Article
Biochemistry & Molecular Biology
Nina Helena Borzecka, Bartosz Nowak, Rafal Pakula, Robert Przewodzki, Jakub Maksymilian Gac
Summary: This study uses numerical simulation to predict the formation process of MTMS colloidal gel, as well as the condensation kinetics and structural properties of the gel. The results show that the model can accurately reflect the kinetics and structure of the gel, and analyze the factors affecting the synthesis of MTMS.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Physics, Fluids & Plasmas
J. M. Tenti, S. N. Hernandez Guiance, I. M. Irurzun
Summary: This work focuses on studying the fractal properties of diffusion-limited aggregation (DLA) clusters grown on spherical surfaces, analyzing the influence of discretization and projection on the fractal dimension of DLA clusters, and discussing the importance of considering these factors in the interpretation of photographic biomedical images.
Article
Chemistry, Multidisciplinary
Emanuel M. Avrahami, Zohar Eyal, Neta Varsano, Ievgeniia Zagoriy, Julia Mahamid, Assaf Gal
Summary: This study investigates the growth process of coccolith crystals using advanced electron microscopy techniques. It reveals that the crystals grow alternately between space filling and skeletonized growth modes, with the final morphology influenced by growth arrest. The findings shed light on the delicate regulation of coccolith crystal morphology.
ADVANCED MATERIALS
(2023)
Article
Mathematics, Interdisciplinary Applications
M. Abdel Baki, L. Badr
Summary: Two-dimensional lead dendritic systems with fractal character were prepared by electroless deposition. The fractal dimension of the dendritic structures is influenced by lead nitrate concentration and medium properties, affecting migration and aggregation of lead particles. The maximum fractal dimension was found for aggregates formed from 0.06 M Pb(NO3)2 in 5% gelatin.
CHAOS SOLITONS & FRACTALS
(2021)
Article
Biotechnology & Applied Microbiology
H. Spencer, A. Gorecki, H. Foley, L. Phillips, M. Y. Abonnel, B. P. Meloni, R. S. Anderton
Summary: This study found that the polyarginine peptide R18 can bind to lysozyme and prevent aggregation through a direct protein interaction. This functionality may have potential implications for promoting protein solubility and treating diseases associated with abnormal protein aggregation, including synucleinopathies such as Parkinson's disease.
APPLIED BIOCHEMISTRY AND MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
S. Macrae Montgomery, Frederic Demoly, Kun Zhou, H. Jerry Qi
Summary: Digital light processing (DLP) is a widely used additive manufacturing technique with high accuracy and print speeds. Grayscale DLP printing is a new development that allows sub-pixel manipulation of printed shapes, enhancing accuracy beyond the typical capabilities. A methodology involving pixel-level grayscale control and a reaction-diffusion model is developed to predict and optimize the printed shapes. This advancement in DLP printing accuracy enables the fabrication of functional and structural components with smaller features or smoother faces.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Biophysics
Neelakant Varma, Abhishek Singh, Vijay K. Ravi, Mukesh Thakur, Satish Kumar
Summary: Deltamethrin interacts with Hen Egg White Lysozyme in vitro, inducing protein aggregation and altering its conformation, subsequently affecting the catalytic activity of the protein.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2021)
Article
Materials Science, Multidisciplinary
Roland Wuerschum
Summary: Direct determination of mean diffusion times by Laplace transform is advantageous in obtaining closed-form expressions for diffusion and reaction-limited loading and unloading of species. This method is particularly useful for complex cases where inverse Laplace transform calculations become laborious. The concept of mean load-ing or unloading time is compared with other time constants, such as mean action time or time lag.
APPLIED PHYSICS A-MATERIALS SCIENCE & PROCESSING
(2023)
Article
Biochemistry & Molecular Biology
Kamile Mikalauskaite, Mantas Ziaunys, Vytautas Smirnovas
Summary: This study examines the impact of the initial folding state of a protein on amyloid fibril formation, revealing a correlation between protein state and the kinetics and structural properties of the resulting fibrils.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
David Robert Daniels
Summary: This study provides an expression for the diffusion-limited reaction rate on a curved surface or membrane and applies it to calculating the receptor-ligand association rate. The research finds that the receptor-ligand reaction rates can be significantly reduced due to the effect of locally induced membrane curvature or geometry.
CHEMICAL PHYSICS LETTERS
(2022)
Article
Pharmacology & Pharmacy
Shavron Hada, Urmila Burlakoti, Ki Hyun Kim, Ji Soo Han, Min Ji Kim, Nam Ah Kim, Seong Hoon Jeong
Summary: Arginine and its derivatives have varying effects on protein aggregation. Arginine and arginine ethyl ester can reduce the stability of IgG, while acetyl arginine can efficiently suppress the formation of subvisible particles.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2023)
Article
Biochemistry & Molecular Biology
Mantas Ziaunys, Andrius Sakalauskas, Tomas Sneideris, Vytautas Smirnovas
Summary: Protein aggregation into amyloid fibrils is associated with various disorders, but the mechanisms behind the conversion of non-harmful proteins into such aggregates are not fully understood. Recent studies suggest that multiple types of protein aggregates may co-exist in tissues of patients with amyloid-related disorders, potentially influencing each other.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Emily Rott, Christian Leppin, Tim Diederichs, Patrick Garidel, Diethelm Johannsmann
Summary: Using QCM-D, the dependence of complex high-frequency viscosity eta on temperature T and concentration c was studied for concentrated solutions of a monoclonal antibody (mAb). Viscoelastic behavior was observed for the mAb solution, while reference materials acted as Newtonian liquids. QCM-D allows for the analysis of relaxation processes that cannot be measured with standard viscometry.
Article
Chemistry, Analytical
Kevin A. Kirk, Alina Vasilescu, Daniel Andreescu, Dinushani Senarathna, Sumona Mondal, Silvana Andreescu
Summary: Proteins are widely used in biomedical and pharmaceutical industries, necessitating the development of rapid and accurate methods for monitoring protein aggregation. This study introduces a novel approach using single-particle collision electrochemistry to track early-stage lysozyme aggregation, providing insights into protein stability and aggregation dynamics. The results demonstrate significant differences in charge transfer between AgNP samples alone and in the presence of non-aggregated and aggregated lysozyme, highlighting the potential of SPCE as an alternative method for studying protein aggregation.
ANALYTICAL CHEMISTRY
(2021)
Article
Materials Science, Multidisciplinary
Todd H. Weisgraber, Martin P. de Beer, Sijia Huang, John J. Karnes, Caitlyn C. Cook, Maxim Shusteff
Summary: This study introduces VirtualVAM, a simulation framework for modeling the tomographic Volumetric Additive Manufacturing (VAM) process. The ability to simulate the production of an entire part provides insight into the interaction between polymerization kinetics and mass transport, which is imperative for improving the resolution and throughput of VAM. We experimentally validate the model and highlight optimization strategies to reduce build errors.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Chemistry, Analytical
Mari Okada, Hiroka Sugai, Shunsuke Tomita, Ryoji Kurita
Article
Instruments & Instrumentation
Shunsuke Tomita, Ryoji Kurita
Summary: The study introduces a pattern-recognition-based protein sensing approach using a simple one-component array composed of charged poly-L-lysine modified with environment-responsive dansyl fluorophores for the identification of proteases. By dissolving the array of PLL-Dnc in buffer solutions with different pH values, fluorescent patterns unique to each protease are produced, enabling the identification of eight proteases through multivariate analysis. The method allows discrimination of mixtures of trypsin and alpha(1)-antitrypsin (ATT) with different compositions, and is expected to have broad applications in screening protein-protein complexes formation and disease-associated protease detection.
SENSORS AND MATERIALS
(2021)
Article
Chemistry, Analytical
Hiroki Okada, Masahiro Mimura, Shunsuke Tomita, Ryoji Kurita
Summary: The study introduces a novel strategy of using chemical additives to modulate probe/analyte interactions for constructing pattern-recognition-based sensing systems. The enhanced fluorescence of dansyl-modified cationic poly-L-lysine upon binding to proteins generates response patterns that accurately identify structurally similar albumin homologues and mammalian cells through multivariate analysis. This inexpensive and accessible strategy offers new opportunities for bioanalytes detection.
ANALYTICAL SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Masahiro Mimura, Shunsuke Tomita, Yoichi Shinkai, Takuya Hosokai, Hiroyuki Kumeta, Tomohide Saio, Kentaro Shiraki, Ryoji Kurita
Summary: Recent studies have shown that DNA quadruplex folding plays a key role in the formation of liquid droplets through interactions with linker histone H1, inducing liquid-liquid phase separation. Quadruplex DNA structures promote droplet formation and decrease molecular motility within the droplets.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Cell Biology
Masahiro Mimura, Shunsuke Tomita, Hiroka Sugai, Yoichi Shinkai, Sayaka Ishihara, Ryoji Kurita
Summary: This study demonstrates the roles of DNA components in liquid-liquid phase separation of proteins and DNAs, including electrostatic interactions between phosphate groups and deoxyribose, as well as interactions involving nucleobases and deoxyriboses. These interactions promote the generation of spherical liquid droplets and modulate the density of DNA within the droplets under low-salt conditions. Additionally, non-spherical assemblies with both mobile and immobile fractions were observed at higher concentrations of a polycationic peptide, linker histone H1, for all DNA oligomers.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Polymer Science
Shunsuke Tomita
Summary: This review introduces a biosensing strategy called the chemical tongue, which mimics the human taste system by using polymeric materials and statistical techniques to recognize various complex biological samples in a unique manner.
Article
Biochemistry & Molecular Biology
Yuto Akahoshi, Hiroka Sugai, Masahiro Mimura, Yoichi Shinkai, Ryoji Kurita, Kentaro Shiraki, Shunsuke Tomita
Summary: In this study, a model liquid-liquid phase separation (LLPS) system was established to investigate the contribution of non-ionic amino acids to LLPS. It was found that eight non-ionic amino acids inhibit LLPS to some extent, while three aromatic amino acids promote LLPS. Furthermore, the promotion effect is primarily due to interactions with DNA nucleobases, as compared to double-stranded DNA and polyacrylic acid.
Article
Chemistry, Analytical
Mao Fukuyama, Suguru Nishinami, Yoko Maruyama, Taiki Ozawa, Shunsuke Tomita, Yumiko Ohhashi, Motohiro Kasuya, Masao Gen, Eri Chatani, Kentaro Shiraki, Akihide Hibara
Summary: This study developed a measurement method for the amyloid droplet nucleation rate based on image analysis, and found that LLPS unexpectedly suppressed amyloid nucleation in the droplets of a prion disease model protein.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Keitaro Kojima, Shunsuke Tomita, Masao Kamimura
Summary: This study is the first to report the uptake of nanoparticles (NPs) into liquid-liquid phase separation (LLPS) droplets in living cells. Fluorescent imaging was used to visualize the uptake of Nile red loaded polystyrene NPs (NR-PSt NPs) into LLPS droplets consisting of adenosine triphosphate (ATP) and poly-L-lysine (PLL). The results showed that the LLPS droplets exhibited a rapid uptake behavior of NPs. Moreover, temperature changes and ionic strength significantly affected the NP uptake behavior and stability of the LLPS droplets.
Article
Chemistry, Multidisciplinary
Ryo Nishihara, Yoshiki Kihara, Kazuki Niwa, Masahiro Mimura, Shunsuke Tomita, Ryoji Kurita
Summary: The enzymatic luminescence reactions of fireflies are accelerated by approximately 10% in the presence of biomolecular condensates containing a positively charged peptide and ATP. This acceleration is attributed to the enrichment of reaction elements, local pH changes, and the promotion of inhibitory intermediate dissociation.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Hiroka Sugai, Shunsuke Tomita, Sayaka Ishihara, Kentaro Shiraki, Ryoji Kurita
Summary: We introduce a pattern-recognition-based sensor that can detect and evaluate cell-derived components in culture media without damaging the cells. By using an array sensor made of a single-polymer probe, fluorescence response patterns of the analyte media were obtained, allowing successful identification of the type and state of the cells through multivariate analysis.
CHEMICAL COMMUNICATIONS
(2022)
Article
Materials Science, Biomaterials
Shunsuke Tomita, Sayaka Ishihara, Ryoji Kurita
Summary: This article presents a polymer-based biosensing technique that can non-invasively analyze the proteins secreted by cultured cells and achieve cell identification, stem cell differentiation monitoring, and detection of cancer cell contamination through analysis of spent media. It provides a solution to the current problem of invasive methods used for cell characterization.
JOURNAL OF MATERIALS CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Shunsuke Tomita, Hiroyuki Kusada, Naoshi Kojima, Sayaka Ishihara, Koyomi Miyazaki, Hideyuki Tamaki, Ryoji Kurita
Summary: This study developed a sensing system based on the chemical-nose strategy to transduce the characteristics of microbiota into fluorescence patterns. By using pattern-recognition algorithms to analyze the fluorescence patterns, different intestinal bacterial strains can be identified, and obesity-associated and sleep disorder-associated gut microbiota can be detected.
Article
Chemistry, Multidisciplinary
Tomoto Ura, Shunsuke Tomita, Kentaro Shiraki
Summary: Dynamic droplet formation through liquid-liquid phase separation (LLPS) is believed to play a role in regulating various biological processes. A model LLPS system coupled with sequential glycolytic enzymatic reactions was developed to demonstrate the dynamic control of liquid droplets, where the droplets compartmentalize different enzymes and trigger their formation, dissolution, and long-term retention by converting scaffold nucleotides. This system provides insights into the role of enzymes associated with LLPS in living cells.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Hiroka Sugai, Shunsuke Tomita, Sayaka Ishihara, Kyoko Yoshioka, Ryoji Kurita
ANALYTICAL CHEMISTRY
(2020)
