Article
Multidisciplinary Sciences
Jennifer Flechsler, Thomas Heimerl, Harald Huber, Reinhard Rachel, Ivan A. Berg
Summary: Prokaryotic cells are more complex than traditionally believed, with various microcompartments encapsulating metabolic enzymes or pathways. The hyperthermophilic Crenarchaeon Ignicoccus hospitalis possesses unique structures like two membranes and an unknown intermembrane compartment. The compartmentalization of metabolic pathways and information processes in this organism represents a unique example in the prokaryotic world.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Oncology
Kosuke Yamaguchi, Xiaoying Chen, Asami Oji, Ichiro Hiratani, Pierre-Antoine Defossez
Summary: Chromatin changes in cancer have significant implications for gene expression, genome stability, and cancer progression, making them important for diagnosis and treatment.
Article
Chemistry, Multidisciplinary
Israel Serrano-Chacon, Bartomeu Mir, Lorenzo Cupellini, Francesco Colizzi, Modesto Orozco, Nuria Escaja, Carlos Gonzalez
Summary: We studied a DNA oligonucleotide that forms two different i-motif structures depending on pH and temperature. At neutral pH, the major structure is stabilized by C:C+ base pairs and G:C:G:C tetrads. At pH 5, a more elongated i-motif structure with C:C+ base pairs and G:T:G:T tetrads is observed. Molecular dynamics calculations showed that the conformational transition between the two structures is driven by the protonation state of key cytosines. This study reveals the pH-dependent plasticity and conformational switch of i-motif structures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Israel Serrano-Chacon, Bartomeu Mir, Lorenzo Cupellini, Francesco Colizzi, Modesto Orozco, Nu'ria Escaja, Carlos Gonzalez
Summary: We studied a DNA oligonucleotide that can form two different i-motif structures, with their stability depending on pH and temperature. The structure at neutral pH is stabilized by C:C+ base pairs and G:C:G:C tetrads. At pH 5, a more elongated structure consisting of C:C+ base pairs and G:T:G:T tetrads is observed. The transition between these two structures is driven by the protonation state of key cytosines.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Jeremy Poulet-Benedetti, Caroline Tonnerre-Doncarli, Anne-Laure Valton, Marc Laurent, Marie Gerard, Natalja Barinova, Nikolaos Parisis, Florian Massip, Franck Picard, Marie-Noelle Prioleau
Summary: In this study, the involvement of three elements (guanine-rich motifs potentially forming G-quadruplexes, nucleosome-free regions, and the histone variant H2A.Z) in the firing of replication origins in vertebrates were investigated. It was found that two guanine-rich motifs on the same DNA strand were sufficient to assemble a functional replication origin without inducing transcription. The guanine-rich motifs were associated with the formation of nucleosome-free regions and enrichment of H2A.Z. These findings suggest the importance of guanine-rich motifs in the organization and duplication of vertebrate genomes.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Leonardo Salicari, Antonio Trovato
Summary: Researchers investigated the presence of entangled motifs in membrane protein structures and found that they occur at a similar frequency as in general proteins. However, the chirality bias of double-winding motifs is reversed in membrane proteins compared to general proteins. These observations may be explained by the differences in co-translational folding mechanisms between membrane and globular proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Lingyu Guan, Vincent Lam, Andrey Grigoriev
Summary: This study identified potential interaction regions of tRNA-derived fragments (tRFs) on a larger scale and proposed a novel model connecting the formation of asymmetric pairs and the potential binding mechanisms of tRFs. The findings suggest a way forward for further experimental elucidation of tRF-binding mechanisms.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Fengxia Li, Eugenio F. Fornasiero, Tal M. Dankovich, Verena Kluever, Silvio O. Rizzoli
Summary: By systematically studying probes initially developed for electron microscopy, researchers found that antibodies coupled to 6 nm gold particles exhibit excellent labeling specificity and reliable detection threshold in nanoSIMS imaging. These tools enable accurate visualization and analysis of samples and can be easily combined with other imaging approaches.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Kang-Hoon Kim, Jubeen Yoon, Christian P. Macks, Han-Eol Park, Jihyun Youn, Jung-uk Lee, Minji An, Jongseong Park, Jaewon Ko, Chang Ho Sohn
Summary: To understand the molecular machinery of synapses, it is important to determine the inventory of synaptic proteins at a subsynaptic resolution. However, the localization of synaptic proteins is challenging due to low expression levels and limited access to immunostaining epitopes. In this study, the exTEM method is introduced to image synaptic proteins in situ by combining TEM with nanoscale resolution and expandable tissue-hydrogel hybrids for enhanced immunolabeling. This method provides insights into the distribution of synapse-organizing proteins and can be widely used to investigate protein nanostructures in densely packed environments.
Article
Multidisciplinary Sciences
Parashar Dhapola, Johan Rodhe, Rasmus Olofzon, Thomas Bonald, Eva Erlandsson, Shamit Soneji, Goran Karlsson
Summary: Scarf is a modularly designed Python package that enables memory-efficient single-cell analysis and can run on low-cost devices. It provides efficient implementations for memory and computation and supports accurate reference-anchored mapping and subsampling of large single-cell datasets.
NATURE COMMUNICATIONS
(2022)
Article
Neurosciences
Jung-Hwa Tao-Cheng, Virginia Crocker, Sandra Lara Moreira, Rita Azzam
Summary: Immunogold labeling is a useful technique for protein localization and quantification at the electron microscopy level. Methodological issues and experiences from studies on protein distribution in cell cultures and brain tissues were summarized. Careful determination of fixation conditions, tissue processing, and evaluation of labeling credibility are crucial for optimal results.
Article
Biology
Jonathan D. Hibshman, Bob Goldstein
Summary: LEA proteins play a crucial role in protecting plants and animals from desiccation. Studies on the nematode C. elegans demonstrate that LEA-1 protein is required in various tissues for resistance against desiccation and osmotic stress. Identification of minimal motifs within LEA-1 suggests the potential for engineering peptides for optimized desiccation protection.
Article
Multidisciplinary Sciences
Saba Parvez, Chelsea Herdman, Manu Beerens, Korak Chakraborti, Zachary P. Harmer, Jing-Ruey J. Yeh, Calum A. MacRae, H. Joseph Yost, Randall T. Peterson
Summary: MIC-Drop is a platform combining droplet microfluidics, single-needle en masse CRISPR ribonucleoprotein injections, and DNA barcoding, enabling large-scale functional genetic screens in zebrafish to efficiently identify genes responsible for morphological or behavioral phenotypes. It has the potential to scale to thousands of genes, facilitating genome-scale reverse genetic screens in model organisms.
Article
Multidisciplinary Sciences
Hannah Schmidbaur, Akane Kawaguchi, Tereza Clarence, Xiao Fu, Oi Pui Hoang, Bob Zimmermann, Elena A. Ritschard, Anton Weissenbacher, Jamie S. Foster, Spencer Nyholm, Paul A. Bates, Caroline B. Albertin, Elly Tanaka, Oleg Simakov
Summary: This study reveals the unique genomic, topological, and regulatory organization of cephalopod genomes, identifies microsyntenies associated with cephalopod nervous system evolution, and suggests that microsyntenic profiling will be central to understanding cephalopod innovations.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Alexander S. Minasyan, Srinivas Chakravarthy, Suchitra Vardelly, Mark Joseph, Evgueni E. Nesterov, Irina V. Nesterova
Summary: This study presents a new approach to enable well-defined conformational transitions in DNA molecular devices. By developing tools for precise folding of multiple DNA quadruplexes within the same oligonucleotide strand, the research demonstrates the facilitation of targeted folding topology by guiding elements. The use of thermodynamic techniques, SEC, SAXS, and electron density maps provides comprehensive characterization of folding/unfolding transitions.
Article
Biochemistry & Molecular Biology
Vera Dugina, Galina Shagieva, Mariya Novikova, Svetlana Lavrushkina, Olga Sokova, Igor Kireev, Pavel Kopnin
Summary: This study investigates the diverse roles of cytoplasmic actins in the progression of chromosomal instability in human breast cancer cells. Beta-cytoplasmic actin depletion leads to chromosomal instability progression, while downregulating gamma-cytoplasmic actin results in chromosome stability and reduced polyploidy and aneuploidy.
Article
Biochemistry & Molecular Biology
Sergey Ulianov, Artem K. Velichko, Mikhail D. Magnitov, Artem Luzhin, Arkadiy K. Golov, Natalia Ovsyannikova, Igor I. Kireev, Alexey S. Gavrikov, Alexander S. Mishin, Azat K. Garaev, Alexander Tyakht, Alexey A. Gavrilov, Omar L. Kantidze, Sergey Razin
Summary: The study found that treatment with 1,6-hexanediol caused changes in chromatin topology, resulting in the mixing of chromatin compartments. Moreover, removing 1,6-hexanediol from the culture medium did not allow chromatin to return to its initial structure, leading to a more compact chromatin compared to untreated cells.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Alexey M. Kopylov, Lika Fab, Olga Antipova, Ekaterina A. Savchenko, Alexander Revishchin, Viktoriya V. Parshina, Svetlana Pavlova, Igor I. Kireev, Andrey Golovin, Dmitry Y. Usachev, Galina Pavlova
Summary: The study investigated the use of RNA aptamers for molecular typing of human glioblastoma multiforme (GBM), demonstrating the specificity of binding between the aptamer and the receptor on tumor cells, and showing the potential application as an escort aptamer for delivering therapeutic agents into tumor cells.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Cell Biology
Artem K. Velichko, Natalia Ovsyannikova, Nadezhda Petrova, Artem Luzhin, Maria Vorobjeva, Alexey S. Gavrikov, Alexander S. Mishin, Igor I. Kireev, Sergey Razin, Omar L. Kantidze
Summary: Replication stress is a major cause of genome instability, and research has shown that replication stress response can also occur in nucleoli. Factors like TOPBP1 and Treacle are recruited inside nucleoli to facilitate ATR signaling in response to replication stress, providing insights into the mechanisms of replication stress response in nucleoli.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Cell Biology
Amir N. Zakirov, Sophie Sosnovskaya, Ekaterina D. Ryumina, Ekaterina Kharybina, Olga S. Strelkova, Oxana A. Zhironkina, Sergei A. Golyshev, Andrey Moiseenko, Igor I. Kireev
Summary: A detailed understanding of the principles of the structural organization of genetic material is crucial for explaining the mechanisms of gene regulation during development. Modern ideas about the spatial organization of the genome are based on microscopic analysis of chromatin structure and molecular data on DNA-DNA interaction. Chromatin structure heterogeneity, depending on functional states and cell cycle progression, adds complexity to the interpretation of structural data and requires selective labeling of different transcriptional states.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Olga Shadrina, Irina Garanina, Andrey Anisenko, Igor Kireev, Marina Gottikh
Summary: DNA-dependent protein kinase (DNA-PK) and its subunits, Ku70, Ku80, and DNA-PKcs, play important roles in various cellular processes. Depletion of these subunits results in different effects on gene expression, with Ku70 playing a more critical role in regulating multiple processes.
Article
Multidisciplinary Sciences
Alexey V. Kostarnoy, Petya G. Gancheva, Igor I. Kireev, Andrey I. Soloviev, Bernd Lepenies, Andrey Y. Kulibin, Ekaterina A. Malolina, Olga N. Scheglovitova, Alexey V. Kondratev, Maria V. Sokolova, Daria Vorobyeva, Nadezhda Filippova, Marina R. Kapkaeva, Maria A. Lagarkova, Pavel S. Metalnikova, Evgeniy Riabenko, Daniil A. Grumov, Maxim A. Bobrov, Elena Vasilieva, Boris S. Naroditsky, Alexander L. Gintsburg
Summary: Cellular lipid uptake is a fundamental physiological process, and we have discovered a previously unknown mechanism of lipid cargo uptake mediated by the receptor Mincle. Our study reveals that Mincle tightly binds a range of self-lipids and forms vesicles in the cytoplasm. Knockout of Mincle leads to a significant decrease in lipid endocytosis, suggesting it as a prospective target for disorders of lipid metabolism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Sophie Sosnovskaya, Amir N. Zakirov, Ekaterina D. Ryumina, Ekaterina Kharybina, Sergei A. Golyshev, Olga S. Strelkova, Oxana A. Zhironkina, Andrei Moiseenko, Anton Orekhov, Igor I. Kireev
Summary: This protocol combines EdU labeling, Ag-amplification of Nanogold particles, and ChromEM staining for visualizing replicative domains in cell culture, allowing for high-efficiency pre-embedding labeling and providing a new method for studying chromatin structure.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Editorial Material
Clinical Neurology
Margarita Zaytseva, Ludmila Papusha, Agnesa Panferova, Andge Valiakhmetova, Anastasia Shekhtman, Sergey Obydennyi, Igor Kireev, Galina Novichkova, Alexander Druy
Article
Biochemistry & Molecular Biology
Anton S. Shakhov, Polina A. Kovaleva, Alexandra S. Churkina, Igor I. Kireev, Irina B. Alieva
Summary: Actin cytoskeleton is crucial for cellular processes, and there are different isoforms in non-muscle cells, β-actin and γ-actin, which have distinct functions and localization in the cytoplasm. Based on super-resolution microscopy, this study demonstrates that β-actin and γ-actin are segregated in the cytoplasm of endothelial cells, with varying degrees of colocalization in different cellular regions. The segregation of actin isoforms is enhanced during the activation of cell lamella in endothelial barrier dysfunction.
Article
Chemistry, Inorganic & Nuclear
Anastasiia S. Garanina, Maria V. Efremova, Alexey E. Machulkin, Evgeny V. Lyubin, Natalia S. Vorobyeva, Oxana A. Zhironkina, Olga S. Strelkova, Igor I. Kireev, Irina B. Alieva, Rustem E. Uzbekov, Viatcheslav N. Agafonov, Igor V. Shchetinin, Andrey A. Fedyanin, Alexander S. Erofeev, Peter V. Gorelkin, Yuri E. Korchev, Alexander G. Savchenko, Maxim A. Abakumov
Summary: This study investigated the remote manipulation of Fe3O4-Au hybrid particles in different magnetic fields and demonstrated their aggregation and disaggregation behavior in aqueous solution. Additionally, the study found that these particles have potential applications in cancer therapy based on their uptake by cancer cells and their effect on cell viability.
Article
Biochemistry & Molecular Biology
Mikhail V. Dubinin, Vlada S. Starinets, Yuliya A. Chelyadnikova, Natalia V. Belosludtseva, Irina B. Mikheeva, Daria K. Penkina, Anastasia D. Igoshkina, Eugeny Yu. Talanov, Igor I. Kireev, Dmitry B. Zorov, Konstantin N. Belosludtsev
Summary: In this study, NS1619 was found to improve potassium ion transport and content in the heart mitochondria of DMD mice. This led to a decrease in oxidative stress and fibrosis level. The findings suggest that NS1619 could be a potential approach for correcting the pathology in DMD.
BIOCHEMISTRY-MOSCOW
(2023)
Meeting Abstract
Biophysics
Vasilii S. Kolmogorov, Nikita A. Savin, Alexei P. Iakovlev, Alexander N. Vaneev, Svetlana V. Lavrushkina, Alexander S. Erofeev, Petr V. Gorelkin, Natalia L. Klyachko, Igor I. Kireev, Alexander G. Majouga, Christopher Edwards, Pavel Novak, Yuri E. Korchev
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
Meeting Abstract
Biophysics
S. Lavrushkina, A. Rudenko, V. Kolmogorov, A. Erofeev, P. Gorelkin, G. Maksimov, I. Kireev
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
Meeting Abstract
Biophysics
Vasilii Kolmogorov, Alexander Vaneev, Yuri M. Efremov, Nikita Savin, Aleksei Iakovlev, Anna Alova, Svetlana Lavrushkina, Alexander Erofeev, Petr Gorelkin, Natalia Klyachko, Igor Kireev, Alexander Majouga, Pavel Novak, Yuri E. Korchev
BIOPHYSICAL JOURNAL
(2021)
