regions Environmental Landscapes Integrated Science (CORELIS). The programme started in 2016. It is implemented jointly by Hamburg university (the lead partner of the project), and university professors from Helsinki (Finland) and Lisbon (Portugal). Researchers from the Austrian National Institute of Polar Research (Austria, and Lund University (Sweden) will join the programme at a later stage. Such an approach will help achieve the synergy of the European and Russian approaches to environmental education. The Russian-Norwegian master programme "Geoecological monitoring and rational use of natural resources in the Northern oil and gas production regions" is a good example of the third form of international environmental education. The programme similar to POMOR and CORELIS. However, it has one distinctive feature - Russian and foreign students study together from the second term only. The authors describe the ways of achieving the learning objectives of these master programmes depending on the students' language skills and their basic knowledge of ecology and nature management

Genetic structure of the protist Physarum albescens (Amoebozoa) revealed by multiple markers and genotyping by sequencing

Myxomycetes are terrestrial protists with many presumably cosmopolitan species dispersing via airborne spores. A truly cosmopolitan species would suffer from outbreeding depression hampering local adaptation, while locally adapted species with limited distribution would be at a higher risk of extinction in changing environments. Here, we investigate intraspecific genetic diversity and phylogeography of Physarum albescens over the entire Northern Hemisphere. We sequenced 324 field collections of fruit bodies for 1-3 genetic markers (SSU, EF1A, COI) and analysed 98 specimens with genotyping by sequencing. The structure of the three-gene phylogeny, SNP-based phylogeny, phylogenetic networks, and the observed recombination pattern of three independently inherited gene markers can be best explained by the presence of at least 18 reproductively isolated groups, which can be seen as cryptic species. In all intensively sampled regions and in many localities, members of several phylogroups coexisted. Some phylogroups were found to be abundant in only one region and completely absent in other well-studied regions, and thus may represent regional endemics. Our results demonstrate that the widely distributed myxomycete species Ph. albescens represents a complex of at least 18 cryptic species, and some of these seem to have a limited geographical distribution. In addition, the presence of groups of presumably clonal specimens suggests that sexual and asexual reproduction coexist in natural populations of myxomycetes

Редкий случай верхушечной формы гипертрофической кардиомиопатии с внутрижелудочковой обструкцией у ребенка

Hypertrophic cardiomyopathy is characterized by primary hypertrophy of myocardium without another cause such as arterial hypertension. We present a rare case of apical hypertrophic cardiomyopathy in 7-year-old girl with minimal nonspecific clinical manifestation (headache after loading). At planned examination typically ECG changes - pronounced repolarization changes and deep (about 10 mm) inverted T waves in precordial leads - were discovered. Transthoracic echocardiography detected local symmetric hypertrophy of left ventricular apex with reduced contractility of this area and intraventricular obstruction with pressure gradient between apical and middle parts of left ventricle 30 mm Hg. This findings were confirmed by ventriculograhy and myocardial scintigraphy. Cardiac magnetic resonance imaging determined marked fibrotic transformation of left ventricular apex. The features of this case are: the young age of the patient and combination of apical hypertrophy with intraventricular obstruction.Гипертрофическая кардиомиопатия характеризуется первичной гипертрофией миокарда при отсутствии других причин этого, в частности артериальной гипертензии. Представлен редкий случай верхушечной гипертрофической кардиомиопатии у девочки 7 лет с минимальными неспецифическими клиническими проявлениями (головные боли, провоцируемые нагрузками). При плановом обследовании были обнаружены типичные изменения на ЭКГ - выраженные нарушения реполяризации миокарда и глубокие (до 10 мм) отрицательные зубцы Т в грудных отведениях. Трансторакальная эхокардиография выявила локальную симметричную гипертрофию верхушечных отделов левого желудочка с нарушением их сократимости и внутрижелудочковую обструкцию с градиентом давления между верхушечным и средним отделами 30 мм рт.ст., что было подтверждено данными вентрикулографии и сцинтиграфии миокарда. МРТ сердца позволила установить наличие выраженной фиброзной трансформации верхушки левого желудочка. Особенностью данного случая являются детский возраст пациентки и сочетание верхушечной гипертрофии миокарда с внутрижелудочковой обструкцией

Problems of industrial development and transport infrastructure of the Republic of Sakha (Yakutia)

Industry of the Republic of Sakha (Yakutia) is mainly represented by the activity of enterprises in mining. In recent years, in the country there was an intensive growth of investments related to the extraction of diamonds, gold, oil and gas. The newly created businesses use the existing transport infrastructure, created in the process of development of traditional diamond-clusters, and coal-gold. There were no significant changes occur in the transport infrastructure