Article
Instruments & Instrumentation
Hongxiao Li, Zhiguang Xiang, Chuan Qin, Yingxin Li, Meixiu Sun
Summary: This study validates the capability of spectra to discriminate between human and non-human blood species, and investigates the predictive ability of a binary classification model for unseen animal species. The results show that the model trained with a limited number of animal species can correctly recognize many unseen animal species, highlighting the importance of careful data selection for model building.
INFRARED PHYSICS & TECHNOLOGY
(2022)
Review
Physics, Multidisciplinary
Thomas Andrew Waigh, Nickolay Korabel
Summary: A wide variety of phenomena in cellular and molecular biology involve anomalous transport, which is often heterogeneous in time and space. Single anomalous exponents and generalized diffusion coefficients fail to adequately describe these phenomena, requiring different experimental techniques and theoretical tools for analysis. High throughput analysis techniques and machine learning play important roles in the study of anomalous transport.
REPORTS ON PROGRESS IN PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Melina Daniilidis, Matthias J. Brandl, Franz Hagn
Summary: Membrane mimetics play a crucial role in studying the structure and function of membrane proteins. In this study, the authors compared the biophysical properties of circularized and linear nanodiscs and found that circularized nanodiscs have improved membrane fluidity and size stability, making them advantageous for high-resolution NMR studies at elevated temperatures.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Brandon J. DeOre, Paul P. Partyka, Fan Fan, Peter A. Galie
Summary: Fluid shear stress is an important factor in regulating vascular permeability, but the mechanisms underlying shear effects on the blood-brain barrier (BBB) are not well understood. This study investigates the impact of shear stress on BBB using an in vitro model and identifies specific molecular components involved in sensing and responding to shear stress. These findings enhance our understanding of the pathologies associated with changes in cerebral perfusion and suggest potential targets for barrier manipulation in vivo.
Article
Chemistry, Multidisciplinary
Hanan Sa'adeh, Awad E. A. Mohamed, Robert Richter, Marcello Coreno, Feng Wang, Kevin C. Prince
Summary: The electronic structure of ammonia-borane has been investigated using various spectroscopic techniques, and the results are consistent with previous calculations and experiments.
Article
Chemistry, Inorganic & Nuclear
Shu-Sheng Xin, Yan-Ling Deng, Chun-Yang Pan
Summary: This study reports the synthesis of three nickel borate compounds with adjustable structures. The compounds exhibit different interlinkage modes and channels with varying sizes and shapes. They also demonstrate different wide band gaps and oxygen reduction reaction (ORR) activities.
DALTON TRANSACTIONS
(2022)
Article
Chemistry, Multidisciplinary
Elke De Zitter, Siewert Hugelier, Sam Duwe, Wim Vandenberg, Alison G. Tebo, Luc Van Meervelt, Peter Dedecker
Summary: Anisotropic environments can significantly impact the spectroscopy and photochemistry of molecules, leading to complex structure-function relationships. By studying fluorescent proteins as model systems, it was found that changes in spectroscopic properties can be attributed to multiple underlying mechanisms. The research highlights the complex interplay between structure and spectroscopy, identifying key modulators like polarity, hydrogen bonding, and presence of water molecules.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Gabriel Ortega, Miguel A. Aguilar, Bishal K. Gautam, Kevin W. Plaxco
Summary: The interactions of proteins with surfaces play a crucial role in biological processes and biotechnologies, with electrostatics being a key factor. The content of charged amino acids in proteins determines the extent of stabilization by surfaces.
Article
Chemistry, Physical
Milan Kumar Hazra, Yaakov Levy
Summary: In this study, the effects of short-range interactions and long-range electrostatic interactions on the stability, structure, and dynamics of liquid-liquid phase separation in protein condensates were investigated using coarse-grained molecular dynamics simulations. It was found that an increase in short-range interactions at the expense of long-range electrostatic interactions led to a decrease in critical temperature of phase separation. Additionally, sequences with a high fraction of short-range interactions exhibited some stabilization, compensating for the loss of long-range interactions. Furthermore, the exchange of long-range electrostatic interactions for short-range interactions impacted the kinetics of breaking intermolecular contacts and intramolecular fluctuations, ultimately affecting the liquid-like behavior of protein condensates.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Physics, Applied
Bingbing Wang, Yulu Chen, Wulin Tong, Yangzhou Zhou, Jiajia Tao, Zewen Wang, Zuoru Dong, Hong Zhou, Zhanglong Fu, DiXiang Shao, Xiaodong Wang, Juncheng Cao
Summary: This study presents a novel blocked-impurity-band hybrid structure for terahertz radiation detection. The modulation effect of sub-wavelength metal grating on light absorption is analyzed, and the optical absorption and spectral response of the hybrid structure detectors are simulated. The results show selective absorption amplification and filtering effects, as well as significant absorption enhancement at specific wavelengths.
APPLIED PHYSICS LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Sungmin Nam, Yung-Hao Lin, Taeyoon Kim, Ovijit Chaudhuri
Summary: In dense collagen gels, single cancer cells generate substantial pushing forces to facilitate cell division without the need for cell spreading or matrix degradation. These forces arise from a combination of interpolar spindle elongation and cytokinetic ring contraction.
Review
Biochemistry & Molecular Biology
Munishwar Nath Gupta, Vladimir N. Uversky
Summary: This article discusses the importance of protein multi-specificity, with a focus on the concept of enzyme specificity and the phenomenon of moonlighting. It provides examples of protein moonlighting and outlines the role of protein plasticity and intrinsic disorder in blurring the distinction between enzymes and other biologically active proteins. Additionally, it updates information on the significant roles of moonlighting in human diseases.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Marco Giulini, Marta Rigoli, Giovanni Mattiotti, Roberto Menichetti, Thomas Tarenzi, Raffaele Fiorentini, Raffaello Potestio
Summary: The increasing computer power and improved accuracy of atomistic force fields have enabled researchers to study biological systems at the molecular level in detail. However, the length and time scales of many processes of interest are still out of reach for current hardware, leading to important questions remaining unanswered. Coarse-grained models, simplified representations of molecules at a lower resolution than atomistic, are commonly used in the investigation of biological physics problems, but the optimal degree of simplification remains a crucial open issue.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Evan Mercier, Xiaolin Wang, Manisankar Maiti, Wolfgang Wintermeyer, Marina Rodnina
Summary: The study reveals that during the synthesis of membrane proteins, the lateral gate fluctuations are highly dynamic, continuously sampling between open and closed states even without ligands. Ribosome binding and transmembrane segment insertion do not stop the gate fluctuations but tend to increase sampling of the open state. Binding of YidC facilitates substantial opening of the gate, aiding in the folding of YidC-dependent polytopic membrane proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Philipp C. Schmid, Oskar Asvany, Thomas Salomon, Sven Thorwirth, Stephan Schlemmer
Summary: Leak-out spectroscopy (LOS) is a novel method of spectroscopy in ion traps where mass-selected, cold ions are excited by an infrared laser and their internal energy is transferred to kinetic energy through collisions with neutral buffer gas particles. The potential of LOS is demonstrated for the first time by recording rotationally resolved spectrum of C-H stretching vibration nu 1 of linear C3H+.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Analytical
Ko-ichiro Miyamoto, Rinya Hiramitsu, Carl Frederik Werner, Tatsuo Yoshinobu
Summary: Stainless steel is crucial in industry due to its resistance to corrosion. However, local corrosion can occur under specific conditions. In this study, a novel measurement system was developed to observe crevice corrosion, and real-time measurements of pH distribution and surface roughness were conducted using pH imaging and infrared light techniques. These measurements provide valuable insights into the propagation of crevice corrosion.
Article
Plant Sciences
Kwame Sarpong Appiah, Richard Ansong Omari, Siaw Onwona-Agyeman, Christiana Adukwei Amoatey, John Ofosu-Anim, Abderrazak Smaoui, Abdelkarim Ben Arfa, Yoko Suzuki, Yosei Oikawa, Shin Okazaki, Keisuke Katsura, Hiroko Isoda, Kiyokazu Kawada, Yoshiharu Fujii
Summary: Plant biodiversity has been explored for potential allelopathic species in weed management. This study investigates the effects of seasonal variation on the carnosic acid concentration and phytotoxicity of rosemary leaves. The results show that rosemary samples collected in summer have the highest inhibitory effects due to their high carnosic acid concentration.
Article
Cell Biology
Meriem Bejaoui, Aprill Kee Oliva, May Sin Ke, Farhana Ferdousi, Hiroko Isoda
Summary: The study demonstrated that dermal papilla cells grown in 3D hanging spheroids have a significant impact on hair growth-related pathways and cell adhesion molecules. DNA microarray analysis was used to compare the effects of different drugs on DPCs, showing that the 3D system enhances the effects of these drugs on hair growth.
Article
Biochemistry & Molecular Biology
Meryem Bouhoute, Yhiya Amen, Meriem Bejaoui, Aprill Kee Oliva Mizushima, Kuniyoshi Shimizu, Hiroko Isoda
Summary: This study investigates the anti-melanogenic effect of a compound called Butyroside D and its underlying mechanism. The results show that Butyroside D downregulates the cAMP, Wnt/beta-catenin, and MAPK signaling pathways, leading to the repression of melanin biosynthesis. Furthermore, Butyroside D inhibits the activation of the cAMP pathway mediated through alpha-melanocyte-stimulating hormone (alpha-MSH) and MC1R, confirming its anti-melanogenic effect on human epidermal melanocytes (HEM) cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Neurosciences
Yuya Sato, Hideaki Yamamoto, Hideyuki Kato, Takashi Tanii, Shigeo Sato, Ayumi Hirano-Iwata
Summary: By utilizing cell engineering technology and neuronal networks in dissociated culture, we constructed modular neuronal networks to investigate the relationship between structure and function. Using high-density microelectrode arrays, we recorded the neural activity of the engineered neuronal networks and found that modular architecture enhances functional complexity by reducing excessive neural correlation between spatially segregated modules. This study highlights the importance of combining cell engineering technologies with high-density microelectrode array recordings in assessing the structure-function relationships in neuronal networks.
FRONTIERS IN NEUROSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Farhana Ferdousi, Kazunori Sasaki, Satoshi Fukumitsu, Hidetoshi Kuwata, Mitsutoshi Nakajima, Hiroko Isoda
Summary: In this study, an untargeted whole-genome transcriptomics analysis was conducted to investigate the effects of carnosic acid (CA) on human amniotic epithelial stem cells (hAESCs). The results showed that CA induced mesoderm-lineage-specific differentiation in hAESCs, particularly in cardiovascular and adipose tissues. Further analysis identified potential molecular targets and upstream regulators of CA in a tissue-specific manner. Overall, this study provides a comprehensive understanding of the molecular mechanisms of CA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Rui Wang, Munkhzul Ganbold, Farhana Ferdousi, Kenichi Tominaga, Hiroko Isoda
Summary: A rare natural compound called oleacein found in unfiltered extra virgin olive oil has been shown to have anti-inflammatory and anti-obesity properties. It can inhibit lipid formation, modulate lipid and glucose metabolism, and enhance anti-inflammatory properties in adipocytes, suggesting its potential application in the management of metabolic disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Takuma Sumi, Hideaki Yamamoto, Yuichi Katori, Koki Ito, Satoshi Moriya, Tomohiro Konno, Shigeo Sato, Ayumi Hirano-Iwata
Summary: Reservoir computing is a machine learning paradigm that utilizes the dynamics of high-dimensional nonlinear systems for processing time-series data. In this study, optogenetics and calcium imaging were used to investigate the computational capabilities of biological neuronal networks (BNNs) through a reservoir computing framework. The modular architecture of BNNs was found to positively correlate with classification accuracy, and BNNs exhibited short-term memory and categorical learning abilities. These findings contribute to our understanding of information representation in BNNs and have implications for the development of physical reservoir computing systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biophysics
Madoka Sato, Masanori Hariyama, Maki Komiya, Kae Suzuki, Yuzuru Tozawa, Hideaki Yamamoto, Ayumi Hirano-Iwata
Summary: This article introduces an idealization method for single-channel electrophysiological recordings that provides valuable information about the gating kinetics of ion channels. The method, called AI2, uses an adaptive integrated approach to process the noisy data and automatically determines the optimal noise reduction settings. The method has been validated and tested on both simulated and experimental data.
BIOPHYSICAL JOURNAL
(2023)
Article
Electrochemistry
Kaoru Hiramoto, Keika Komatsu, Ryota Shikuwa, An Konno, Yusuke Sato, Ayumi Hirano-Iwata, Kosuke Ino, Hitoshi Shiku
Summary: Multicellular spheroids are important models in vitro for studying biological and pathological processes. Monitoring their cellular activities without labeling is challenging, but electrochemiluminescence (ECL) has the potential to track the activities of spheroids by displaying secreted molecules adhering to an electrode.
ELECTROCHIMICA ACTA
(2023)
Article
Biochemistry & Molecular Biology
Michitaka Fujiwara, Farhana Ferdousi, Hiroko Isoda
Summary: With the progression of an aging society, cognitive aging has become an urgent concern. This study uses the senescence-accelerated mouse-prone 8 (SAMP8) model to investigate molecular changes in the brain cortex, identifying key functional alterations and candidate genes associated with brain aging, as well as pivotal hub genes involved in these functional domains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Nutrition & Dietetics
Jieun Yoon, Kazunori Sasaki, Iku Nishimura, Haruna Hashimoto, Tomohiro Okura, Hiroko Isoda
Summary: This study examined the effects of desert olive tree pearls (DOTPs) on the cognitive function of middle-aged and older adults. Results showed that DOTPs significantly improved complex attention and alleviated cognitive problems faced by middle-aged and older adults in Japan.
Article
Nutrition & Dietetics
Shinji Kondo, Farhana Ferdousi, Jinchang Zhao, Sofya Suidasari, Miki Yokozawa, Ken Yamauchi, Ken-ichi Tominaga, Hiroko Isoda
Summary: Olive leaf extract has shown potential as a hematinic agent by increasing red blood cell count and hemoglobin levels. It also does not have significant adverse effects on liver and kidney functions. Oleuropein and oleuroside have been identified as the active components in olive leaf extract for inducing erythroid differentiation.
Article
Multidisciplinary Sciences
Hideaki Yamamoto, F. Paul Spitzner, Taiki Takemuro, Victor Buendia, Hakuba Murota, Carla Morante, Tomohiro Konno, Shigeo Sato, Ayumi Hirano-Iwata, Anna Levina, Viola Priesemann, Miguel A. Munoz, Johannes Zierenberg, Jordi Soriano
Summary: High-level information processing in the mammalian cortex requires both segregated processing in specialized circuits and integration across multiple circuits. One possible way to implement these demands is by flexibly switching between states with different levels of synchrony. The control of complex synchronization patterns in neuronal networks remains elusive, but this study provides insights by manipulating and stimulating networks of cortical neurons in vitro. Results show that a modular architecture enhances the network's sensitivity to external asynchronous stimulation and that the depletion of synaptic resources in stimulated neurons is the underlying mechanism for this effect.
Article
Chemistry, Physical
Michio Niwano, Teng Ma, Kazuki Iwata, Daisuke Tadaki, Hideaki Yamamoto, Yasuo Kimura, Ayumi Hirano-Iwata
Summary: The interfacial layer structure of bulk nanobubbles was determined, revealing the presence of three-, four-, and five-membered ring clusters of water molecules. It was hypothesized that a specific interfacial layer with a hydrogen bond network stabilizes the nanobubbles. The hardness of the interfacial layer was found to be dependent on the encapsulated gas species.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
