Papers -
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Direct Formation of ZIF-8 Crystal Thin Films on the Surface of a Zinc Ion-Doped Polymer Substrate Reviewed
T. Tsuruoka, K. Araki, K. Kawauchi, Y. Takashima, K. Akamatsu
Inroganics 12 ( 21 ) 2024
Authorship：Last author
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Changes in gene expression due to product-related impurities of nucleic acid therapeutics
ISHIDA Kazuya, UCHIDA Yasunori, YOSHIDA Tokuyuki, AKAHORI Yumi, SAITO Emi, NANKAI Hirokazu, KARASAWA Kaoru, INAGAKI Chie, IWASAKI Noriyuki, HIGO Daisuke, TAKAHARA Kentaro, KAWAKAMI Junji, OBIKA Satoshi, INOUE Takao
Annual Meeting of the Japanese Society of Toxicology 51.1 P-302 2024
Publisher：The Japanese Society of Toxicology
Nucleic acid therapeutics contain impurities derived from nucleotide deletion or insertion, such as N-1 (single nucleotide deletion) and N+1 (single nucleotide insertion) impurities. Although they can hybridize with off-target RNAs, it is unclear whether N-1/N+1 impurities alter gene expression and contribute to off-target toxicity.
In this study, we prepared samples of antisense oligonucleotides with varying impurity content. Then, we confirmed the accurate mass corresponding to each N-1/N+1 impurity and determined their relative amount by LC-MS. Next, samples were introduced into human cells for comprehensive gene expression analysis. The results showed that many genes fully complementary to the N-1/N+1 impurities were down-regulated. This was probably caused by the fully complementary binding of the N-1/N+1 impurities and/or the partially complementary binding of the desired product with one nucleotide incompatibility. For some genes, the knockdown efficiency became higher with increasing content of the fully complementary N-1/N+1 impurities, strongly suggesting that the knockdown was caused by the binding of the N-1/N+1 impurities.
These results indicate that N-1/N+1 impurities can change gene expression. Comprehensive gene expression analyses will enable us to estimate the genes whose expression is altered by the binding of the desired product and the N-1/N+1 impurities. By considering the toxicological risk when the expression of these genes is changed, it will be possible to evaluate the risk of the N-1/N+1 impurities together with the desired product. -
Shunsuke Yamada, Yohei Takashima, Takaaki Tsuruoka, Kensuke Akamatsu
RSC Applied Interfaces 2024
Publisher：Royal Society of Chemistry (RSC)
An interfacial model has been developed for describing ion transport kinetics at the membrane/solution interface in the new solid-electrodeposition system.
DOI： 10.1039/d4lf00112e
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Asuka Nishibe, Ryohei Akiyoshi, Akinori Saeki, Kazuyoshi Ogasawara, Takaaki Tsuruoka, Daisuke Tanaka
Chemical Communications 2024
Publisher：Royal Society of Chemistry (RSC)
The impact of inorganic (–Cd–S–)<sub>n</sub> assemblies on semiconductive properties is demonstrated by systematically synthesizing one-dimensional Cd(ii) benzenethiolate coordination polymers.
DOI： 10.1039/d3cc05689a
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Structural transformation of silver(i)–thiolate coordination polymer film at solid–liquid interfaces
Myu Fukuoka, Yohei Takashima, Kensuke Akamatsu, Aude Demessence, Takaaki Tsuruoka
CrystEngComm 2024
DOI： 10.1039/D4CE01023J
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Ryosuke Fujiwara, Yuta Ikeda, Takuto Kawaguchi, Yohei Takashima, Takaaki Tsuruoka, Kensuke Akamatsu
Energies 17 ( 1 ) 190 - 190 2023.12
Publisher：MDPI AG
SnTe is the most widely studied p-type thermoelectric (TE) alternative to PbTe. In this study, we prepared a nanostructured SnTe bulk material via spark plasma sintering from a precursor synthesized by a chemical precipitation process without using organic molecules. The sintered sample comprised tiny grains (100–300 nm) with high-density grain boundaries. Eventually, because the material would contain no impurities acting as scattering nodes of charge carriers, the material exhibited a relatively high electrical conductivity of 7.07 × 105 Sm−1 at 310 K. The material demonstrated low lattice thermal conductivity (0.87 Wm−1K−1 at 764 K), which can be owing to the increasing phonon scattering at grain boundaries. The maximum ZT was 0.31 at 764 K in the measured temperature range. This study provides a method for the design of phase-pure and surfactant-free SnTe thermoelectric materials that exhibit low lattice thermal conductivity and high carrier mobility using a chemical synthetic approach.
DOI： 10.3390/en17010190
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Loss of p53 function promotes DNA damage-induced formation of nuclear actin filaments Reviewed
Torii T, Sugimoto W, Itoh K, Kinoshita N, Gessho M, Goto T, Uehara I, Nakajima W, Budirahardja Y, Miyoshi D, Nishikata T, Tanaka N, Kawauchi K
Cell Death and Disease 14 766 2023.11
Joint Work
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Comparison of evolutionary relationships between Branchiostoma floridae, Ciona intestinalis, and Homo sapiens globins provide evidence of gene co-option and convergent evolution Reviewed
Yano N, Minamoto T, Yamaguchi H, Goto T, Nishikata T
International Journal of Molecular Science 24 16009 2023.11
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RNA 高次構造を標的とした光線力学療法の展望 Invited
取井猛流・木下菜月・橋本佳樹・杉本渉・川内敬子・三 好大輔
38 ( 13 ) 1154 - 1156 2023.11
Authorship：Last author, Corresponding author
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Sequencing of Morpholino Antisense Oligonucleotides Using Electron Capture Dissociation Mass Spectrometry Reviewed
Kaoru Karasawa, Eva Duchoslav, Lyle Burton, Junji Kawakami, Takashi Baba
Analytical Chemistry 95 ( 44 ) 16352 - 16358 2023.10
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Mitochondrial Dynamics of Bcl-2 Family Proteins during 17-β-Estradiol-Induced Apoptosis Correlate with the Malignancy of Endometrial Cancer Cells Reviewed
Takahiro Yaguchi, Misaki Kameno, Hirofumi Taira, Junji Kawakami
Biochemstry 62 ( 21 ) 3041 - 3049 2023.10
Authorship：Last author
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Loss of p53 function promotes DNA damage-induced formation of nuclear actin filaments Reviewed International journal
Takeru Torii, Wataru Sugimoto, Katsuhiko Itoh, Natsuki Kinoshita, Masaya Gessho, Toshiyuki Goto, Ikuno Uehara, Wataru Nakajima, Yemima Budirahardja, Daisuke Miyoshi, Takahito Nishikata, Nobuyuki Tanaka, Hiroaki Hirata, Keiko Kawauchi
Cell Death & Disease 14 ( 11 ) 766766 - 766 2023.8
Tumor suppressor p53 plays a central role in response to DNA damage. DNA-damaging agents modulate nuclear actin dynamics, influencing cell behaviors; however, whether p53 affects the formation of nuclear actin filaments remains unclear. In this study, we found that p53 depletion promoted the formation of nuclear actin filaments in response to DNA-damaging agents, such as doxorubicin (DOXO) and etoposide (VP16). Even though the genetic probes used for the detection of nuclear actin filaments exerted a promotive effect on actin polymerization, the detected formation of nuclear actin filaments was highly dependent on both p53 depletion and DNA damage. Whilst active p53 is known to promote caspase-1 expression, the overexpression of caspase-1 reduced DNA damage-induced formation of nuclear actin filaments in p53-depleted cells. In contrast, co-treatment with DOXO and the pan-caspase inhibitor Q-VD-OPh or the caspase-1 inhibitor Z-YVAD-FMK induced the formation of nuclear actin filament formation even in cells bearing wild-type p53. These results suggest that the p53-caspase-1 axis suppresses DNA damage-induced formation of nuclear actin filaments. In addition, we found that the expression of nLifeact-GFP, the filamentous-actin-binding peptide Lifeact fused with the nuclear localization signal (NLS) and GFP, modulated the structure of nuclear actin filaments to be phalloidin-stainable in p53-depleted cells treated with the DNA-damaging agent, altering the chromatin structure and reducing the transcriptional activity. The level of phosphorylated H2AX (γH2AX), a marker of DNA damage, in these cells also reduced upon nLifeact-GFP expression, whilst details of the functional relationship between the formation of nLifeact-GFP-decorated nuclear actin filaments and DNA repair remained to be elucidated. Considering that the loss of p53 is associated with cancer progression, the results of this study raise a possibility that the artificial reinforcement of nuclear actin filaments by nLifeact-GFP may enhance the cytotoxic effect of DNA-damaging agents in aggressive cancer cells through a reduction in gene transcription.
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Kenji Usui, Makoto Ozaki, Kan Hirao, Tsubasa Kosaka, Natsumi Endo, Shuhei Yoshida, Shin-ichiro Yokota, Yonejiro Arimoto, Ryuji Osawa, Nobuhiro Nakanishi, Kin-ya Tomizaki, Tomohiro Umetani, Fumihiro Kayamori
Scientific Reports 13 12027 2023.7
Authorship：Last author, Corresponding author
Microwaves are used for diverse applications such as mobile phones, ovens, and therapy devices. However, there are few reports on the effects of microwaves on diseases other than cancer, and on physiological processes. Here, we focused on CaCO3 mineralization as a model of biomineralization and attempted to elucidate the effect of microwaves on CaCO3 mineralization using peptides. We conducted AFM, ζ potential, HPLC, ICP-AES, and relative permittivity measurements. Our findings show that microwaves alter the nanomorphology of the CaCO3 precipitate, from sphere-like particles to string-like structures. Furthermore, microwaves have little effect on the mineralization when the mineralization ability of a peptide is high, but a large effect when the precipitation ability is low. Our findings may be applicable to not only the treatment of teeth and bones but also the development of organic–inorganic nanobiomaterials. This methodology can be expanded to other molecular/atomic reactions under various microwave conditions to alter reaction activity parameters.
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Thixotropic β-Chitin Nanofiber Hydrogel with a Living Body-Responsive Self-Hardening Property and Its Application as a Sprayable Antiadhesion Barrier Reviewed International journal
Koji Nagahama, Kaho Tobiishi, Natsumi Ueda, Tatsuya Dode, Shahidul Islam Sobuj, Fumiya Yuasa, Kazuhiko Yamashita, Takahito Nishikata
ACS Applied Bio Materials 6 ( 7 ) 2636 - 2643 2023.7
Authorship：Lead author, Corresponding author
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Effect of linearly polarized microwaves on nanomorphology of calcium carbonate mineralization using peptides Reviewed
Kenji Usui, Makoto Ozaki, Kan Hirao, Tsubasa Kosaka, Natsumi Endo, Shuhei Yoshida, Shin-ichiro Yokota, Yonejiro Arimoto, Ryuji Osawa, Nobuhiro Nakanishi, Kin-ya Tomizaki, Tomohiro Umetani, Fumihiro Kayamori
Scientific Reports 13 12027 2023.7
Microwaves are used for diverse applications such as mobile phones, ovens, and therapy devices. However, there are few reports on the effects of microwaves on diseases other than cancer, and on physiological processes. Here, we focused on CaCO3 mineralization as a model of biomineralization and attempted to elucidate the effect of microwaves on CaCO3 mineralization using peptides. We conducted AFM, ζ potential, HPLC, ICP-AES, and relative permittivity measurements. Our findings show that microwaves alter the nanomorphology of the CaCO3 precipitate, from sphere-like particles to string-like structures. Furthermore, microwaves have little effect on the mineralization when the mineralization ability of a peptide is high, but a large effect when the precipitation ability is low. Our findings may be applicable to not only the treatment of teeth and bones but also the development of organic–inorganic nanobiomaterials. This methodology can be expanded to other molecular/atomic reactions under various microwave conditions to alter reaction activity parameters.
DOI： 10.1038/s41598-023-37473-7
Other Link： https://www.nature.com/articles/s41598-023-37473-7
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Inhibitory Effect of Adsorption of Streptococcus mutans onto Scallop-Derived Hydroxyapatite Reviewed
Momoko Usuda, Mariko Kametani, Masakazu Hamada, Yuto Suehiro, Saaya Matayoshi, Rena Okawa, Shuhei Naka, Michiyo Matsumoto-Nakano, Tatsuya Akitomo, Chieko Mitsuhata, Kazuya Koumoto, Keiko Kawauchi, Takahito Nishikata, Masatoshi Yagi, Toshiro Mizoguchi, Koki Fujikawa, Taizo Taniguchi, Kazuhiko Nakano and Ryota Nomura
Int J Mol Sci 24 11371 2023.7
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Inhibitory Effect of Adsorption of Streptococcus mutans onto Scallop-Derived Hydroxyapatite Reviewed
Usuda M, Kametani M, Hamada M, Suehiro Y, Matayoshi S, Okawa R, Naka S, Matsumoto-Nakano M, Akitomo T, Mitsuhata C, Koumoto K, Kawauchi K, Nishikata T, Yagi M, Mizoguchi T, Fujikawa K, Taniguchi T, Nakano K, Nomura R
International Journal of Molecular Science 24 11371 2023.7
Joint Work
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Inhibitory Effect of Adsorption of Streptococcus mutans onto Scallop-Derived Hydroxyapatite. Reviewed International journal
Momoko Usuda, Mariko Kametani, Masakazu Hamada, Yuto Suehiro, Saaya Matayoshi, Rena Okawa, Shuhei Naka, Michiyo Matsumoto-Nakano, Tatsuya Akitomo, Chieko Mitsuhata, Kazuya Koumoto, Keiko Kawauchi, Takahito Nishikata, Masatoshi Yagi, Toshiro Mizoguchi, Koki Fujikawa, Taizo Taniguchi, Kazuhiko Nakano, Ryota Nomura
International journal of molecular sciences 24 ( 14 ) 2023.7
Hydroxyapatite adsorbs various substances, but little is known about the effects on oral bacteria of adsorption onto hydroxyapatite derived from scallop shells. In the present study, we analyzed the effects of adsorption of Streptococcus mutans onto scallop-derived hydroxyapatite. When scallop-derived hydroxyapatite was mixed with S. mutans, a high proportion of the bacterial cells adsorbed onto the hydroxyapatite in a time-dependent manner. An RNA sequencing analysis of S. mutans adsorbed onto hydroxyapatite showed that the upregulation of genes resulted in abnormalities in pathways involved in glycogen and histidine metabolism and biosynthesis compared with cells in the absence of hydroxyapatite. S. mutans adsorbed onto hydroxyapatite was not killed, but the growth of the bacteria was inhibited. Electron microscopy showed morphological changes in S. mutans cells adsorbed onto hydroxyapatite. Our results suggest that hydroxyapatite derived from scallop shells showed a high adsorption ability for S. mutans. This hydroxyapatite also caused changes in gene expression related to the metabolic and biosynthetic processes, including the glycogen and histidine of S. mutans, which may result in a morphological change in the surface layer and the inhibition of the growth of the bacteria.
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Thixotropic β‑Chitin Nanofiber Hydrogel with a Living BodyResponsive Self-Hardening Property and Its Application as a Sprayable Antiadhesion Barrier Reviewed
Nagahama K, Tobiishi K, Ueda N, Dode T, Sobuj SI, Yuasa F, Yamashita K, Nishikata T
American Chemical Society Applied Bio Materials 2023 ( 6 ) 2636 - 2643 2023.7
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Comparison of Analysis Data of Model Oligonucleotide Therapeutics Obtained with Different Types of Liquid Chromatograph-Mass Spectrometers Reviewed
Kenji HIROSE, Tokuyuki YOSHIDA, Maki TERASAKI, Hiroshi SEZAKI, Kaoru KARASAWA, Noriyuki IWASAKI, Kentaro TAKAHARA, Naomi TAKIGUCHI, Mitsuaki SEKIGUCHI, Hirokazu NANKAI, Emi SAITO, Hideaki SATO, Takashi OSAWA, Takao YAMAGUCHI, Kosuke ITO, Junji KAWAKAMI, Satoshi OBIKA, Takao INOUE
Pharmaceutical and Medical Device Regulatory Science 54 ( 5 ) 439 - 454 2023.7