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25 pages, 3982 KiB

Open AccessCommunication

PARP3 Affects Nucleosome Compaction Regulation

by Alexander Ukraintsev, Mikhail Kutuzov, Ekaterina Belousova, Marie Joyeau, Victor Golyshev, Alexander Lomzov and Olga Lavrik

Int. J. Mol. Sci. 2023, 24(10), 9042; https://doi.org/10.3390/ijms24109042 - 20 May 2023

Cited by 3 | Viewed by 2043

Abstract

Genome compaction is one of the important subject areas for understanding the mechanisms regulating genes’ expression and DNA replication and repair. The basic unit of DNA compaction in the eukaryotic cell is the nucleosome. The main chromatin proteins responsible for DNA compaction have already been identified, but the regulation of chromatin architecture is still extensively studied. Several authors have shown an interaction of ARTD proteins with nucleosomes and proposed that there are changes in the nucleosomes’ structure as a result. In the ARTD family, only PARP1, PARP2, and PARP3 participate in the DNA damage response. Damaged DNA stimulates activation of these PARPs, which use NAD⁺ as a substrate. DNA repair and chromatin compaction need precise regulation with close coordination between them. In this work, we studied the interactions of these three PARPs with nucleosomes by atomic force microscopy, which is a powerful method allowing for direct measurements of geometric characteristics of single molecules. Using this method, we evaluated perturbations in the structure of single nucleosomes after the binding of a PARP. We demonstrated here that PARP3 significantly alters the geometry of nucleosomes, possibly indicating a new function of PARP3 in chromatin compaction regulation. Full article

(This article belongs to the Special Issue Current Research on Chromatin Structure and Function)

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15 pages, 4148 KiB

Open AccessArticle

Gas-Fueled Binary Energy System with Low-Boiling Working Fluid for Enhanced Power Generation

by Valentin Morenov, Ekaterina Leusheva, Alexander Lavrik, Anna Lavrik and George Buslaev

Energies 2022, 15(7), 2551; https://doi.org/10.3390/en15072551 - 31 Mar 2022

Cited by 10 | Viewed by 2356

Abstract

This article discusses methods of enhanced power generation using a binary power system with low-boiling fluid as an intermediate energy carrier. The binary power system consists of micro-gas and steam power units and is intended for remote standalone power supply. Trifluotrichloroethane was considered as the working agent of the binary cycle. The developed system was modeled by two parts in MATLAB Simulink and Aspen HYSYS. The model in Aspen HYSYS calculates the energy and material balance of the binary energy system. The model in MATLAB Simulink investigates the operation of power electronics in the energy system for quality power generation. The results of the simulation show that the efficiency of power generation in the range of 100 kW in the developed system with micro-turbine power units reaches 50%. Full article

(This article belongs to the Special Issue Recent Progress in Bio-Energy with Carbon Capture and Storage)

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15 pages, 6103 KiB

Open AccessFeature PaperArticle

Ensuring the Sustainability of Arctic Industrial Facilities under Conditions of Global Climate Change

by George Buslaev, Pavel Tsvetkov, Alexander Lavrik, Andrey Kunshin, Elizaveta Loseva and Dmitry Sidorov

Resources 2021, 10(12), 128; https://doi.org/10.3390/resources10120128 - 15 Dec 2021

Cited by 23 | Viewed by 4533

Abstract

Global climate change poses a challenge to the mineral development industry in the Arctic regions. Civil and industrial buildings designed and constructed without consideration of warming factors are beginning to collapse due to changes in the permafrost structure. St. Petersburg Mining University is developing technical and technological solutions for the construction of remote Arctic facilities and a methodology for their design based on physical and mathematical predictive modeling. The article presents the results of modeling the thermal regimes of permafrost soils in conditions of thermal influence of piles and proposes measures that allow a timely response to the loss of bearing capacity of piles. Designing pile foundations following the methodology proposed in the article to reduce the risks from global climate change will ensure the stability of remote Arctic facilities located in the zone of permafrost spreading. Full article

(This article belongs to the Special Issue Resource Provision of the Sustainable Development under Global Shocks)

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19 pages, 2898 KiB

Open AccessArticle

Optimizing the Size of Autonomous Hybrid Microgrids with Regard to Load Shifting

by Alexander Lavrik, Yuri Zhukovskiy and Pavel Tcvetkov

Energies 2021, 14(16), 5059; https://doi.org/10.3390/en14165059 - 17 Aug 2021

Cited by 34 | Viewed by 2811

Abstract

The article proposes a method of multipurpose optimization of the size of an autonomous hybrid energy system consisting of photovoltaic, wind, diesel, and battery energy storage systems, and including a load-shifting system. The classical iterative Gauss–Seidel method was applied to optimize the size of a hybrid energy system in a remote settlement on Sakhalin Island. As a result of the optimization according to the minimum net present value criterion, several optimal configurations corresponding to different component combinations were obtained. Several optimal configurations were also found, subject to a payback period constraint of 5, 6, and 7 years. Optimizing the size of the hybrid power system with electric load shifting showed that the share of the load not covered by renewable energy sources decreases by 1.25% and 2.1%, depending on the parameters of the load shifting model. Net present cost and payback period also decreased, other technical and economic indicators improved; however, CO₂ emissions increased due to the reduction in the energy storage system. Full article

(This article belongs to the Special Issue Planning and Operation of Renewable Energy Systems)

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23 pages, 2545 KiB

Open AccessArticle

Design, Synthesis, and Biological Investigation of Novel Classes of 3-Carene-Derived Potent Inhibitors of TDP1

by Irina V. Il’ina, Nadezhda S. Dyrkheeva, Alexandra L. Zakharenko, Alexander Yu. Sidorenko, Nikolay S. Li-Zhulanov, Dina V. Korchagina, Raina Chand, Daniel M. Ayine-Tora, Arina A. Chepanova, Olga D. Zakharova, Ekaterina S. Ilina, Jóhannes Reynisson, Anastasia A. Malakhova, Sergey P. Medvedev, Suren M. Zakian, Konstantin P. Volcho, Nariman F. Salakhutdinov and Olga I. Lavrik

Molecules 2020, 25(15), 3496; https://doi.org/10.3390/molecules25153496 - 31 Jul 2020

Cited by 29 | Viewed by 4518

Abstract

Two novel structural types of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors with hexahydroisobenzofuran 11 and 3-oxabicyclo [3.3.1]nonane 12 scaffolds were discovered. These monoterpene-derived compounds were synthesized through preliminary isomerization of (+)-3-carene to (+)-2-carene followed by reaction with heteroaromatic aldehydes. All the compounds inhibit the TDP1 enzyme at micro- and submicromolar levels, with the most potent compound having an IC₅₀ value of 0.65 μM. TDP1 is an important DNA repair enzyme and a promising target for the development of new chemosensitizing agents. A panel of isogenic clones of the HEK293FT cell line knockout for the TDP1 gene was created using the CRISPR-Cas9 system. Cytotoxic effects of topotecan (Tpc) and non-cytotoxic compounds of the new structures were investigated separately and jointly in the TDP1 gene knockout cells. For two TDP1 inhibitors, 11h and 12k, a synergistic effect was observed with Tpc in the HEK293FT cells but was not found in TDP1 −/− cells. Thus, it is likely that the synergistic effect is caused by inhibition of TDP1. Synergy was also found for 11h in other cancer cell lines. Thus, sensitizing cancer cells using a non-cytotoxic drug can enhance the efficacy of currently used pharmaceuticals and, concomitantly, reduce toxic side effects. Full article

(This article belongs to the Special Issue Advances in Anticancer Drug Discovery)

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10 pages, 2864 KiB

Open AccessArticle

Upgrading the Baryonic Matter at the Nuclotron Experiment at NICA for Studies of Dense Nuclear Matter

by Peter Senger, Dmitrii Dementev, Johann Heuser, Mikhail Kapishin, Evgeny Lavrik, Yuri Murin, Anna Maksymchuk, Hans Rudolf Schmidt, Christian Schmidt, Anna Senger and Alexander Zinchenko

Particles 2019, 2(4), 481-490; https://doi.org/10.3390/particles2040029 - 15 Nov 2019

Cited by 22 | Viewed by 3537

Abstract

The Nuclotron at the Joint Institute for Nuclear Research in Dubna can deliver gold beams with kinetic energies between 2 and 4.5 A GeV. In heavy-ion collisions at these energies, it is expected that the nuclear fireball will be compressed by up to approximately four times the saturation density. This offers the opportunity to study the high-density equation-of-state (EOS) of nuclear matter in the laboratory, which is needed for our understanding of the structure of neutron stars and the dynamics of neutron star mergers. The Baryonic Matter at the Nuclotron (BM@N) experiment will be upgraded to perform multi-differential measurements of hadrons including (multi-) strange hyperons, which are promising probes of the high-density EOS, and of new phases of quantum chromodynamic (QCD) matter. The layout of the upgraded BM@N experiment and the results of feasibility studies are presented. Full article

(This article belongs to the Special Issue Relativistic and Ultrarelativistic Nuclear Collisions: Dynamics and Phase Transitions)

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