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Molecular Biology 2025年第1期59卷 17-25页

作者： Aristova, E.O. Volkhin, I.A. Denisova, A.A. Nikitin, P.A. Petrukhin, E.R. Faculty of Bioengineering and Bioinformatics Moscow State University Moscow 119234 Russian Federation Life Sciences Research Center Moscow Institute of Physics and Technology (National Research University) Moscow oblast Dolgoprudny 141700 Russian Federation Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow 119071 Russian Federation

Abstract: According to classic ideas, new genes emerge from old genes by duplication or horizontal transfer. Analyses of a large number of genomes in recent decades have shown that some genes have no visible homologs and have presumably emerged de novo from previously noncoding sequences. The review considers possible mechanisms of de novo gene formation, the properties of protein sequences encoded by such genes, and features of their expression and selection. The problem of identification of de novo arising gene is discussed separately. © Pleiades Publishing, Ltd. 2025.

关键词： de novo gene orphan gene pervasive transcription pervasive translation

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Making Synchrosqueezing Locally Adaptive in The Time-Frequency Plane

Making Synchrosqueezing Locally Adaptive in The Time-Frequen...

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International Conference on Acoustics, Speech, and Signal Processing (ICASSP)

作者： Marcelo A. Colominas Sylvain Meignen Universidad Nacional de Entre Ríos (UNER) Faculty of Engineering Institute for Research and Development in Bioengineering and Bioinformatics (IBB) CONICET Argentina Jean Kuntzmann Laboratory University Grenoble Alpes and CNRS France

In this work, we explore the problem of making synchrosqueezing transform adaptive. To deal with multicomponent signals, existing methods use a fixed order N, thus assuming all the modes making up the signal have order N polynomial phases. To go beyond this limitation, we introduce a new criterion based on the concentration of the representation to locally choose the best order for the synchrosqueezing transform. We study the performance of the proposed approach in terms of the error with respect to the ideal time-frequency representation, both on synthetic and real signals.

关键词： Greedy algorithms Time-frequency analysis Transforms Signal processing Acoustics Proposals Speech processing

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Osteogenic activity of bone: Novel approach of polyvinylidene fluoride films, marrow blood supply, and ultrasound stimulation

SPE Polymers

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SPE Polymers 2023年第4期4卷 175-185页

作者： Zuchuat, Jésica Halter, Christian Zalazar, Martín Faculty of Engineering National University of Entre Ríos Entre Ríos Argentina Institute for Research and Development in Bioengineering and Bioinformatics UNER – CONICET Entre Ríos Argentina

Electric fields used in bone stimulation are based on the application of direct current, but some drawbacks exist, such as the need for an external power source. Piezoelectric poly(vinylidene fluoride) (PVDF) has attracted interest for biomedical applications due to its flexibility, low toxicity, and the piezoelectric response to mechanical stimuli. This study aimed to investigate the effects of PVDF films on bone regeneration in rabbit tibias to assess the potential improvement in osteogenesis. An initial exploratory experiment was performed to determine optimal parameters for regulating the marrow blood supply. The second experiment focused on examining the effects of ultrasound stimulation on the implant's osteogenic capacity. The results showed that PVDF films have a notable impact on the extraskeletal bone formation and bone density in a secluded microenvironment with and without microperforations. At 60 days after surgery, tibias with marrow blood supply reached higher bone volumes and density and they were consistent with the cellular activity. Our results suggest that piezoelectric PVDF films have osteogenic characteristics and can be used to enhance new bone formation in a secluded space, thus reinforcing their biocompatibility nature. Additional studies are required to analyze the benefits of ultrasound stimulation. © 2023 The Authors. SPE Polymers published by Wiley Periodicals LLC on behalf of Society of Plastics Engineers.

关键词： bone tissue engineering osteogenesis piezoelectric polyvinylidene fluoride ultrasound

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Using DNA-logging to determine inflow profile in horizontal wells

Using DNA-logging to determine inflow profile in horizontal ...

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SPE Russian Petroleum Technology Conference 2021, RPTC 2021

作者： Posdyshev, Arsenii Stanislavovich Shelyakin, Pavel Vladimirovich Shaikhutdinov, Nurislam Maratovich Popov, Aleksey Alekseevich Logacheva, Maria Dmitrievna Tutukina, Maria Nikolaevna Gelfand, Mikhail Sergeevich Skoltech Center for Hydrocarbon Recovery Russia Genomics of Adaptive Immunity Department Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Russia Skoltech Center of Life Sciences Russia MSU Faculty of Bioengineering and Bioinformatics Russia

ISBN: (纸本)9781613998304

The purpose of this work is to adapt and apply Next Generation Sequencing methods in oil and gas well field studies. Relatively recent NGS methods provide a description of a geological formation by analyzing millions of DNA sequences and represent an entirely new way to obtain information about oil and gas reservoirs and the composition of their fluids, which could significantly change the approach to exploration and field development. We present the results of pilot work to determine the inflow profile in a horizontal well based on DNA markers. The technology is based on the comparison of bacterial DNA from drill cuttings obtained while drilling with DNA from microorganisms of fluids obtained during production at the wellhead. Because of their high selectivity, individual microbes live only under certain conditions (salinity, oil saturation, temperature) and can be used as unique natural biomarkers. The comparison of DNA samples of drilling cutting and produced fluid allows for identification of the segment of the horizontal well from which the main flow comes, as well as identifying the type of incoming fluid (water, oil, gas) without stopping the operation process and without conducting expensive downhole operations. As a result of these studies, the microbial communities of the oil-bearing sands and formation fluids of the Cretaceous deposits (group BS) in Western Siberia were identified, and the relative numerical ratio of microorganisms in the formations was determined. It was shown that the microbiome diversity changes with depth, and depends on the lithological composition, and sequencing data obtained from cuttings samples correlate with data from wellhead samples of produced fluid. Thus, the practical applicability of DNA sequencing for solving field problems in oil and gas field development, in particular for determining the inflow profile in horizontal wells, was confirmed. Copyright 2021, Society of Petroleum Engineers.

关键词： Horizontal wells

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Exploiting Structural Constraints of Proteolytic Catalytic Triads for Fast Supercomputer Scaffold Probing in Enzyme Design Studies 7th

Exploiting Structural Constraints of Proteolytic Catalytic T...

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7th Russian Supercomputing Days Conference, RuSCDays 2021

作者： Zlobin, Alexander Ermidis, Alexander-Pavel Maslova, Valentina Belyaeva, Julia Golovin, Andrey Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Moscow117997 Russia Sirius University of Science and Technology Sochi354340 Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow119991 Russia

ISBN: (纸本)9783030928636

Evolutionary constraints on the effectiveness of enzymatic function result in well-defined architectures of active sites. In this study we show that these constraints are fully pronounced even at the backbone level. We explore the possibility of defining catalytic triads in proteases just by their relative backbone orientations to dramatically speed up the scaffold search problem of de novo enzyme design. An order of magnitude speed-up achieved this way paves a way to a routine scanning of the whole structural proteome including modeled structures. © 2021, Springer Nature Switzerland AG.

关键词： Enzymes

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Impact of phytoconstituents on oral health practices:a post COVID-19 observation

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Food Science and Human Wellness 2024年第5期13卷 2386-2400页

作者： Harsh Kumar Reena Singh Daljeet Singh Dhanjal Chirag Chopra Natália Cruz-Martins Gheyath K.Nasrallah Amin F.Majdalawieh Sivakumar Manickam Shahida Anusha Siddiqui Dinesh Kumar Indu Sharma Varun Sharma School of Bioengineering&Food Technology Shoolini University of Biotechnology and Management SciencesSolan 173229India School of Bioengineering and Biosciences Lovely Professional UniversityPunjab 144402India Faculty of Medicine University of PortoPorto 4200-319Portugal Institute for Research and Innovation in Health(i3S) University of PortoPorto 4200-135Portugal Institute of Research and Advanced Training in Health Sciences and Technologies(CESPU) RuaCentral de GandraGandra 4585-116Portugal TOXRUN-Toxicology Research Unit University Institute of Health SciencesCESPUCRLGandra 4585-116Portugal Biomedical Research Center Qatar UniversityDoha 2713Qatar Department of Biomedical Science College of Health SciencesQatar UniversityDoha 2713Qatar Department of Biology Chemistryand Environmental SciencesCollege of Arts and SciencesAmerican University of SharjahSharjah 26666United Arab Emirates Petroleum and Chemical Engineering Faculty of EngineeringUniversiti Teknologi BruneiBandar Seri Begawan BE1410Brunei Campus Straubing for Biotechnology and Sustainability Technical University of MunichStraubing 94315Germany Genetic Heritage Group New York UniversityAbu Dhabi 129188United Arab Emirates Bioinformatics Division NMC Genetics India Pvt.Ltd.Gurugram 122001India

Appropriate oral hygiene significantly reduces the possibility of oral ***,dental caries and periodontal diseases are major oral health issues causing chronic diseases due to poor oral ***,herbal compounds have gained interest in maintaining oral *** of burdock root(Arctium),noni fruit(Morinda citrifolia),and neem leaf(Azadirachta indica)are now used as intracanal medicaments in endodontics and *** amboinicus species and other plants produces essential oil likeβ-caryophyllene,p-cymene,andγ-terpinene can exhibit antibacterial activity;highlighting phytoconstituents plays a vital role in oral *** COVID-19 pandemic highlighted the importance of hygiene and sanitization,to curb *** cavity is among the gateways for virus entry into *** is a potential reservoir of SARS-CoV-2,and there is an increased risk of infection if there is any fissure in the *** enables entry of virus into the vascular system through gingival or periodontal pocket,possibly reaching lung periphery then to lung vessels by interacting with endothelial surface receptors triggering pulmonary vasoconstriction and lung damage due to endothelial *** review aims to draw attention to the possible route of SARS-CoV-2 infection via the oral cavity and the importance of oral hygiene against COVID-19.

关键词： COVID-19 SARS-CoV-2 Oral Hygiene Microbiota Phytochemicals

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Molecular Modeling of Penicillin Acylase Binding with a Penicillin Nucleus by High Performance Computing: Can Enzyme or its Mutants Possess β-lactamase Activity?

Supercomputing Frontiers and Innovations

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Supercomputing Frontiers and Innovations 2022年第2期9卷 68-78页

作者： Kirilin, Evgeny M. Bochkova, Anna A. Panin, Nikolay V. Pochinok, Igor V. Švedas, Vytas Lomonosov Moscow State University Belozersky Institute of Physicochemical Biology Moscow Russia Lomonosov Moscow State University Research Computing Center Moscow Russia Lomonosov Moscow State University Faculty of Bioengineering and Bioinformatics Moscow Russia

High-performance computing has been used for molecular modeling of penicillin acylase interaction with a penicillin nucleus 6-aminopenicillanic acid (6-APA) to assess whether the wild-type enzyme or its mutants could possess β-lactamase activity. Applying parallel hybrid GPU/CPU computing technologies for metadynamics calculations with the PLUMED library in conjunction with AMBER software suite it has been shown that trace amounts of wild-type penicillin acylas-e6-APA complexes leading to a β-lactamase reaction can be formed. Higher β-lactamase activity can be observed in enzyme mutants by introducing charged residue in the substrate binding pocket and its proper positioning with respect to a catalytic nucleophile, including stabilization of the tetrahedral intermediate in the oxyanion hole. Thus, it has been shown that the certain mutations facilitate the orientation of the substrate required for the manifestation of β-lactamase activity in the penicillin acylase active center. © The Authors 2022. This paper is published with open access at ***

关键词： Molecular modeling

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RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome (vol 2023 baad025, 2023)

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DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2023年第2023期2023卷 baad025页

作者： Ryabykh, G. K. Kuznetsov, S., V Korostelev, Y. D. Sigorskikh, A., I Zharikova, A. A. Mironov Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Leninskiye Gory Moscow 119234 Russia Kharkevich Institute for Information Transmission Problems RAS Bolshoy Karetny per. Moscow 127051 Russia National Medical Research Center for Therapy and Preventive Medicine Petroverigsky per. Moscow 101000 Russia

Every year there is more and more evidence that non-coding RNAs play an important role in biological processes affecting various levels of organization of living systems: from the cellular (regulation of gene expression, remodeling and maintenance of chromatin structure, co-transcriptional suppression of transposons, splicing, post-transcriptional RNA modifications, etc.) to cell populations and even organismal ones (development, aging, cancer, cardiovascular and many other diseases). The development and creation of mutually complementary databases that will aggregate, unify and structure different types of data can help to reach the system level of studying non-coding RNAs. Here we present the RNA-Chrom manually curated analytical database, which contains the coordinates of billions of contacts of thousands of human and mouse RNAs with chromatin. Through the user-friendly web interface (https://***/), two approaches to the analysis of the RNA–chromatin interactome were implemented. Firstly, to find out whether the RNA of interest to a user contacts with chromatin, and if so, with which genes or DNA loci? Secondly, to find out which RNAs are in contact with the DNA locus of interest to a user (and probably participate in its regulation), and if there are such, what is the nature of their interaction? For a more detailed study of contact maps and their comparison with other data, the web interface allows a user to view them in the UCSC Genome *** URLhttps://***/

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Limits on inferring gene regulatory networks from single-cell measurements of unstable mRNA levels

Limits on inferring gene regulatory networks from single-cel...

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IEEE Conference on Decision and Control

作者： Tarun Mahajan Michael Saint-Antoine Roy D. Dar Abhyudai Singh Department of Bioengineering University of Illinois at Urbana-Champaign Urbana IL USA Center for Bioinformatics and Computational Biology University of Delaware Newark DE USA Faculty of Department of Bioengineering University of Illinois at Urbana-Champaign Urbana IL USA Faculty of Electrical and Computer Engineering Biomedical Engineering and Mathematical Sciences University of Delaware Newark DE USA

ISBN: (数字)9781665467612

ISBN: (纸本)9781665467629

Gene regulatory network inference from single-cell expression data, such as single-cell RNA sequencing, is a popular problem in computational biology. Despite diverse methods spanning information theory, machine learning, and statistics, it is unsolved. This is attributable to measurement errors, lack of perturbation data, or difficulty in causal inference. Yet the role of kinetic parameters of gene expression is unknown. We show how the relative stability of mRNA and protein hampers inference. We use a simple model of gene expression to show that a more stable protein than mRNA deteriorates correlation between the mRNA of a transcription factor and its target gene. This can also happen when mRNA and protein are on the same timescale. Relative difference in timescales affects true interactions more strongly than false positives. Besides correlation, we find that information-theoretic nonlinear measures are also prone to this problem.

关键词： Proteins Sequential analysis Measurement errors Correlation RNA Perturbation methods Machine learning

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Computational Alchemy Using Accelerated GPU Calculations: Fine Structural Tuning Inhibitors of L,D-transpeptidase 2 from Mycobacterium tuberculosis

Supercomputing Frontiers and Innovations

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Supercomputing Frontiers and Innovations 2022年第3期9卷 72-86页

作者： Baldin, Semen M. Shegolev, Vsevolod O. Švedas, Vytas K. Lomonosov Moscow State University Belozersky Institute of Physicochemical Biology Moscow Russia Lomonosov Moscow State University Research Computing Center Moscow Russia Lomonosov Moscow State University Faculty of Chemistry Moscow Russia Lomonosov Moscow State University Faculty of Bioengineering and Bioinformatics Moscow Russia

The computational alchemy is based on equilibrium methods of molecular dynamics (MD), including thermodynamic integration (TI) or free energy perturbation (FEP). It makes it possible to evaluate the energy characteristics of a subtile alchemical transformation of the prototype compound structures in order to modulate their functional properties, what can be used searching for new analogues of enzyme inhibitors. In recent years, the method is gaining new opportunities due to high-performance computing as different MD engines got the ability to perform TI or FEP calculations using GPU acceleration. We have tested the method on two experimentally studied enzyme-inhibitor systems: penicillin acylase from E. coli (PaEc) and Influenza A virus neuraminidase (NaIAv) and performed computational alchemy calculations for pairs of their known inhibitors. Thus, the validated methodology was then applied to estimate binding of L,Dtranspeptidase 2 from M. tuberculosis (LdtMt2) to the structural analogs of inhibitors previously discovered in our group. We have found that the performance of computational alchemy predictions is highly dependent on properly chosen simulation parameters and at optimal performance the difference between the calculated and experimentally determined relative binding energies is less than 1 kcal/mol. Thus, for optimal application to novel enzyme—inhibitor or receptor—ligand systems, we recommend prior adaptation of this method, based on validation of force field combinations as well as water models, to experimentally determined binding data of structurally related inhibitors/ligands to the molecular target of interest, if available, and then to proceed to the study of new compounds. High-performance computational alchemy can be used as a useful integrative part of the methodology searching for new enzyme inhibitors or receptor ligands and optimizing their structure at drug design © The Authors 2022. This paper is published with open access at ***

关键词： Molecular dynamics

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