?
ArdA genes from pKM101 and from B. bifidum chromosome have a different range of regulated genes
Heliyon. 2023. Vol. 9. No. 12. Article e22986.
Gladysheva-Azgari M., Sharko F., Evteeva M. A., Kuvyrchenkova A. P., Boulygina E., Tsygankova S., Slobodova N., Pustovoit K. S., Melkina O., Nedoluzhko A., Korzhenkov A. A., A.A. Kudryavtseva, I.V. Manukhov
The ardA genes are present in a wide variety of conjugative plasmids and play an important role in overcoming the restriction barrier. To date, there is no information on the chromosomal ardA genes. It is still unclear whether they keep their antirestriction activity and why bacterial chromosomes contain these genes. In the present study, we confirmed the antirestriction function of the ardA gene from the Bifidobacterium bifidum chromosome. Transcriptome analysis in Escherichia coli showed that the range of regulated genes varies significantly for ardA from conjugative plasmid pKM101 and from the B. bifidum chromosome. Moreover, if the targets for both ardA genes match, they often show an opposite effect on regulated gene expression. The results obtained indicate two seemingly mutually exclusive conclusions. On the one hand, the pleiotropic effect of ardA genes was shown not only on restriction-modification system, but also on expression of a number of other genes. On the other hand, the range of affected genes varies significally for ardA genes from different sources, which indicates the specificity of ardA to inhibited targets.
Ekaterina D. Riumina, Klink G. V., Alekseeva E. et al., PNAS, США 2026 Vol. 123 No. 35 P. 1–20
The role of escape from the cytotoxic T cell (CTL) response in SARS-CoV-2 evolution remains controversial. Here, we study the origin and spread of SARS-CoV-2 variants whose mutations reduce presentation by the HLA class I alleles common in human populations. We find that 35% of mutations that are characteristic of the variants of concern, and ...
Added: October 2, 2026
Aly Ismailov, Poptsova M., Plos One 2026 Vol. 21 No. 9 Article e0355902
Added: October 2, 2026
Knyazev E., Чеботарева О. Е., М.: Издательский дом НИУ ВШЭ, 2026.
This teaching and learning guide provides a concise overview of the theoretical and practical aspects of the basic skills required to work in a biological laboratory. It also includes protocols for practical classes conducted as part of the introductory professional training placement for first-year students in the Bachelor’s programme in Cell and Molecular Biotechnology at ...
Added: September 30, 2026
Ryskina H., Knyazev E., Вопросы биологической, медицинской и фармацевтической химии 2026 Т. 29 № 9 С. 84–91
Introduction. The active integration of rapidly developing omics and computer technologies in the 21st century has led to a breakthrough in understanding the principles of the functioning of living systems. One of the dynamically developing integrative areas in biology is biological modeling. The fundamental paradigm has been the methodology that allows for the prediction of ...
Added: September 29, 2026
Gureev M., Advanced Science 2026 P. 1–13
Targeted protein degradation represents a promising therapeutic strategy, yet its broader application is often limited by the scarcity of usable E3 ligases. Glutathione peroxidase 4 (GPX4) is a key target for inducing ferroptosis, but achieving sustained and potent inhibition remains challenging with conventional enzymatic inhibitors. Herein, we report the first small‐molecule GPX4 degraders that incorporate ...
Added: September 26, 2026
Diachkova E., Nikulin D., Кубкин Я. В. et al., American Journal of Respiratory and Critical Care Medicine 2026 Vol. 212
Accurate classification of a patient with pulmonary hypertension (PH) into one of five groups is fundamental for appropriate disease management strategies. The time from disease onset to correct diagnosis is unacceptably long in many cases. Chronic thromboembolic pulmonary hypertension (CTEPH) develops as a consequence of venous thromboemboli, resulting in a more pronounced hereditary predisposition to ...
Added: September 23, 2026
Xu Y., Ryabov F., Alexandrov I. et al., USA 2026 Vol. 6 No. 8 Article 101324
Центромеры обеспечивают расхождение хромосом, однако организацию их хроматина в пределах повторяющейся альфа-сателлитной ДНК долгое время было трудно изучать. Для решения этой задачи мы создали гаплотип-разрешённые аннотации сателлитной ДНК для полной диплоидной сборки генома человека T2T-HG002. Затем с помощью метода направленного метилирования с секвенированием длинных прочтений (DiMeLo-seq) мы картировали центромерный белок A (CENP-A), модификацию H3K9me3 и ...
Added: September 23, 2026
Hebbar P., Ryabov F., Alexandrov I. et al., Cell 2026 Vol. 189 P. 4891–4908.e12
The common marmoset is a New World monkey widely used to study primate evolution and human disease. We present a telomere-to-telomere (T2T) reference assembly for the species, plus three near-T2T haplotypes. These resolve previously inaccessible regions, including the centromeres, sex chromosomes, subterminal satellites, acrocentric chromosomes, and the major histocompatibility complex (MHC). We find marmoset centromeres ...
Added: September 23, 2026
Shaitan A., Ke Y., Shutao C. et al., 2026 No. 24 Article 181
Background Therapeutic peptides exert pivotal effects in diverse biological processes, and have attracted significant interest in the field of biomedicine in recent years. However, most existing methods often fail to adequately capture the intricate interactions among amino acid residues and the contextual dependencies within peptide sequences, which hampers the extraction of deep semantic representations and ...
Added: September 18, 2026
Anton Rogachev, Sysoeva O., Frontiers in Systems Neuroscience 2025 Vol. 19 Article 1658243
Added: September 17, 2026
Anton Rogachev, Sysoeva O., Cognitive Systems Research 2024 Vol. 86 Article 101236
Receptive speech is the ability to understand speech addressed to a person. It is a crucial process for a child’s cognitive development. We examine the relationship between receptive speech and neural tracking of natural speech in 52 children aged 3–8 years to infer the neurophysiological mechanisms underlying speech development. We registered a 32-channel electroencephalogram (EEG) ...
Added: September 17, 2026
Чеботарева О. Е., Пирогов А. А., Antipenko I. et al., Доклады российской академии наук. Науки о жизни 2026 Т. 529 № 1 С. 389–395
Preeclampsia (PE) is a severe obstetric complication caused by chronic placental ischaemia. Genome-wide profiling of microRNA isoforms in two trophoblast hypoxia models (CoCl2 and the oxyquinoline derivative neuradapt, BeWo b30 cells) and clinical PE samples (placental tissue, syncytiotrophoblast vesicles) revealed concordant downregulation of hsa-miR-143-3p isoforms. Under a strict fold-change threshold, the canonical isoform (21 nt) ...
Added: September 16, 2026
Poddiakov A., / Series Social Science Research Network "Social Science Research Network". 2026. No. 7437658.
Clarity of knowledge and reasoning is necessary in many cases. Yet vagueness in scientific thinking related to surprise, curiosity, "ability to engage with not-knowing" (de Freitas) and abductive reasoning is also a crucially important source of scientific creativity which supplements combinatorial logic when dealing with the already known. Starting from studies by C. S. Peirce ...
Added: September 15, 2026
Bug D. S., Kuzovenkova D. A., Tishkov A. V. et al., Biochemical Genetics 2026
Deciphering the evolutionary history of genes is foundational for biomedical research, enabling the identification of compensatory mutations in disease-associated genes and the selection of evolutionarily relevant model organisms. However, challenges of multi-isoform handling, the presence of incomplete genomes/proteomes initial datasets, and problems of evolutionary history representation are still present. To address these issues, we introduce ...
Added: September 14, 2026
Ребрейкина А. Б., Liaukovich K., Современная зарубежная психология 2024 Т. 13 № 2 С. 33–43
Создание методик диагностики на основе анализа движений глаз является особенно актуальным для оценки когнитивных функций у детей, которые не могут дать речевой или моторный ответ в силу своего возраста или из-за нарушений развития. Для таких детей использование объективных методов оценки когнитивных функций на основе айтрекинга может стать полезным диагностическим инструментом, дополняющим традиционные поведенческие опросники и ...
Added: September 8, 2026
Ребрейкина А. Б., Liaukovich K., Современная зарубежная психология 2023 Т. 12 № 4 С. 51–61
Активное развитие метода видеоокулографии, т. е. регистрации движений глаз, создает возможности для создания новых подходов для развития когнитивных функций и обучения. Методики, основанные на видеоокулографии, могут быть полезны не только для детей с серьезными нарушениями моторных функций, но и детей с нарушениями развития когнитивных функций, прежде всего внимания, так как контроль движений глаз тесно связан ...
Added: September 8, 2026
Портнова Г. В., Liaukovich K., Васильева Л. Н. et al., Журнал высшей нервной деятельности им. И.П. Павлова 2022 Т. 72 № 4 С. 504–519
Когнитивная и эмоциональная нагрузка в ходе увеличения сложности задач приводит к активации различных звеньев вегетативной нервной системы и может сопровождаться как увеличением эффективности решения задач, так и способствовать дестабилизации эмоционального состояния и уменьшению продуктивности. Увеличение когнитивной нагрузки при условии высокой мотивации испытуемых является стрессовым фактором и выражается в различной реакции симпатического и парасимпатического звеньев в ...
Added: September 8, 2026
Shaitan A., Ke Y., Hongjun Y. et al., PLoS Computational Biology 2026 Article e1013836
The interaction between peptides and human leukocyte antigen class II (HLA-II)
molecules plays a pivotal role in adaptive immune responses, as HLA-II mediates
the recognition of exogenous antigens and initiates T cell activation through peptide
presentation. Accurate prediction of peptide-HLA-II binding serves as a cornerstone
for deciphering cellular immune responses, and is essential for guiding the optimization
of antibody therapeutics. ...
Added: September 7, 2026
Anna A. Kudryavtseva, Cséfalvay E., Gnuchikh E. Y. et al., Frontiers in Microbiology 2023 Vol. 14 Article 1133144
ArdB, ArdA, and Ocr proteins inhibit the endonuclease activity of the type I restriction-modification enzymes (RMI). In this study, we evaluated the ability of ArdB, ArdA, and Ocr to inhibit different subtypes of Escherichia coli RMI systems (IA, IB, and IC) as well as two Bacillus licheniformis RMI systems. Furthermore we explored, the antirestriction activity of ArdA, ArdB, and ...
Added: May 23, 2023
Манухов И. В., Кудрявцева А. А., Biochemistry. Biokhimiia 2020
Abstract—The antirestriction ArdB protein inhibits the endonuclease activity of type I restriction/modification (RM) systems in vivo; however, the mechanism of inhibition remains unknown. In this study, we showed that recombinant ArdB from Escherichia coli cells copurified with DNA. When overexpressed in E. coli cells, a portion of ArdB protein formed insoluble DNAfree aggregates. Only native ...
Added: October 19, 2022
Манухов И. В., Кудрявцева А. А., FEMS Microbiology Letters 2018
Antirestriction proteins of the ArdB group (ArdB, KlcA) specifically inhibit restriction (endonuclease) activity of restriction-modification (RM) type I systems. Antirestriction activity of KlcA and ArdB, encoded in transmissible plasmids RP4 (IncPα) and R64 (IncI1), respectively, has been determined. We show that the protein KlcA (RP4), an amino acid sequence identical to that of the protein ...
Added: October 19, 2022
Манухов И. В., Кудрявцева А. А., Molecular Biology 2017
Abstract⎯Antirestriction proteins of the ArdB/KlcA family are specific inhibitors of restriction (endonuclease) activity of type-I restriction/modification enzymes. The effect of conserved amino acid residues on the antirestriction activity of the ArdB protein encoded by the transmissible R64 (IncI1) plasmid has been investigated. An analysis of the amino acid sequences of ArdB homologues demonstrated the presence ...
Added: October 19, 2022
Hada A., Hota S., Luo J. et al., Cell Reports 2019 Vol. 28 No. 1 P. 282–294
Nucleosomes are the fundamental building blocks of chromatin that regulate DNA access and are composed of histone octamers. ATP-dependent chromatin remodelers like ISW2 regulate chromatin access by translationally moving nucleosomes to different DNA regions. We find that histone octamers are more pliable than previously assumed and distorted by ISW2 early in remodeling before DNA enters nucleosomes ...
Added: March 17, 2021
Antonov I., Medvedeva Y., Genes 2020 Vol. 11 No. 12 P. 1–11
Although thousands of mammalian long non-coding RNAs (lncRNAs) have been reported in the last decade, their functional annotation remains limited. A wet-lab approach to detect functions of a novel lncRNA usually includes its knockdown followed by RNA sequencing and identification of the deferentially expressed genes. However, identification of the molecular mechanism(s) used by the lncRNA ...
Added: March 12, 2021