Article
Multidisciplinary Sciences
Sithara S. Wijeratne, Michelle F. Marchan, Jason S. Tresback, Radhika Subramanian
Summary: This study uses atomic force microscopy (AFM) to observe the dynamic reorganization of microtubule arrays by depolymerizing enzymes. Previously unseen destabilization modes of microtubule arrays by depolymerases are discovered. The study reveals that different depolymerases exhibit distinct depolymerization patterns, leading to either large-scale destabilization or length regulation of microtubule arrays.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Jingyi Wang, Jiawen Zhang, Sijia Li, Dengfeng Liu, Akhilesh Bhambhani, Hongbo Zeng
Summary: This article highlights the importance of characterizing the morphology and intermolecular interactions of RNA and lipid molecules using atomic force microscopy (AFM), as well as the application of AFM in this field. The first section introduces the use of AFM imaging to obtain high-resolution morphologies and nanostructures of RNA molecules in air and liquid, and discusses the application of AFM force spectroscopy to understand the nanomechanical properties and molecular interactions of RNA molecules. The second section focuses on the studies of lipid and RNA-lipid complexes using AFM, including sample preparation and factors influencing their morphology and structure. The future perspectives and challenges in the characterization of RNA and lipid using AFM techniques are also discussed.
ADVANCES IN COLLOID AND INTERFACE SCIENCE
(2023)
Article
Nanoscience & Nanotechnology
Keivan Asadi, Junghoon Yeom, Hanna Cho
Summary: Investigating internal resonance (IR) mechanisms in micro/nanoresonators reveals that intermodal coupling between second and third flexural modes in asymmetric structures provides an optimal condition for strong IR, with high energy transfer to the resonated mode. This study introduces design strategies that can be easily integrated into typical micro/nanoelectromechanical systems, offering potential for paradigm-shifting applications in micro/nanosystems.
MICROSYSTEMS & NANOENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Audrey Cochard, Adham Safieddine, Pauline Combe, Marie-Noelle Benassy, Dominique Weil, Zoher Gueroui
Summary: This study develops a method to manipulate the localization of RNA in cells using bioengineered motor-condensates, thereby providing new tools for studying the impact of RNA localization on cellular functions.
Editorial Material
Multidisciplinary Sciences
Telmo O. Paiva, Albertus Viljoen, Yves F. Dufrene
Summary: Advancements in atomic force microscopy (AFM) techniques and methodologies in microbiology have enhanced our understanding of microbial cell surfaces. Recent studies have shown that AFM imaging of cells and membranes at or near molecular resolution enables detailed visualization of membrane-drug interactions.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Dmitry K. Zharkov, Andrey V. Leontyev, Artemi G. Shmelev, Larisa A. Nurtdinova, Anton P. Chuklanov, Niaz I. Nurgazizov, Victor G. Nikiforov
Summary: We conducted luminescence response studies on a single YVO4:Yb, Er particle with a size of 1 μm. Yttrium vanadate nanoparticles are known for their low sensitivity to surface quenchers, making them suitable for biological applications. YVO4:Yb, Er nanoparticles were synthesized using the hydrothermal method and exhibited bright green upconversion luminescence. The study found significant differences between the collective luminescent response of an ensemble of nanoparticles and that of a single particle, indicating highly individual upconversion properties of single particles. It emphasizes the importance of studying and calibrating the individual photophysical properties of upconversion particles when using them as single sensors for local parameters of a medium.
Article
Physics, Applied
Shiquan Lin, Zhong Lin Wang
Summary: Inspired by TENG, scanning TENG is proposed for local surface charge density measurement using atomic force microscopy. The technique taps a conductive tip above a charged dielectric surface to induce an AC, with Fourier analysis showing a linear relation to surface charge density. Results demonstrate its power in probing nanoscale charge transfer in contact-electrification.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Physical
Miles F. Beaux, Reuben J. Peterson, Igor O. Usov
Summary: Atomic force microscopy was used to map the topography and qualitative mechanical characteristics of gallium-stabilized delta-phase plutonium coupons. The initial rough and heterogeneous surface of plutonium was observed, along with distinct striation patterns in qualitative nanomechanical mapping. Investigation suggested that the striations were not measurement artifacts or plutonium-specific features, and were influenced by mechanical working of the surface.
SURFACES AND INTERFACES
(2021)
Article
Chemistry, Physical
Francisco J. Solis, Monica Olvera de la Cruz
Summary: This article discusses the interactions between charged particles and induced polarization charge on solid-liquid or liquid-liquid interfaces with dielectric contrast, as well as the self-energy of charged particles near rough surfaces. Results show that the local convexity and concavity of the surface affect the repulsion of ions.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Cell Biology
Elma Sakinatus Sajidah, Keesiang Lim, Tomoyoshi Yamano, Goro Nishide, Yujia Qiu, Takeshi Yoshida, Hanbo Wang, Akiko Kobayashi, Masaharu Hazawa, Firli R. P. Dewi, Rikinari Hanayama, Toshio Ando, Richard W. Wong
Summary: Small extracellular vesicles (sEVs) play a crucial role in cell communication and can be used for drug delivery and structural characterization of nanoparticles. The high-speed atomic force microscopy (HS-AFM) can evaluate the structural changes of sEVs under different physicochemical stresses.
JOURNAL OF EXTRACELLULAR VESICLES
(2022)
Article
Mechanics
Abbasali Abouei Mehrizi, Qiao Liu, Hao Wang
Summary: The extended thin-film region adjacent to the contact line plays a crucial role in heat transfer and wetting dynamics by enhancing heat transfer and influencing contact line morphology. The study focused on advancing contact line morphology induced by water vapor condensation at low rates. Results showed that the morphology of the liquid film in this process differs from nonvolatile cases, with a precursor nanofilm and nanodroplets detected beyond the contact line.
Article
Multidisciplinary Sciences
Alex Evilevitch, Sophia Hohlbauch
Summary: This study investigated the mechanical response of the nucleus during the initial stage of herpesvirus infection by using atomic force microscopy. It was found that the chromatin becomes stiffer while the nuclear lamina becomes softer after the injection of viral DNA, which may contribute to maintaining nuclear integrity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Lin Wu, Dian Chen, Jienyu Ding, Yu Liu
Summary: This study used stopped-flow fluorescence to track structural switches in the full-length adenine riboswitch in real time, revealing that adenine binds more rapidly than helix P4 and the binding pocket, followed by stabilization of the binding pocket, P4, and annealing of P1. Additionally, a transient intermediate consisting of an unwound P1 was detected during adenine binding in both the WT riboswitch and a functional mutant, providing insights into the conformational changes triggered by a ligand in the riboswitch RNA.
Article
Chemistry, Analytical
Xinyu Li, Li Zhao, Rongrong Feng, Xiaowei Du, Zelin Guo, Yu Meng, Yulan Zou, Wenchao Liao, Qiyuan Liu, Yaohuan Sheng, Gaowei Zhao, Haijian Zhong, Weidong Zhao
Summary: Using atomic force microscopy, it was found that Na(V)1.5 is irregularly distributed on the surfaces of both normal and cancer breast cells, with higher expression on cancer cells. The stability of the Na(V)1.5-antibody complex is higher on normal breast cells compared to cancer breast cells. These findings provide insights into the interactions of ion channel-antibody systems and the role of sodium channels in tumor metastasis and invasion.
ANALYTICAL METHODS
(2023)
Article
Chemistry, Multidisciplinary
Niklas A. Weber, Hendrik Schmidt, Tim Sievert, Christian Jooss, Friedrich Guethoff, Vasily Moshneaga, Konrad Samwer, Matthias Krueger, Cynthia A. Volkert
Summary: This study investigates the mechanism of friction at sliding contacts, proposing that friction can be explained by considering the damping of stick-slip pulses. The findings provide a basis for reconciling controversies in literature studies on friction and suggest possible tactics for controlling friction.
Article
Cell Biology
Dmitry A. Kretov, Daria A. Mordovkina, Irina A. Eliseeva, Dmitry N. Lyabin, Dmitry N. Polyakov, Vandana Joshi, Benedicte Desforges, Loic Hamon, Olga I. Lavrik, David Pastre, Patrick A. Curmi, Lev P. Ovchinnikov
Article
Biochemistry & Molecular Biology
S. Pankivskyi, D. Pastre, E. Steiner, V Joshi, A. Rynditch, L. Hamon
Summary: SAM68 is an mRNA-binding protein involved in mRNA processing in the nucleus, and its interaction with ITSN1 can enhance its solubility, regulating the processing of a fraction of nuclear mRNAs. ITSN1 and mRNA may act together to promote SAM68 solubilization, which is important for SAM68-controlled splicing events related to higher neuronal functions or cancer progression.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Maria V. Sukhanova, Anastasia S. Singatulina, David Pastre, Olga I. Lavrik
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Multidisciplinary Sciences
Leonardo David Herrera-Zuniga, Liliana Marisol Moreno-Vargas, Luck Ballaud, Jose Correa-Basurto, Diego Prada-Gracia, David Pastre, Patrick A. Curmi, Jean Michel Arrang, Rachid C. Maroun
SCIENTIFIC REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Konstantin N. Naumenko, Mariya Sukhanova, Loic Hamon, Tatyana A. Kurgina, Elizaveta E. Alemasova, Mikhail M. Kutuzov, David Pastre, Olga Lavrik
Article
Biology
Anastasiia Samsonova, Krystel El Hage, Benedicte Desforges, Vandana Joshi, Marie-Jeanne Clement, Guillaume Lambert, Helene Henrie, Nicolas Babault, Pierrick Craveur, Rachid C. Maroun, Emilie Steiner, Ahmed Bouhss, Alexandre Maucuer, Dmitry N. Lyabin, Lev P. Ovchinnikov, Loic Hamon, David Pastre
Summary: Samsonova et al. demonstrate a cooperative association of Lin28 and YB-1 for target mRNA through their cold-shock domain, suggesting that this association may contribute to translational plasticity during development and adaptation of cancer cells to adverse environments.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Asaki Kobayashi, Marie-Jeanne Clement, Pierrick Craveur, Krystel El Hage, Jean de Matha Salone, Guillaume Bollot, David Pastre, Alexandre Maucuer
Summary: Splicing factor mutations are common in various cancers, and cells with these mutations are vulnerable to certain drugs. Through virtual screening and experimental validation, researchers discovered a small molecule, UHMCP1, that can disrupt specific splicing factor interactions, affecting RNA splicing and cell viability.
Article
Biochemistry & Molecular Biology
Karina Budkina, Krystel El Hage, Marie-Jeanne Clement, Benedicte Desforges, Ahmed Bouhss, Vandana Joshi, Alexandre Maucuer, Loic Hamon, Lev P. Ovchinnikov, Dmitry N. Lyabin, David Pastre
Summary: The study reveals that YB-1 can unwind mRNA secondary structures under cellular stress by utilizing its cold-shock domain and C-terminal domain. YB-1 aids in stress granule disassembly during recovery, and its overexpression inhibits stress granule assembly in cancer cells by promoting mRNA translation initiation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Juan Carlos Rengifo-Gonzalez, Krystel El Hage, Marie-Jeanne Clement, Emilie Steiner, Vandana Joshi, Pierrick Craveur, Dominique Durand, David Pastre, Ahmed Bouhss
Summary: The study reveals that the tandem RNA recognition motifs of TDP-43 cooperatively bind to long GU-repeats, maintaining its solubility. The cooperative binding of TDP-43 to mRNA is crucial for preserving its solubility in the nucleus and miscibility in cytoplasmic stress granules.
Article
Biology
Krystel El Hage, Nicolas Babault, Olek Maciejak, Benedicte Desforges, Pierrick Craveur, Emilie Steiner, Juan Carlos Rengifo-Gonzalez, Helene Henrie, Marie-Jeanne Clement, Vandana Joshi, Ahmed Bouhss, Liya Wang, Cyril Bauvais, David Pastre
Summary: RNA-protein interactions (RPIs) hold promise as therapeutic targets, but lack of methods and feedback between computational and experimental techniques hampers drug discovery. In this study, we address these challenges by developing an approach that combines computational techniques and cell-based scoring to identify small RPI inhibitors, focusing on the Y-box binding protein 1 (YB-1). We validated 22 hits using molecular dynamics simulations and nuclear magnetic resonance spectroscopy, and found that 11 significantly interfere with mRNA binding to YB-1 in cells. One of the leads is an FDA-approved PARP-1 inhibitor. This work demonstrates the potential of our integrative approach for rational development of RPI inhibitors.
Article
Biology
Binita Goswami, Deepika Ahuja, David Pastre, Partho Sarothi Ray
Summary: Post-transcriptional regulation of p53, controlled by miR-125b and HuR, determines its expression in response to DNA damage. miR-125b represses p53 mRNA translation, while its reduction upon DNA damage relieves the repression, leading to pulsatile expression of p53. The decrease in miR-125b level is caused by enhanced exosomal export mediated by HuR, while the subsequent increase is due to p53-mediated transcriptional upregulation and enhanced processing. The reciprocal feedback loops between miR-125b and p53 contribute to the fine-tuned temporal regulation of p53 expression.
COMMUNICATIONS BIOLOGY
(2023)
Article
Cell Biology
Evgeniya M. Mamontova, Marie-Jeanne Clement, Maria V. Sukhanova, Vandana Joshi, Ahmed Bouhss, Juan Carlos Rengifo-Gonzalez, Benedicte Desforges, Loic Hamon, Olga I. Lavrik, David Pastre
Summary: In this study, it was discovered that the RNA-binding protein FUS is directed to PAR through its RNA recognition motif, enhancing PAR synthesis. Specific residues in the FUS RRM were found to be PARylated by PARP-1 to control PAR synthesis levels. A model was proposed where FUS is released from nascent mRNA during transcriptional arrest and recruited by DNA-damage activated PARP-1 to stimulate PAR synthesis. This model offers new perspectives on the role of FET proteins in cancers and neurodegenerative diseases.
