Article
Biophysics
Soochul Shin, Sun Han, Juyoung Kim, Yumi Shin, Ji-Joon Song, Sungchul Hohng
Summary: SIMUL is a multiplexed ctDNA detection technique that can sensitively and specifically detect multiple single-nucleotide mutations in early cancer stages. It accurately measures mutant fractions and holds immense potential for clinical applications.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Chemistry, Analytical
Yu P. Zhang, Evgeniia Lobanova, Derya Emin, Sergey V. Lobanov, Antonina Kouli, Caroline H. Williams-Gray, David Klenerman
Summary: This study introduces a new method for the diagnosis of early Parkinson's disease. The results show that the proportion of soluble alpha-synuclein aggregates can distinguish between Parkinson's disease patients and control groups, with Parkinson's disease patients having a higher proportion of larger and rounder alpha-synuclein aggregates. By combining the number and morphology of the aggregates, a new biomarker with improved accuracy for early Parkinson's disease diagnosis was constructed.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Young-Sun Kwon, Jin-Sung Ko, Se-Young Oh, Young Taek Han, Sangmee Ahn Jo
Summary: Alzheimer's disease (AD) is characterized by blood-brain barrier dysfunction. Our study focused on oleracones, a group of flavonoids isolated from Portulaca oleracea L. extract, which has anti-inflammatory and antioxidant effects. We found that oleracone F treatment improved memory dysfunction in AD model transgenic mice by reducing amyloid plaques, amyloid precursor protein levels, and inflammation in the brain. In vitro studies also showed that oleracones D, E, and F blocked the elevation of VCAM-1 protein induced by TNF-alpha, inhibiting leukocyte adhesion. Overall, oleracones ameliorated cognitive impairment by reducing leukocyte infiltration to the brain and modulating brain inflammation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Ye Lin, Fatemeh Sharifi, Sean B. Andersson
Summary: The paper introduces a method based on SMC-EM technology that can simultaneously localize the position of biological macromolecules and estimate motion model parameters. The research results indicate that under low signal conditions, the SMC-EM method outperforms other methods, while at higher signal-to-background ratios, both SMC-EM and MLE-based methods perform equally well and are significantly better than fitting to the MSD.
BIOMEDICAL OPTICS EXPRESS
(2021)
Article
Chemistry, Physical
J. J. Erik Maris, Donglong Fu, Florian Meirer, Bert M. Weckhuysen
Summary: This article reviews the development of spatial and temporal characterization of nanoporous solids using single-molecule localization microscopy, illustrating how this approach can be used to track molecular diffusion and reaction behaviors in nanoporous solids.
ADSORPTION-JOURNAL OF THE INTERNATIONAL ADSORPTION SOCIETY
(2021)
Article
Multidisciplinary Sciences
Yiming Li, Wei Shi, Sheng Liu, Ivana Cavka, Yu-Le Wu, Ulf Matti, Decheng Wu, Simone Koehler, Jonas Ries
Summary: Global fitting algorithm globLoc for multi-channel SMLM significantly improves localization precision and color assignment, by extracting maximum information from correlated signals in multi-channel data through flexible parameter sharing and modeling.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Daniel J. Lightwood, Rebecca J. Munro, John Porter, David McMillan, Bruce Carrington, Alison Turner, Anthony Scott-Tucker, Elizabeth S. Hickford, Antje Schmidt, David Fox, Alison Maloney, Tom Ceska, Tim Bourne, James O'Connell, Alastair D. G. Lawson
Summary: TNF can be inhibited by small molecules that stabilize the TNF trimer in an asymmetric conformation. The authors also developed a monoclonal antibody that selectively binds this inactive form of TNF, enabling both target engagement assessment and structural characterization of TNF binding to TNF receptor 1.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Pranesh Padmanabhan, Andrew Kneynsberg, Esteban Cruz, Rumelo Amor, Jean-Baptiste Sibarita, Jurgen Gotz
Summary: We found that Tau exhibits spatial and kinetic heterogeneity near the plasma membrane, forming nanometer-sized hot spots, which are longer-lasting than its interaction with microtubules. These hot spots are different from Tau condensation on microtubules and independent of cholesterol.
Article
Physics, Multidisciplinary
M. Omidian, S. Leitherer, N. Neel, M. Brandbyge, J. Kroeger
Summary: Through experiments and calculations, we found that under an external electric field, the polar covalent bond between a gold atom and a carbon atom on graphene exhibits different strengths and stabilities depending on the orientation of the field.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Kirill Vasilev, Benjamin Doppagne, Tomas Neuman, Anna Roslawska, Herve Bulou, Alex Boeglin, Fabrice Scheurer, Guillaume Schull
Summary: The authors demonstrate the internal Stark effect by observing spectral shifts in the fluorescence spectrum of a phthalocyanine molecule caused by electrostatic fields generated within the molecule itself. This phenomenon of tuning chromophores' optical properties using electrostatic fields is known as the internal Stark effect (ISE) and plays a crucial role in optimizing complex functions in living organisms. By sequentially removing central protons from a free-base phthalocyanine chromophore with a scanning tunneling microscope, the authors were able to measure the Stark shift in the emission energy caused by the charges confined within the chromophore.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Takahiro K. Fujiwara, Taka A. Tsunoyama, Shinji Takeuchi, Ziya Kalay, Yosuke Nagai, Thomas Kalkbrenner, Yuri L. Nemoto, Limin H. H. Chen, Akihiro C. E. Shibata, Kokoro Iwasawa, Ken P. Ritchie, Kenichi G. N. Suzuki, Akihiro Kusumi
Summary: The ultrafast camera developed by Fujiwara et al. has significantly improved the time resolution of single-molecule localization microscopy, revealing the dynamic nano-architecture of focal adhesions and leading to the model of compartmentalized focal adhesion protein islands.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Limin Xiang, Rui Yan, Kun Chen, Wan Li, Ke Xu
Summary: Using single-molecule displacement/diffusivity mapping (SMdM), we analyzed the diffusion of a typical fluorescent protein (FP) in living mammalian cells at nanoscale resolution. We found that the diffusion coefficients in the endoplasmic reticulum (ER) and mitochondrion are about 40% of that in the cytoplasm, with higher spatial inhomogeneities in the cytoplasm. Furthermore, we discovered that positive net charges impede diffusions in the ER lumen and mitochondrial matrix, while negative net charges do not.
Article
Multidisciplinary Sciences
Linfei Li, Jeremy F. Schultz, Sayantan Mahapatra, Zhongyi Lu, Xu Zhang, Nan Jiang
Summary: By using ultrahigh vacuum tip-enhanced Raman spectroscopy (UHV-TERS), single oxygen adatoms on a boron monolayer (borophene) can be identified and mapped with a spatial resolution of approximately 4.8 angstrom and single bond sensitivity. This technique enables the atomically defined, chemically homogeneous, and thermally reversible oxidation of borophene via atomic oxygen in UHV. Additionally, it reveals the propensity of borophene towards molecular oxygen activation at room temperature and phase-dependent chemical properties. Overall, this work demonstrates the powerful utility of UHV-TERS in probing the local chemistry of surface adsorbates in the atomic regime and has important applications in heterogeneous catalysis, on-surface molecular engineering, and low-dimensional materials.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Soeren Doose
Summary: Single-molecule localization microscopy has become an important tool in biomedical research. The LOCAN Python library provides well-defined data structures and analysis methods for analyzing localization data in a script or computable notebook.
Article
Chemistry, Physical
Mengdi Hou, Fulin Xing, Jianyu Yang, Fen Hu, Leiting Pan, Jingjun Xu
Summary: This study develops a method called ultrastructure expansion single-molecule localization microscopy (U-ExSMLM) to dissect the membrane cytoskeleton structure of human erythrocytes at molecular resolution. The method provides direct evidence for cytoskeleton asymmetry in erythrocytes and offers future opportunities for studying the ultrastructure of membrane cytoskeleton.
Article
Multidisciplinary Sciences
Audrey Durand, Theresa Wiesner, Marc-Andre Gardner, Louis-Emile Robitaille, Anthony Bilodeau, Christian Gagne, Paul De Koninck, Flavie Lavoie-Cardinal
NATURE COMMUNICATIONS
(2018)
Article
Cell Biology
Stephen D. Glasgow, Simon Labrecque, Ian Beamish, Sarah Aufmkolk, Julien Gibon, Dong Han, Stephanie N. Harris, Paul Dufresne, Paul W. Wiseman, R. Anne McKinney, Philippe Seguela, Paul De Koninck, Edward S. Ruthazer, Timothy E. Kennedy
Article
Neurosciences
Christian Tardif, Gabriel Nadeau, Simon Labrecque, Daniel Cote, Flavie Lavoie-Cardinal, Paul De Koninck
Article
Cell Biology
Charleen Salesse, Julien Charest, Helene Doucet-Beaupre, Anne-Marie Castonguay, Simon Labrecque, Paul De Koninck, Martin Levesque
Article
Multidisciplinary Sciences
Flavie Lavoie-Cardinal, Anthony Bilodeau, Mado Lemieux, Marc-Andre Gardner, Theresa Wiesner, Gabrielle Laramee, Christian Gagne, Paul De Koninck
SCIENTIFIC REPORTS
(2020)
Article
Neurosciences
Theresa Wiesner, Anthony Bilodeau, Renaud Bernatchez, Andreanne Deschenes, Bastian Raulier, Paul De Koninck, Flavie Lavoie-Cardinal
FRONTIERS IN NEURAL CIRCUITS
(2020)
Article
Biology
Cedric Bressan, Alessandra Pecora, Dave Gagnon, Marina Snapyan, Simon Labrecque, Paul De Koninck, Martin Parent, Armen Saghatelyan
Review
Biochemical Research Methods
Jeffrey K. Cornuault, Gabriel Byatt, Marie-Eve Paquet, Paul De Koninck, Sylvain Moineau
Summary: The zebrafish model is gaining attention for investigating microbiota-host interactions due to its low cost, ability to assess large cohorts, and availability of optical methodologies. Recent findings have revealed the modulation of zebrafish gut microbiota by exogenous microbes, nutrition, and environmental factors. This model also shows potential for assessing the impact of gut microbiota on brain development.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Valerie Van Steenbergen, Flavie Lavoie-Cardinal, Youcef Kazwiny, Marianna Decet, Tobie Martens, Patrik Verstreken, Werend Boesmans, Paul De Koninck, Pieter Vanden Berghe
Summary: The correct distribution of organelles and vesicles in cells is crucial for cell functioning. In polarized cells such as neurons, the transport of mitochondria, which play a key role in producing energy and buffering calcium, is especially important. This study found that the molecular conformation of tubulin affects mitochondrial transport in neurons. The position of a mitochondrion within or at the rim of a microtubule bundle determines the impact of tubulin conformation on mitochondrial transport.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Computer Science, Artificial Intelligence
Anthony Bilodeau, Constantin V. L. Delmas, Martin Parent, Paul De Koninck, Audrey Durand, Flavie Lavoie-Cardinal
Summary: This study proposes a weakly supervised MICRoscopy Analysis neural network (MICRA-Net) that can be trained on a simple main classification task using image-level annotations to solve more complex tasks such as semantic segmentation. MICRA-Net relies on extracted latent information from a trained model to achieve similar performances as established architectures, reducing the annotation burden in microscopy datasets.
NATURE MACHINE INTELLIGENCE
(2022)
Proceedings Paper
Education, Scientific Disciplines
Andreanne Deschenes, Flavie Lavoie-Cardinal, Mario Methot, Paul De Koninck
FIFTEENTH CONFERENCE ON EDUCATION AND TRAINING IN OPTICS AND PHOTONICS (ETOP 2019)
(2019)
Proceedings Paper
Computer Science, Artificial Intelligence
Louis-Emile Robitaille, Audrey Durand, Marc-Andre Gardner, Christian Gagne, Paul De Koninck, Flavie Lavoie-Cardinal
THIRTY-SECOND AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE / THIRTIETH INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE / EIGHTH AAAI SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE
(2018)
Proceedings Paper
Computer Science, Artificial Intelligence
Louis-Emile Robitaille, Audrey Durand, Marc-Andre Gardner, Christian Gagne, Paul De Koninck, Flavie Lavoie-Cardinal
THIRTY-SECOND AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE / THIRTIETH INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE / EIGHTH AAAI SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE
(2018)
Article
Biochemistry & Molecular Biology
Sarah Malvaut, Simona Gribaudo, Delphine Hardy, Linda Suzanne David, Laura Daroles, Simon Labrecque, Marie-Anne Lebel-Cormier, Zayna Chaker, Daniel Cote, Paul De Koninck, Martin Holzenberger, Alain Trembleau, Isabelle Caille, Armen Saghatelyan
Article
Biochemistry & Molecular Biology
Pei-Yang Gao, Ya-Nan Ou, Yi-Ming Huang, Zhi-Bo Wang, Yan Fu, Ya-Hui Ma, Qiong-Yao Li, Li-Yun Ma, Rui-Ping Cui, Yin-Chu Mi, Lan Tan, Jin-Tai Yu
Summary: Liver function may play a role in the progression of Alzheimer's disease. The study found that as AD progressed, certain liver function markers increased while others decreased. The relationship between liver function and CSF AD biomarkers indicates a potential mediation effect on cognition.
JOURNAL OF NEUROCHEMISTRY
(2024)