Review
Chemistry, Multidisciplinary
Fan Xu, Ben L. Feringa
Summary: Photoresponsive supramolecular polymers are highly organized assemblies with photosensitive molecules as monomers, showing reversible changes in geometry, dipole moment, and chirality upon light stimuli. They have broad applications in smart materials, including light-driven soft actuators, fluorescent anticounterfeiting, and light-triggered electronic devices. This review focuses on the light-activated molecules used in photoresponsive supramolecular polymers and the different changes induced by light. It also highlights the disassembly, reassembly, actuation, emission, and chirality transfer of these polymers. Future opportunities and challenges, such as using visible/near IR light and enabling biomedical applications, are also discussed.
ADVANCED MATERIALS
(2023)
Article
Multidisciplinary Sciences
Qingrui Duan, Qingxi Zhang, Kun Nie, Rui Huang, Jianhua Yang, Peikun He, Zihui Tie, Haifeng Huang, Guixian Ma, Yuhu Zhang, Yuyuan Gao, Lijuan Wang
Summary: We demonstrated for the first time that alpha-syn PFF spreads from BMVECs to pericytes through tunneling nanotubes (TNTs) and myosin. Inhibition of myosin 1d (Myo1d) can prevent the transfer of alpha-syn PFF from BMVECs to pericytes. Targeting Myo1d may be a promising approach to prevent the spreading of alpha-syn from blood to the brain.
Editorial Material
Multidisciplinary Sciences
Leonid A. Mirny
Summary: The study reveals that loop extrusion, essential for chromosome folding and function, also plays a crucial part in repairing double-strand DNA breaks.
Review
Cell Biology
Maryne Dupuy, Francois Lamoureux, Mathilde Mullard, Anais Postec, Laura Regnier, Marc Baud'huin, Steven Georges, Benedicte Brounais-Le Royer, Benjamin Ory, Francoise Redini, Franck Verrecchia
Summary: Ewing sarcoma (ES) is the second most common primary malignant bone tumor in children, adolescents, and young adults in Europe, with a survival rate of 70% for localized forms using conventional treatment. However, resistance to chemotherapy and pulmonary metastases greatly reduce the survival rate. ES is characterized by a chromosomal translocation that leads to the fusion protein EWS-FLI1, which plays a crucial role in the development of ES. This review provides an overview of ES from a clinical and biological perspective.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Mechanics
Xining Xu, Yunxin Zhang
Summary: Through numerical calculations, we found that the dynamics and output power of randomly flashing ratchets exhibit symmetry with respect to the shift between the two potentials Delta(max) + Delta(min), where Delta(max) and Delta(min) are the shifts between the two peaks and two bottoms respectively. The mean velocity and output power reach optimal performance when Delta(max) + Delta(min) = 1.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Review
Oncology
Ray Manneh Kopp, Paula Espinosa-Olarte, Teresa Alonso-Gordoa
Summary: Neuroendocrine neoplasms (NENs) are a heterogeneous group of tumors with diverse behavior, biology, and prognosis, challenging to diagnose and requiring a multidisciplinary approach. The combination of pathology, molecular biomarkers, and novel imaging techniques leads to an accurate diagnosis and better treatment approach. Recent advances in molecular characterization and imaging techniques, such as (68)Gallium-DOTATATE PET-CT, have improved diagnostic sensitivity and opened up new treatment strategies.
Article
Chemistry, Physical
Ligesh Theeyancheri, Subhasish Chaki, Tapomoy Bhattacharjee, Rajarshi Chakrabarti
Summary: To study the behavior of deformable active agents in porous media, we computationally investigate the dynamics of linear chains and rings made of active Brownian monomers. We find that flexible linear chains and rings migrate smoothly and undergo swelling, while semiflexible linear chains shrink at lower activities and swell at higher activities. Semiflexible rings, on the other hand, shrink and get trapped at lower activities, but escape at higher activities. This demonstrates the interplay between activity and topology in controlling the structure and dynamics of linear chains and rings in porous media.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
Xin Shi, Anna-Katharina Pumm, Jonas Isensee, Wenxuan Zhao, Daniel Verschueren, Alejandro Martin-Gonzalez, Ramin Golestanian, Hendrik Dietz, Cees Dekker
Summary: Researchers have demonstrated a self-assembled DNA nanostructure that exhibits flow-driven rotary motion when docked onto a nanopore. These artificial nanoengines operate autonomously under physiological conditions, providing a new approach to constructing energy-transducing motors at nanoscale interfaces.
Article
Biochemistry & Molecular Biology
Antonina Hafner, Minhee Park, Scott E. Berger, Sedona E. Murphy, Elphege P. Nora, Alistair N. Boettiger
Summary: Population-level analyses have shown the significant roles of CTCF and cohesin in mammalian genome organization. However, their contributions at the single-cell level were not fully understood until now. This study used super-resolution microscopy to explore the effects of CTCF and cohesin removal, revealing their distinct contributions to loop stacking and the organization of the genome at the single-cell level.
Article
Chemistry, Multidisciplinary
Emanuele Penocchio, Giulio Ragazzon
Summary: Molecular nonequilibrium systems have great potential for future nanotechnology, but their development is hindered by the lack of an informative representation. We extended the energy span model, an approach pertaining to catalytic networks, to provide an insightful visual representation of kinetic asymmetry in system dynamics. Our approach applies to both chemically and photochemically driven systems, ranging from unimolecular motors to simple self-assembly schemes. The obtained diagrams offer immediate access to information needed for guiding experiments and understanding the effects of design changes.
Editorial Material
Multidisciplinary Sciences
Orsolya Barabas, Phoebe A. A. Rice
Summary: CRISPR-Cas is a bacterial defense system that can either protect host cells by attacking invading DNA or assist in the safe insertion of DNA into the genome. The structures of this specific type of CRISPR-Cas system have been successfully visualized.
Editorial Material
Multidisciplinary Sciences
Felicia Kuperwaser, Itai Yanai
Summary: A comprehensive cell atlas of gene expression and regulation in human embryos has provided a unique opportunity for innovative investigation of development through multi-organ and multi-modal analysis.
Editorial Material
Multidisciplinary Sciences
Fahad Rashid, James Berger
Summary: High-resolution structures of bacterial Rho protein in complex with an RNA polymerase enzyme and partner proteins confirm the long-held model of Rho's role in gene transcription termination.
Article
Nanoscience & Nanotechnology
Stefano Corra, Marina Tranfic Bakic, Jessica Groppi, Massimo Baroncini, Serena Silvi, Emanuele Penocchio, Massimiliano Esposito, Alberto Credi
Summary: This study presents a theoretical model and experimental evidence for the operation of an out-of-equilibrium photoactivated artificial molecular pump. The relationship between light energy input and the deviation of the dissipative state from thermodynamic equilibrium in this artificial system is quantitatively analyzed.
NATURE NANOTECHNOLOGY
(2022)
Editorial Material
Multidisciplinary Sciences
Pavel V. Baranov, John F. Atkins
Summary: Messenger RNA has 64 possible codons, three of which usually stop protein synthesis. However, certain organisms can utilize all codons to determine amino acids, partially due to an unexpected characteristic of transfer RNA.
Review
Biochemistry & Molecular Biology
Jan Jurcik, Barbara Sivakova, Ingrid Cipakova, Tomas Selicky, Erika Stupenova, Matus Jurcik, Michaela Osadska, Peter Barath, Lubos Cipak
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Barbara Sivakova, Jan Jurcik, Veronika Lukacova, Tomas Selicky, Ingrid Cipakova, Peter Barath, Lubos Cipak
Summary: The LFQ phosphoproteomics workflow presented in this study, based on sequential Fe-IMAC phosphopeptide enrichment, strong anion exchange (SAX), and porous graphitic carbon (PGC) fractionation strategies, enabled the identification of 8353 phosphosites in the fission yeast Schizosaccharomyces pombe, with 1274 sites being newly discovered. The results demonstrate that the combination of PGC and SAX fractionation strategies significantly enhances the robustness and specificity of LFQ phosphoproteomics studies, providing valuable insights into the complexity of protein kinase functions in S. pombe.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ivana Misova, Alexandra Pitelova, Jaroslav Budis, Juraj Gazdarica, Tatiana Sedlackova, Anna Jordakova, Zsigmond Benko, Maria Smondrkova, Nina Mayerova, Karoline Pichlerova, Lucia Strieskova, Martin Prevorovsky, Juraj Gregan, Lubos Cipak, Tomas Szemes, Silvia Bagelova Polakova
Summary: In homologous recombination, the Dbl2 protein is found to be essential for regulating gene expression and participating in gene silencing pathways along with the HIRA histone chaperone complex. Furthermore, deletion of Dbl2 results in alterations in chromatin structure and levels of histone methylation.
NUCLEIC ACIDS RESEARCH
(2021)
Editorial Material
Biochemistry & Molecular Biology
Juraj Gregan
Summary: Understanding the spatial organization of genomes is crucial in cell biology, but distinguishing relationships between sister chromatids has been challenging due to limitations in sequencing-based techniques. Recent developments have provided insights into the organization of sister chromatids.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Barbora Mikolaskova, Matus Jurcik, Ingrid Cipakova, Tomas Selicky, Jan Jurcik, Silvia Bagelova Polakova, Erika Stupenova, Andrej Dudas, Barbara Sivakova, Jana Bellova, Peter Barath, Lucia Aronica, Juraj Gregan, Lubos Cipak
Summary: By studying the interactions between Nrl1 and RNA-processing proteins, as well as the regulation of Nrl1 through phosphorylation, two mechanisms involved in the regulation of the spliceosome-associated factor Nrl1 have been identified: domain-specific interactions and post-translational modification by phosphorylation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Andrea Sevcovicova, Jana Plava, Matej Gazdarica, Eva Szabova, Barbora Huraiova, Katarina Gaplovska-Kysela, Ingrid Cipakova, Lubos Cipak, Juraj Gregan
Summary: The study revealed that phosphorylation sites on the Swi5-Sfr1 complex contribute to its partially functional state during meiosis, but the functional relevance of this phosphorylation remains to be determined.
Editorial Material
Biochemistry & Molecular Biology
Lubos Cipak
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Michaela Osadska, Tomas Selicky, Miroslava Kretova, Jan Jurcik, Barbara Sivakova, Ingrid Cipakova, Lubos Cipak
Summary: Cohesin, a multi-subunit protein complex, plays important roles in various cellular processes. Recent studies have shown that cohesin's functions are not only dependent on protein-protein interactions and modifications, but also involve RNA processing factors. Mutations, changes in expression, and alterations in the interactions between cohesin and RNA processing factors can impact chromosome segregation and genome stability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Tomas Selicky, Matus Jurcik, Barbora Mikolaskova, Alexandra Pitelova, Nina Mayerova, Miroslava Kretova, Michaela Osadska, Jan Jurcik, Roman Holic, Lenka Kohutova, Jana Bellova, Zsigmond Benko, Juraj Gregan, Silvia Bagelova Polakova, Peter Barath, Lubos Cipak, Ingrid Cipakova
Summary: This study demonstrates the important role of the Gpl1-Gih35-Wdr83 complex in regulating pre-mRNA splicing in the fission yeast S. pombe, through knock-out strategy, affinity purification, and yeast-two-hybrid assay.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biology
Miroslava Kretova, Tomas Selicky, Ingrid Cipakova, Lubos Cipak
Summary: Pre-mRNA splicing is a crucial process in eukaryotic cells to generate mature messenger RNAs for protein synthesis. The splicing process involves the removal of non-coding regions (introns) and joining of coding regions (exons) in pre-mRNAs. The spliceosome, composed of various proteins and factors, carries out the specific steps of splicing. Recent studies have revealed that post-translational modifications of splicing factors play significant roles in the regulation of pre-mRNA splicing, including phosphorylation, acetylation, methylation, ubiquitination, and sumoylation.