Article
Biochemistry & Molecular Biology
David Ngai, Amanda L. Mohabeer, Amanda Mao, Marsel Lino, Michelle P. Bendeck
Summary: DDR1 regulates its own expression through the YAP/TAZ signaling pathway. In response to increased matrix stiffness, collagen stimulation, or RhoA activation, YAP/TAZ translocates to the nucleus and binds to chromatin, promoting transcription of the DDR1 gene.
Article
Materials Science, Multidisciplinary
Aram Bahmani, J. William Pro, Florent Hannard, Francois Barthelat
Summary: This study examines the assembly process and mechanisms of hard cubic grains using vibration as a potential method for rapid fabrication of structured materials. The results show that the acceleration normalized by gravity cannot fully capture the phase transitions or the mechanisms governing cubes packing and that amplitude and frequency must be considered independently. Cube rotation and bouncing play crucial roles in the assembly process.
Article
Chemistry, Multidisciplinary
Kyunglim Pyo, Maria Francisca Matus, Eero Hulkko, Pasi Myllyperkio, Sami Malola, Tatu Kumpulainen, Hannu Hakkinen, Mika Pettersson
Summary: Understanding the dynamics of FRET in fluorophore-functionalized nanomaterials is crucial for their applications in biomedical imaging and optical sensing. This study investigates the structural dynamics of noncovalently bound azadioxotriangulenium dye and gold nanoclusters, revealing their energy transfer mechanism and providing new insights at an atomistic level. Experimental and computational methods were used to resolve distinct subpopulations involved in the energy transfer process, and molecular dynamics simulations explained the observed phenomena. The observed energy transfer rates were in accordance with the well-known 1/R(6) distance dependence for FRET.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Mathematics
Radomir Halas, Jozef Pocs, Jana Pocsova
Summary: This paper focuses on three important classes of aggregation functions, including the lattice of all aggregation functions, the lattice of idempotent aggregation functions, and the lattice of Sugeno integrals. The lattice structures of these classes are characterized using join-dense subsets, and the minimality of these sets is also discussed.
Article
Cell Biology
Shan Wang, Emelie Englund, Pontus Kjellman, Zhen Li, Johannes Kumra Ahnlide, Carmen Rodriguez-Cupello, Mattia Saggioro, Ryu Kanzaki, Kristian Pietras, David Lindgren, Hakan Axelson, Christelle N. Prinz, Vinay Swaminathan, Chris D. Madsen
Summary: Wang et al. have identified CCM3 as a negative regulator of YAP/TAZ activation and mechanotransduction in focal adhesions, with crucial roles in controlling mesenchymal/stromal stem cell differentiation and metastasis. CCM3 functions as a gatekeeper in focal adhesions, regulating mechanotransduction and YAP/TAZ signaling by competing with focal adhesion kinase for binding to paxillin. Loss of CCM3 in cancer-associated fibroblasts leads to exacerbated tissue remodelling and metastasis dissemination in mouse models of breast cancer.
NATURE CELL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Ines H. Kaltheuner, Kanchan Anand, Jonas Moecking, Robert Duester, Jinhua Wang, Nathanael S. Gray, Matthias Geyer
Summary: Abemaciclib, a CDK inhibitor for breast cancer treatment, also targets HIPKs and DYRK1A. HIPKs play a role in signal pathway regulation, and DYRK1A is inhibited by Abemaciclib in vitro to a similar extent as Cdk4/Cdk6.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Wan Xu, Xiao-Di Liu, Miriam Pena-Alvarez, Hua-Chao Jiang, Philip Dalladay-Simpson, Benoit Coasne, Julien Haines, Eugene Gregoryanz, Mario Santoro
Summary: The study reveals that zeolite can accommodate a high concentration of H-2 molecules under high pressure, forming a unique glassy-like structure that is unattainable in pure hydrogen. Raman spectroscopy shows that the microporosity of the zeolite remains intact under high pressure, with intermolecular interactions influenced by the zeolite framework.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Multidisciplinary Sciences
V Freret-Lorgeril, C. Bonadonna, E. Rossi, A. P. Poulidis, M. Iguchi
Summary: Characterizing the size and settling velocity of volcanic ash during eruptions is crucial for predicting its dispersion. Using an optical disdrometer for real-time monitoring, this study assesses its accuracy in detecting volcanic ash during fallout. Results show that with proper adjustments, the disdrometer data can provide useful information about the grain size of individual ash particles and filter out aggregates, improving the accuracy of the assessment.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Physical
Bing-shuang Qian, Wen-de Tian, Kang Chen
Summary: The study reveals that the absorption process of particles into a dense porous medium exhibits three distinct types of behavior, depending on the competition of propelling strength versus repulsive barrier and the contrast between permeation and propelling persistence time scales. These behaviors lead to different ways of particle transportation and cluster formation in the medium.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Astronomy & Astrophysics
Pierfrancesco Di Cintio, Mario Pasquato, Alicia Simon-Petit, Suk-Jin Yoon
Summary: This study introduces a new method for simulating collisional gravitational N-body systems and validates some predictions of star cluster evolution before, during, and after core collapse. The results show a power-law relation between the size of the core and the time left to core collapse, a non-monotonic dependence of the collapse time on the mass-function slope, and post-collapse phenomena such as core rebound and evolution of inner density slope. Furthermore, the presence of an intermediate-mass black hole inhibits core collapse.
ASTRONOMY & ASTROPHYSICS
(2022)
Article
Multidisciplinary Sciences
Qinchuan Wang, Erick O. Hernandez-Ochoa, Meera C. Viswanathan, Ian D. Blum, Danh C. Do, Jonathan M. Granger, Kevin R. Murphy, An-Chi Wei, Susan Aja, Naili Liu, Corina M. Antonescu, Liliana D. Florea, C. Conover Talbot, David Mohr, Kathryn R. Wagner, Sergi Regot, Richard M. Lovering, Peisong Gao, Mario A. Bianchet, Mark N. Wu, Anthony Cammarato, Martin F. Schneider, Gabriel S. Bever, Mark E. Anderson
Summary: Antagonistic pleiotropy theory suggests that aging-related diseases are caused by evolved genetic traits that provide advantages in early life. The study of CaMKII shows that its activation by reactive oxygen species was acquired along the vertebrate stem lineage, contributing to the early and continued evolutionary success of vertebrates. This highlights a trade-off where enhanced sensitivity to adverse effects of ROS in diseases and aging is balanced by positive traits that facilitated evolutionary success.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Junsheng Xin, Jing Xu, Chen Zhu, Yupeng Tian, Qiong Zhang, Xi Kang, Manzhou Zhu
Summary: Ligand engineering was used to activate intramolecular interactions and restrict intramolecular rotation of metal nanoclusters, resulting in improved thermal stability, emission intensity, and non-linear optical properties.
Article
Chemistry, Multidisciplinary
Yuan Yuan Liu, Xin Zhang, Kai Li, Qiu Chen Peng, Yu Jing Qin, Hong Wei Hou, Shuang Quan Zang, Ben Zhong Tang
Summary: The study reports butterfly-like molecules of OAP with typical AIE characteristics achieved through the RIV mechanism. OAP AIEgens can be synthesized easily using commercially available materials, making them ideal ligands for constructing MOFs. The OAP-based MOFs have potential applications in gas response, information storage, and white light-emitting devices.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Physical
Julia A. Giannini, Ethan M. Stanifer, M. Lisa Manning
Summary: This study examines structural indicators for predicting plasticity in active materials, developing a computational model and extending a linear response method. The research highlights the significant impact of strong pressure gradients and self-generated free boundaries on the linear response of the system in predicting plasticity in active packings.
Article
Engineering, Chemical
Konstantin Pougatch, Sean Delfel, Majid Hosseini, Benny Moyls, Ardalan Sadighian, Adrian Revington
Summary: A novel mathematical model based on first principles is developed to simulate the flocculation process of dense clay slurries. The model takes into account all major physical processes during flocculation, including polymer mixing, floc formation, fractal growth of aggregates, floc breakage, rheological changes, and flow regime changes. The model uses Population Balance Method to track the evolution of floc size distribution numerically, and is applied to a batch flocculation process in a mixing vessel with an impeller for analysis and comparison with experiments. The model aids in understanding the complex interactions between different phenomena during flocculation.
CHEMICAL ENGINEERING SCIENCE
(2021)
Article
Physics, Applied
Daniel C. Jones, Yuriy Alexandrov, Nathan Curry, Sunil Kumar, Peter M. P. Lanigan, Colin D. McGuinness, Matthew W. Dale, Daniel J. Twitchen, David Fisher, Mark A. A. Neil, Christopher Dunsby, Paul M. W. French
Summary: This study utilized phasor analysis and nonlinear iterative fitting to analyze spectral and lifetime data of CVD diamond, mapping variations in concentrations of nitrogen vacancy (NV) defects and identifying SiV- luminescence. These techniques are crucial for reliable fabrication of quantum devices with well-defined and characterized quantum electronic properties.
JOURNAL OF PHYSICS D-APPLIED PHYSICS
(2021)
Review
Pharmacology & Pharmacy
Yuewei Xu, Anke Nijhuis, Hector C. Keun
Summary: RBM39 is a crucial RNA-binding protein involved in cell cycle progression and tumor regression, while aryl sulphonamides act as molecular glues targeting RBM39 and show potential for anticancer therapy.
BRITISH JOURNAL OF PHARMACOLOGY
(2022)
Article
Biochemical Research Methods
Ranjan Kalita, William Flanagan, Jonathan Lightley, Sunil Kumar, Yuriy Alexandrov, Edwin Garcia, Mark Hintze, Michalis Barkoulas, Chris Dunsby, Paul M. W. French
Summary: The proposed technique utilizes a polarization-sensitive camera to simultaneously acquire four images for calculating phase-contrast images. This polarisation-resolved differential phase contrast (pDPC) microscopy technique can be easily integrated with fluorescence microscopy.
JOURNAL OF BIOPHOTONICS
(2021)
Article
Microscopy
Jonathan Lightley, Frederik Gorlitz, Sunil Kumar, Ranjan Kalita, Arinbjorn Kolbeinsson, Edwin Garcia, Yuriy Alexandrov, Vicky Bousgouni, Riccardo Wysoczanski, Peter Barnes, Louise Donnelly, Chris Bakal, Christopher Dunsby, Mark A. A. Neil, Seth Flaxman, Paul M. W. French
Summary: The study introduces a robust, long-range optical autofocus system for microscopy utilizing machine learning, which can address the issue of defocusing in experiments with long image data acquisition times. Through training a convolutional neural network (CNN) to account for fluctuations in the optical system, the system achieves high accuracy over a wide defocus range and demonstrates application in automated multiwell plate single molecule localization microscopy.
JOURNAL OF MICROSCOPY
(2021)
Article
Multidisciplinary Sciences
Anke Nijhuis, Arti Sikka, Orli Yogev, Lili Herendi, Cristina Balcells, Yurui Ma, Evon Poon, Clare Eckold, Gabriel N. Valbuena, Yuewei Xu, Yusong Liu, Barbara Martins da Costa, Michael Gruet, Chiharu Wickremesinghe, Adrian Benito, Holger Kramer, Alex Montoya, David Carling, Elizabeth J. Want, Yann Jamin, Louis Chesler, Hector C. Keun
Summary: This study demonstrates that high-risk neuroblastoma is sensitive to indisulam, a drug that targets both RNA splicing and cellular metabolism. The researchers show that indisulam induces the loss of RBM39, accumulation of splicing errors, and growth inhibition in neuroblastoma models. Analysis of RNA sequencing and metabolic profiling data reveals disruptions to cell cycle and metabolism in response to indisulam. The authors also demonstrate complete tumor regression without relapse in mice models treated with indisulam, confirming the therapeutic potential of targeting both metabolism and RNA splicing in high-risk neuroblastoma.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Mathew Van de Pette, Antonio Galvao, Steven J. Millership, Wilson To, Andrew Dimond, Chiara Prodani, Grainne McNamara, Ludovica Bruno, Alessandro Sardini, Zoe Webster, James McGinty, Paul French, Anthony G. Uren, Juan Castillo-Fernandez, Rosalind M. John, Anne C. Ferguson-Smith, Matthias Merkenschlager, Gavin Kelsey, Amanda G. Fisher, William Watkinson
Summary: This study demonstrates that a high-fat diet in pregnant mice can lead to the release of silencing of the Dlk1 gene locus in multiple generations of offspring. The authors found that this occurs through changes in microRNA expression and transcriptional changes in the developing oocytes. These findings highlight how diet can impact the fetal epigenome, affecting the properties of successive generations of offspring through intergenerational or trans-generational mechanisms.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Connor Darling, Samuel P. X. Davis, Sunil Kumar, Paul M. W. French, James McGinty
Summary: This paper presents a single-shot adaptive Optical Projection Tomography (OPT) system for high-speed imaging of dynamic mesoscopic biological samples. The system has the advantages of low cost and no need for sample rotation.
JOURNAL OF BIOPHOTONICS
(2023)
Article
Biology
Hannah J. J. Gleneadie, Beatriz Fernandez-Ruiz, Alessandro Sardini, Mathew Van de Pette, Andrew Dimond, Rab K. K. Prinjha, James McGinty, Paul M. W. French, Hakan Bagci, Matthias Merkenschlager, Amanda G. G. Fisher
Summary: Duchenne muscular dystrophy (DMD) is a genetic disorder caused by mutations in the dystrophin gene (Dmd), leading to progressive muscle weakening. A study using mouse models and myoblasts found that chromatin-modifying drugs can increase the expression of utrophin (Utrn), a protein that can compensate for Dmd deficiency. Inhibitors of PRC2 and ERK1/2 were identified to enhance Utrn expression, offering potential therapeutic strategies for DMD.
COMMUNICATIONS BIOLOGY
(2023)
Article
Microscopy
J. Lightley, S. Kumar, M. Q. Lim, E. Garcia, F. Goerlitz, Y. Alexandrov, T. Parrado, C. Hollick, E. Steele, K. Rossmann, J. Graham, J. Broichhagen, I. A. Mcneish, C. A. Roufosse, M. A. A. Neil, C. Dunsby, P. M. W. French
Summary: 'openFrame' is a modular, low-cost, open-hardware microscopy platform that can be configured or adapted to most light microscopy techniques and allows for rapid prototyping and automation.
JOURNAL OF MICROSCOPY
(2023)
Proceedings Paper
Engineering, Biomedical
Connor Darling, Samuel P. X. Davis, Sunil Kumar, Paul M. W. French, James McGinty
Summary: This method presents a single-shot volumetric imaging technique utilizing optical projection tomography. With the implementation of compressive sensing and machine learning, it is capable of recording up to 70 (camera limited) 1x1x1.9mm volumes per second.
ADVANCES IN MICROSCOPIC IMAGING III
(2021)
Proceedings Paper
Engineering, Biomedical
R. Kalita, J. Lightley, S. Kumar, Y. Alexandrov, E. Garcia, W. Flanagan, M. A. A. Neil, C. Dunsby, P. M. W. French
Summary: This robust and low-cost implementation of differential phase microscopy utilises a polarisation-sensitive camera to simultaneously capture 4 images, from which the phase gradients and quantitative phase image can be calculated.
ADVANCES IN MICROSCOPIC IMAGING III
(2021)
Meeting Abstract
Respiratory System
Riccardo Wysoczanski, Jonathan Baker, Peter Fenwick, Chris Dunsby, Paul French, Peter Barnes, Louise Donnelly
EUROPEAN RESPIRATORY JOURNAL
(2021)
Meeting Abstract
Pathology
E. Garcia, J. Lightley, S. Kumar, R. Kalita, F. Gorlitz, Y. Alexandrov, T. Cook, C. Dunsby, M. Neil, C. Roufosse, P. French
Article
Biochemistry & Molecular Biology
Ben Jones, Emma Rose McGlone, Zijian Fang, Phil Pickford, Ivan R. Correa, Atsuro Oishi, Ralf Jockers, Asuka Inoue, Sunil Kumar, Frederik Gorlitz, Chris Dunsby, Paul M. W. French, Guy A. Rutter, Tricia Tan, Alejandra Tomas, Stephen R. Bloom
Summary: The study found that GLP-1R, GIPR, and GCGR agonists with reduced beta-arrestin recruitment can prolong G protein-dependent cAMP/PKA signaling and increase insulin secretion. However, this effect is only seen at high agonist concentrations, and further research is needed to maximize the use of this strategy for therapeutic purposes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Optics
Taylor M. Cannon, Joao L. Lagarto, Benjamin T. Dyer, Edwin Garcia, Douglas J. Kelly, Nicholas S. Peters, Alexander R. Lyon, Paul M. W. French, Chris Dunsby
Summary: The study characterized the fluorescence properties of NADH under various microenvironmental conditions, revealing how temperature, pH, and binding partners impact the fluorescence signature of NADH, leading to competing effects of different parameters and increasing the complexity of the fluorescence data.