Article
Chemistry, Multidisciplinary
Alexandre Chappard, Craig Leighton, Rebecca S. S. Saleeb, Kiani Jeacock, Sarah R. R. Ball, Katie Morris, Owen Kantelberg, Ji-Eun Lee, Elsa Zacco, Annalisa Pastore, Margaret Sunde, David J. J. Clarke, Patrick Downey, Tilo Kunath, Mathew H. H. Horrocks
Summary: Protein misfolding and aggregation are common features of neurogenerative disorders. Single-molecule techniques have allowed the characterization of these protein aggregates, previously inaccessible with traditional methods. In this study, we employed a high affinity antibody labeled with orthogonal fluorophores, along with fast-flow microfluidics and single-molecule confocal microscopy, to specifically detect alpha-synuclein in biologically relevant samples.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
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
Biochemical Research Methods
Arindam Ghosh, Alexey Chizhik, Narain Karedla, Joerg Enderlein
Summary: Super-resolution fluorescence imaging is commonly used to study the spatial organization of biological structures at molecular scales, achieving resolutions beyond the classical optical limit. Various methods have been developed for super-resolution imaging along the optical axis, with some reaching nanometer accuracy in 3D localization. However, these approaches can be technically complex and have limited applicability. Metal-induced energy transfer imaging offers a simpler alternative for nanometer-scale axial localization of fluorophores.
Article
Multidisciplinary Sciences
Aleksandr Barulin, Prithu Roy, Jean-Benoit Claude, Jerome Wenger
Summary: The authors introduce optical horn antennas, a nanophotonic platform, for the label-free detection of UV autofluorescence from single proteins. This technique allows for real-time monitoring of protein unfolding and dissociation.
NATURE COMMUNICATIONS
(2022)
Article
Biophysics
Tanmay Chatterjee, Alexander Johnson-Buck, Nils G. Walter
Summary: Sensitive assays of protein biomarkers play a critical role in clinical diagnostics and biomedical research. Nucleic acid aptamers generated by SELEX have shown promise as an alternative to immunoreagents for detection, offering advantages in synthesis and reproducibility. SiMREPS, a single molecule recognition platform, allows for high sensitivity detection of biomarkers without requiring high-affinity probes. This study demonstrates the applicability of aptamers as detection probes in SiMREPS for two clinically relevant biomarkers, VEGF165 and IL-8, with detection limits in the low femtomolar range.
BIOSENSORS & BIOELECTRONICS
(2022)
Review
Chemistry, Analytical
Hui Wang, Cuilin Zhu, Di Li
Summary: The emergence of single-molecule techniques has greatly advanced research in enzymology. Single-molecule enzymology studies the individual behavior of a single enzyme molecule, which is hidden under the overall average. This review summarizes the emerging developments of several single-molecule techniques, such as TIRFM, confocal microscopy, FCS, and magnetic/optical tweezers, in real-time monitoring of the catalytic process of single enzymes. It explores various enzymatic catalytic behaviors and mechanisms that differ from bulk experiments, providing a deeper understanding of enzymatic reaction mechanisms through the analysis of single-molecule enzymatic kinetics coupled with conformational changes. Additionally, this review critically discusses the future challenges of imaging and monitoring single enzymatic reactions in cellular environments.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Stefan Niekamp, Nico Stuurman, Nan Zhang, Ronald D. Vale
Summary: The study reveals that during motility, the motor protein dynein exhibits variability in the movement between its domains, with the AAA ring and MTBDs not always stepping simultaneously and taking differently sized steps. This variability results in a large number of unexpected conformational states of dynein during motility. The flexibility between major dynein domains is found to be critical for dynein motility.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Antonio Garcia, Shannon J. Saluga, David J. Dibble, Pia A. Lopez, Nozomi Saito, Suzanne A. Blum
Summary: This study for the first time imaged the selectivity of individual molecular catalysts for two different reactions in real time at the single-catalyst level, revealing that catalyst selectivity may be unexpectedly spatially and time-variable in ruthenium-catalyzed polymerization.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Klara Strobl, Ekaterina Selivanovitch, Pablo Ibanez-Freire, Francisco Moreno-Madrid, Iwan A. T. Schaap, Rafael Delgado-Buscalioni, Trevor Douglas, Pedro J. de Pablo
Summary: This study explores a method for studying molecular function in confined environments by packing biomolecules inside virus capsids and monitoring the emission signal of green fluorescent proteins using atomic force microscopy and total internal reflection fluorescence microscopy. The results show that mechanical and electronic quenching can be decoupled by using different tips, revealing insights into the behavior of green fluorescent proteins within virus capsids.
Article
Biochemical Research Methods
Jack W. Shepherd, Sarah Lecinski, Jasmine Wragg, Sviatlana Shashkova, Chris MacDonald, Mark C. Leake
Summary: This study used cutting-edge genomically integrated FRET biosensing to determine localized molecular crowding in single live yeast cells, finding that crowding is reduced when yeast is grown in elevated glucose concentrations. Simulations indicated that the cell membrane is largely inaccessible to these sensors, and that cytosolic crowding is broadly uniform across each cell over a timescale of seconds.
Article
Optics
Prakash Joshi, Partha Pratim Mondal
Summary: Molecular assembly in cellular environments is crucial for understanding biological mechanisms. Biophysical parameters directly linked to cellular states require a multimodel approach for accurate estimation.
Article
Biology
Yufeng Zhou, John H. Lewis, Zhe Lu, Kenton J. Swartz
Summary: This study successfully tracked the multistate conformational changes of the membrane protein AdiC using a high-resolution fluorescence-polarization-microscopy method. By monitoring the emission-polarization changes of a fluorophore label, four conformations of AdiC were resolved and their probabilities were quantified in the presence of different concentrations of the substrate arginine. The acquired data allowed for the determination of all equilibrium constants and provided insights into the energetic relations among the four states.
Article
Chemistry, Multidisciplinary
George N. Samaan, Mckenzie K. Wyllie, Julian M. Cizmic, Lisa-Maria Needham, David Nobis, Katrina Ngo, Susan Andersen, Steven W. Magennis, Steven F. Lee, Byron W. Purse
Summary: A new tricyclic pyrimidine nucleoside analogue named ABN was designed and synthesized, which exhibited improved brightness and fluorescence properties in water, becoming the brightest and most red-shifted nucleobase analogue known in duplex DNA. Single-molecule fluorescence measurements of ABN showed excellent photostability with high count rates, offering robust and accessible single-molecule fluorescence detection capabilities.
Article
Chemistry, Analytical
Xinyu Zhou, Rui Wang, Zijian Wan, Pengfei Zhang, Shaopeng Wang
Summary: In this study, we demonstrate multiplexed protein detection and parallel protein interaction analysis through evanescent scattering microscopy (ESM). ESM allows label-free digital single-molecule counting for binding kinetics measurement, improving counting efficiency and accuracy. We show that digital single-molecule counting can differentiate proteins with different molecular weights, enabling real-time monitoring of protein binding processes in solution. Additionally, we show that this strategy can analyze the kinetics of two different protein interaction processes simultaneously, both on surfaces and in solution. This work may provide a way to investigate complex protein interactions, such as the competition between biomarker-antibody binding in biofluids and biomarker-protein binding on cellular membranes.
ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Yoonsuk Hyun, Doory Kim
Summary: With the development of super-resolution imaging techniques, understanding protein structure at the nanoscale in terms of clustering and organization in a cell is crucial. This review categorizes computational cluster analysis methods for single-molecule localization microscopy (SMLM) images into classical and machine learning-based methods, and discusses possible future directions for machine learning-based cluster analysis methods for SMLM data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Dentistry, Oral Surgery & Medicine
Y. Matsuda, J. Miura, M. Shimizu, T. Aoki, M. Kubo, S. Fukushima, M. Hashimoto, F. Takeshige, T. Araki
JOURNAL OF DENTAL RESEARCH
(2016)
Article
Chemistry, Analytical
De Xing Lioe, Kamel Mars, Shoji Kawahito, Keita Yasutomi, Keiichiro Kagawa, Takahiro Yamada, Mamoru Hashimoto
Article
Materials Science, Multidisciplinary
Shoichiro Fukushima, Taichi Furukawa, Hirohiko Niioka, Masayoshi Ichimiya, Takumi Sannomiya, Jun Miyake, Masaaki Ashida, Tsutomu Araki, Mamoru Hashimoto
OPTICAL MATERIALS EXPRESS
(2016)
Article
Chemistry, Multidisciplinary
Doan Thi Kim Dung, Shoichiro Fukushima, Taichi Furukawa, Hirohiko Niioka, Takumi Sannomiya, Kaori Kobayashi, Hiroshi Yukawa, Yoshinobu Baba, Mamoru Hashimoto, Jun Miyake
Article
Chemistry, Analytical
Kamel Mars, De Xing Lioe, Shoji Kawahito, Keita Yasutomi, Keiichiro Kagawa, Takahiro Yamada, Mamoru Hashimoto
Article
Biochemical Research Methods
Takeo Minamikawa, Yoshinori Murakami, Naokazu Matsumura, Hirohiko Niioka, Shuichiro Fukushima, Tsutomu Araki, Mamoru Hashimoto
JOURNAL OF SPECTROSCOPY
(2017)
Article
Biochemical Research Methods
K. Hirose, T. Aoki, T. Furukawa, S. Fukushima, H. Niioka, S. Deguchi, M. Hashimoto
BIOMEDICAL OPTICS EXPRESS
(2018)
Article
Biochemistry & Molecular Biology
Naoki Yamato, Mana Matsuya, Hirohiko Niioka, Jun Miyake, Mamoru Hashimoto
Article
Multidisciplinary Sciences
Naoki Yamato, Hirohiko Niioka, Jun Miyake, Mamoru Hashimoto
SCIENTIFIC REPORTS
(2020)
Article
Optics
Hiroki Ogawa, Mamoru Hashimoto
Summary: A method of suppressing four-wave mixing in an optical fiber bundle to achieve coherent anti-Stokes Raman scattering (CARS) endomicroscopy was proposed and demonstrated, with successful CARS imaging of a polystyrene bead and effective suppression of background emission.
Article
Chemistry, Physical
Shun Kizawa, Mamoru Hashimoto
Summary: The study introduces a novel concept of elliptical focal spot for efficient signal acquisition, enabling high-speed coherent anti-Stokes Raman scattering (CARS) microspectroscopy even in short exposure times. The system's ultrafast imaging capabilities have broad applications in the field of biology, with minimal photodamage to living cells.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Computer Science, Information Systems
Shukri Bin Korakkottil Kunhi Mohd, De Xing Lioe, Keita Yasutomi, Keiichiro Kagawa, Mamoru Hashimoto, Shoji Kawahito
Summary: This paper proposes an SRS double-demodulation lock-in amplifier implemented with CMOS image sensor technology, which integrates two-stage 1/f noise and offset reduction circuits with a high-speed lateral electric field modulation (LEFM) photo-demodulator. The lock-in amplifier demodulates at 40 MHz with a sampling frequency of 20 MHz, suppressing the circuit's 1/f noise to achieve higher detection sensitivity. Both simulation and measurement results verify the functionality of the prototype chip and demonstrate its ability to reject laser common mode components while emphasizing differences.
Proceedings Paper
Engineering, Biomedical
Naoki Yamato, Mana Matsuya, Hirohiko Niioka, Jun Miyake, Mamoru Hashimoto
Summary: This study presents an improvement in the imaging speed of coherent Raman endoscopic imaging using deep-learning-based segmentation. By investigating the relationship between the exposure time of input images and the quality of output images, the imaging speed was significantly accelerated.
BIOMEDICAL VIBRATIONAL SPECTROSCOPY 2022: ADVANCES IN RESEARCH AND INDUSTRY
(2022)
Article
Optics
Keigo Hirose, Shuichiro Fukushima, Taichi Furukawa, Hirohiko Niioka, Mamoru Hashimoto
Proceedings Paper
Optics
DeXing Lioe, Kamel Mars, Taishi Takasawa, Keita Yasutomi, Keiichiro Kagawa, Mamoru Hashimoto, Shoji Kawahito
HIGH-SPEED BIOMEDICAL IMAGING AND SPECTROSCOPY: TOWARD BIG DATA INSTRUMENTATION AND MANAGEMENT
(2016)