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Illumina-based transcriptomic analysis of the fast-growing leguminous tree Acacia crassicarpa: functional gene annotation and identification of novel SSR-markers

Shougo Ishio, Kazutaka Kusunoki, Michiko Nemoto, Tadayoshi Kanao, Takashi Tamura

Frontiers in Plant Science 15 2024年8月

掲載種別：研究論文（学術雑誌）出版者・発行元：Frontiers Media SA

Acacia crassicarpa is a fast-growing leguminous tree that is widely cultivated in tropical areas such as Indonesia, Malaysia, Australia, and southern China. This tree has versatile utility in timber, furniture, and pulp production. Illumina sequencing of A. crassicarpa was conducted, and the raw data of 124,410,892 reads were filtered and assembled de novo into 93,317 unigenes, with a total of 84,411,793 bases. Blast2GO annotation, Benchmark Universal Single-Copy Ortholog evaluation, and GO-term classification produced a catalogue of unigenes for studying primary metabolism, phytohormone signaling, and transcription factors. Massive transcriptomic analysis has identified microsatellites composed of simple sequence repeat (SSR) loci representing di-, tri-, and tetranucleotide repeat units in the predicted open reading frames. Polymorphism was induced by PCR amplification of microsatellite loci located in several genes encoding auxin response factors and other transcription factors, which successfully distinguished 16 local trees of A. crassicarpa tested, representing potentially exploitable molecular markers for efficient tree breeding for plantation and biomass exploitation.

DOI： 10.3389/fpls.2024.1339958

The Multiphasic Teeth of Chiton Articulatus, an Abrasion-Resistant and Self-Sharpening Tool for Hard Algae Collection 査読

Devis Montroni, Ezra Sarmiento, Ruoheng Zhao, Phani Saketh Dasika, John Michael Connolly, Richard Wuhrer, Yugang Zhang, Mikhail Zhernenkov, Taifeng Wang, Brenda Paola Ramirez-Santana, Leigh Sheppard, Omar Hernando Avila-Poveda, Atsushi Arakaki, Michiko Nemoto, Pablo Zavattieri, David Kisailus

Advanced Functional Materials 2024年

掲載種別：研究論文（学術雑誌）

Chiton articulatus is a species of mollusk living in the tropical Pacific intertidal rocky shores of Mexico. This species feeds on solid waste organic sources, including hard crustose algae that grow on rocky substrates, by grazing on them with its radula, a flexible chitinous membrane lined with mineralized major lateral teeth. In this study, the composition, morphology, and resulting mechanics of the mature teeth of this species, which have yet to be examined, are revealed. The results show the presence of multiphasic mature teeth, each consisting of aligned hard magnetite nanoparticles on the leading edge of the tooth underneath which are magnetite lamellae, followed by goethite, lepidocrocite, and eventually hydroxyapatite near the trailing edge. This multiregional structure demonstrates a gradation in hardness as well as different microstructural features integrated with tough interfaces. The combination of these microstructural and phase arrangements results in an abrasion-resistant tough structure with a self-sharpening ability. The results of this work will help contribute to developing new bioinspired designs while also helping to understand the evolution and feeding habits of these intriguing invertebrates.

DOI： 10.1002/adfm.202401658

Nuclear Transformation of the Marine Pennate Diatom Nitzschia sp. Strain NIES-4635 by Multi-Pulse Electroporation 査読

Koki Okada, Yu Morimoto, Yukine Shiraishi, Takashi Tamura, Shigeki Mayama, Takashi Kadono, Masao Adachi, Kentaro Ifuku, Michiko Nemoto

Marine Biotechnology 2023年12月

Fibrous anisotropy and mineral gradients Within the radula stylus of chiton: Controlled stiffness and damage tolerance in a flexible biological composite 査読

Jung-Eun Lee, John Connolloy, Wen Yang, Guillaume Freychet, Taifeng Wang, Steven A. Herrera, Satoshi Murata, Phani Saketh Dasika, Devis Montroni, Anna Pohl, Chenhui Zhu, Mikhail Zhernenkov, Richard Wuhrer, Leigh Sheppard, Michiko Nemoto, Atsushi Arakaki, Pablo Zavattieri, David Kisailus

JOURNAL OF COMPOSITE MATERIALS 2022年8月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：SAGE PUBLICATIONS LTD

Over hundreds of millions of years, organisms have evolved architected structures via precise control over hierarchically assembled components, including the integration of dissimilar materials. One such example is found in the radula system of chitons, intertidal mollusks that feed on algae growing on the rock. Their radula consists of multiple rows of ultrahard teeth, each integrated with a foldable belt-like substrate via a stiff, yet flexible stylus, which is essential for efficient rasping during the feeding process. Here, we investigate the nano and micro-scale components and architectures as well as regional mechanical properties of the stylus, and their subsequent role during the rasping of Cyptochiton stelleri. Three important factors were determined to contribute to the regio-specific stiffness of the stylus: the presence of mineral components, highly oriented chitinous fibers, and a chemically cross-linked protein matrix. All these factors are varied throughout the stylus. There is a high mineral content on the trailing edge close to the tooth and a cross-linked matrix on the leading edge, both with orientational specific oriented chitin fibers that provide force transduction to the tooth. Conversely, there is a significant lack of mineral or cross-linked matrix in the proximal end as well as a low degree of fiber orientation, resulting in a flexible region that can accommodate torsion and flexure during rasping. Understanding the graded composite structure of the stylus and applying this unique design to various engineering fields such as soft robotics, biotechnology, and the medical industry, can inspire the production of high-performance materials.

DOI： 10.1177/00219983221121867

Evaluation of the Geenius HIV 1/2 confirmatory assay for HIV-2 samples isolated in Japan 査読

Urara Shigemi, Yoshimi Yamamura, Masakazu Matsuda, Reiko Okazaki, Mai Kubota, Shiro Ibe, Michiko Nemoto, Masami Maejima-Kitagawa, Sayaka Sukegawa, Mayumi Imahashi, Tadashi Kikuchi, Wataru Sugiura, Yasumasa Iwatani, Atsuko Hachiya, Yoshiyuki Yokomaku

Journal of Clinical Virology 152 105189 - 105189 2022年7月

Nanoarchitected Tough Biological Composites from Assembled Chitinous Scaffolds 査読

Wei Huang, Devis Montroni, Taifeng Wang, Satoshi Murata, Atsushi Arakaki, Michiko Nemoto, David Kisailus

ACCOUNTS OF CHEMICAL RESEARCH 55 ( 10 ) 1360 - 1371 2022年5月

記述言語：英語出版者・発行元：AMER CHEMICAL SOC

Over hundreds of millions of years, organisms have derived specific sets of traits in response to common selection pressures that serve as guideposts for optimal biological designs. A prime example is the evolution of toughened structures in disparate lineages within plants, invertebrates, and vertebrates. Extremely tough structures can function much like armor, battering rams, or reinforcements that enhance the ability of organisms to win competitions, find mates, acquire food, escape predation, and withstand high winds or turbulent flow. From an engineering perspective, biological solutions are intriguing because they must work in a multifunctional context. An organism rarely can be optimally designed for only one function or one environmental condition. Some of these natural systems have developed well-orchestrated strategies, exemplified in the biological tissues of numerous animal and plant species, to synthesize and construct materials from a limited selection of available starting materials. The resulting structures display multiscale architectures with incredible fidelity and often exhibit properties that are similar, and frequently superior, to mechanical properties exhibited by many engineered materials. These biological systems have accomplished this feat through the demonstrated ability to tune size, morphology, crystallinity, phase, and orientation of minerals under benign processing conditions (i.e., near-neutral pH, room temperature, etc.) by establishing controlled synthesis and hierarchical 3D assembly of nano- to microscaled building blocks. These systems utilize organic-inorganic interactions and carefully controlled microenvironments that enable kinetic control during the synthesis of inorganic structures. This controlled synthesis and assembly requires orchestration of mineral transport and nucleation. The underlying organic framework, often consisting of polysaccharides and polypeptides, in these composites is critical in the spatial and temporal regulation of these processes. In fact, the organic framework is used not only to provide transport networks for mineral precursors to nucleation sites but also to precisely guide the formation and phase development of minerals and significantly improve the mechanical performance of otherwise brittle materials.Over the past 15 years, we have focused on a few of these extreme performing organisms, (Wang et al., Adv. Fund. Mater. 2013, 23, 2908; Weaver et al., Science 2012, 336, 1275; Huang et al., Nat. Mater. 2020, 19, 1236; Rivera et al., Nature 2020, 586, 543) investigating not only their ultrastructural features and mechanical properties but in some cases, how these assembled structures are mineralized. In specific instances, comparative analyses of multiscale structures have pinpointed which design principles have arisen convergently; when more than one evolutionary path arrives at the same solution, we have a good indication that it is the best solution. This is required for survival under extreme conditions. Indeed, we have found that there are specific architectural features that provide an advantage toward survival by enabling the ability to feed effectively or to survive against predatory attacks. In this Account, we describe 3 specific design features, nanorods, helicoids, and nanoparticles, as well as the interfaces in fiber-reinforced biological composites. We not only highlight their roles in the specific organisms but also describe how controlled syntheses and hierarchical assembly using organic (i.e., often chitinous) scaffolds lead to these integrated macroscale structures. Beyond this, we provide insight into multifunctionality: how nature leverages these existing structures to potentially add an additional dimension toward their utility and describe their translation to biomimetic materials used for engineering applications.

DOI： 10.1021/acs.accounts.2c00110

Mesocrystalline Ordering and Phase Transformation of Iron Oxide Biominerals in the Ultrahard Teeth of Cryptochiton stelleri 査読

Taifeng Wang, Wei Huang, Cong Huy Pham, Satoshi Murata, Steven Herrera, Nathan D. Kirchhofer, Bassim Arkook, Dejan Stekovic, Mikhail E. Itkis, Nir Goldman, Luis Zepeda-Ruiz, Mikhail Zhernenkov, Michiko Nemoto, Atsushi Arakaki, David Kisailus

SMALL STRUCTURES 3 ( 4 ) 2022年4月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：WILEY

Biological organisms naturally synthesize complex, hierarchical, multifunctional materials through mineralization processes at ambient conditions and under physiological pH. One such example is the ultrahard and wear-resistant radular teeth found in mollusks, which are used to scape against the rock to feed on algae. Herein, the biologically controlled structural development of the hard, outer magnetite-containing shell of the chitin teeth is revealed. Specifically, the formation of a series of mesocrystalline iron oxide phases, templated by chitin-binding proteins, is identified. The initial domains, consisting of ferrihydrite mesocrystals with a spherulite-like morphology, undergo a solid-state phase transformation to form magnetite while maintaining mesocrystallinity, likely via a shear-induced solid-state reaction, without any noticeable architectural changes. Subsequent growth via Ostwald ripening leads to nearly single-crystalline rod-like elements. In addition, an interpenetrating organic matrix is identified that, at early stages of tooth development, potentially contains iron-binding proteins that guide the self-assembly of the mesocrystalline mineral and influence the preferred orientation of the later-formed magnetite nanorods, which ultimately determines the mechanical behavior of the mature chiton teeth.

DOI： 10.1002/sstr.202100202

Correction to: Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases. 国際誌

Michiko Nemoto, Sayako Iwaki, Hisao Moriya, Yuki Monden, Takashi Tamura, Kenji Inagaki, Shigeki Mayama, Kiori Obuse

Marine biotechnology (New York, N.Y.) 23 ( 1 ) 157 - 157 2021年2月

Multiple mutations in RNA polymerase β-subunit gene (rpoB) in Streptomyces incarnatus NRRL8089 enhance production of antiviral antibiotic sinefungin: modeling rif cluster region by density functional theory. 査読国際誌

Saori Ogawa, Hitomi Shimidzu, Koji Fukuda, Naoki Tsunekawa, Toshiyuki Hirano, Fumitoshi Sato, Kei Yura, Tomohisa Hasunuma, Kozo Ochi, Michio Yamamoto, Wataru Sakamoto, Kentaro Hashimoto, Hiroyuki Ogata, Tadayoshi Kanao, Michiko Nemoto, Kenji Inagaki, Takashi Tamura

Bioscience, biotechnology, and biochemistry 2021年1月

記述言語：英語掲載種別：研究論文（学術雑誌）

Streptomyces incarnatus NRRL8089 produces the antiviral, antifungal, antiprotozoal nucleoside antibiotic sinefungin. To enhance sinefungin production, multiple mutations were introduced to the rpoB gene encoding RNA polymerase (RNAP) β-subunit at the target residues, D447, S453, H457, and R460. Sparse regression analysis using elastic-net lasso-ridge penalties on previously reported H457X mutations identified a numeric parameter set, which suggested that H457R/Y/F may cause production enhancement. H457R/R460C mutation successfully enhanced the sinefungin production by 3-fold, while other groups of mutations, such as D447G/R460C or D447G/H457Y, made moderate or even negative effects. To identify why the rif cluster residues have diverse effects on sinefungin production, an RNAP/DNA/mRNA complex model was constructed by homology modeling and molecular dynamics simulation. The 4 residues were located near the mRNA strand. Density functional theory-based calculation suggested that D447, H457, and R460 are in direct contact with ribonucleotide, and partially positive charges are induced by negatively charged chain of mRNA.

DOI： 10.1093/bbb/zbab011

Impact of long-term antiretroviral therapy on gut and oral microbiotas in HIV-1-infected patients. 査読国際誌

Mayumi Imahashi, Hirotaka Ode, Ayumi Kobayashi, Michiko Nemoto, Masakazu Matsuda, Chieko Hashiba, Akiko Hamano, Yoshihiro Nakata, Mikiko Mori, Kento Seko, Masashi Nakahata, Ayumi Kogure, Yasuhito Tanaka, Wataru Sugiura, Yoshiyuki Yokomaku, Yasumasa Iwatani

Scientific reports 11 ( 1 ) 960 - 960 2021年1月

記述言語：英語掲載種別：研究論文（学術雑誌）

In HIV-1-infected patients, antiretroviral therapy (ART) is a key factor that may impact commensal microbiota and cause the emergence of side effects. However, it is not fully understood how long-term ART regimens have diverse impacts on the microbial compositions over time. Here, we performed 16S ribosomal RNA gene sequencing of the fecal and salivary microbiomes in patients under different long-term ART. We found that ART, especially conventional nucleotide/nucleoside reverse transcriptase inhibitor (NRTI)-based ART, has remarkable impacts on fecal microbial diversity: decreased α-diversity and increased ß-diversity over time. In contrast, dynamic diversity changes in the salivary microbiome were not observed. Comparative analysis of bacterial genus compositions showed a propensity for Prevotella-enriched and Bacteroides-poor gut microbiotas in patients with ART over time. In addition, we observed a gradual reduction in Bacteroides but drastic increases in Succinivibrio and/or Megasphaera under conventional ART. These results suggest that ART, especially NRTI-based ART, has more suppressive impacts on microbiota composition and diversity in the gut than in the mouth, which potentially causes intestinal dysbiosis in patients. Therefore, NRTI-sparing ART, especially integrase strand transfer inhibitor (INSTI)- and/or non-nucleotide reverse transcriptase inhibitor (NNRTI)-containing regimens, might alleviate the burden of intestinal dysbiosis in HIV-1-infected patients under long-term ART.

DOI： 10.1038/s41598-020-80247-8

Radular stylus of Cryptochiton stelleri: A multifunctional lightweight and flexible fiber-reinforced composite. 査読国際誌

Anna Pohl, Steven A Herrera, David Restrepo, Ryo Negishi, Jae-Young Jung, Chris Salinas, Richard Wuhrer, Tomoko Yoshino, Joanna McKittrick, Atsushi Arakaki, Michiko Nemoto, Pablo Zavattieri, David Kisailus

Journal of the mechanical behavior of biomedical materials 111 103991 - 103991 2020年7月

記述言語：英語掲載種別：研究論文（学術雑誌）

Chitons are herbivorous invertebrates that use rows of ultrahard magnetite-based teeth connected to a flexible belt (radula) to rasp away algal deposits growing on and within rocky outcrops along coastlines around the world. Each tooth is attached to the radula by an organic structure (stylus) that provides mechanical support during feeding. However, the underlying structures within the stylus, and their subsequent function within the chiton have yet to be investigated. Here, we investigate the macrostructural architecture, the regional material and elemental distribution and subsequent nano-mechanical properties of the stylus from the Northern Pacific dwelling Cryptochiton stelleri. Using a combination of μ-CT imaging, optical and electron microscopy, as well as elemental analysis, we reveal that the stylus is a highly contoured tube, mainly composed of alpha-chitin fibers, with a complex density distribution. Nanoindentation reveals regiospecific and graded mechanical properties that can be correlated with both the elemental composition and material distribution. Finite element modeling shows that the unique macroscale architecture, material distribution and elemental gradients have been optimized to preserve the structural stability of this flexible, yet robust functionally-graded fiber-reinforced composite tube, providing effective function during rasping. Understanding these complex fiber-based structures offers promising blueprints for lightweight, multifunctional and integrated materials.

DOI： 10.1016/j.jmbbm.2020.103991

Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases. 査読国際誌

Michiko Nemoto, Sayako Iwaki, Hisao Moriya, Yuki Monden, Takashi Tamura, Kenji Inagaki, Shigeki Mayama, Kiori Obuse

Marine biotechnology (New York, N.Y.) 2020年6月

担当区分：責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

Silica cell walls of diatoms have attracted attention as a source of nanostructured functional materials and have immense potential for a variety of applications. Previous studies of silica cell wall formation have identified numerous involved proteins, but most of these proteins are species-specific and are not conserved among diatoms. However, because the basic process of diatom cell wall formation is common to all diatom species, ubiquitous proteins and molecules will reveal the mechanisms of cell wall formation. In this study, we assembled de novo transcriptomes of three diatom species, Nitzschia palea, Achnanthes kuwaitensis, and Pseudoleyanella lunata, and compared protein-coding genes of five genome-sequenced diatom species. These analyses revealed a number of diatom-specific genes that encode putative endoplasmic reticulum-targeting proteins. Significant numbers of these proteins showed homology to silicanin-1, which is a conserved diatom protein that reportedly contributes to cell wall formation. These proteins also included a previously unrecognized SET domain protein methyltransferase family that may regulate functions of cell wall formation-related proteins and long-chain polyamines. Proteomic analysis of cell wall-associated proteins in N. palea identified a protein that is also encoded by one of the diatom-specific genes. Expression analysis showed that candidate genes were upregulated in response to silicon, suggesting that these genes play roles in silica cell wall formation. These candidate genes can facilitate further investigations of silica cell wall formation in diatoms.

DOI： 10.1007/s10126-020-09976-1

Antiviral effect of sinefungin on in vitro growth of feline herpesvirus type 1. 査読

Yudai Kuroda, Haruka Yamagata, Michiko Nemoto, Kenji Inagaki, Takashi Tamura, Ken Maeda

The Journal of antibiotics 72 ( 12 ) 981 - 985 2019年12月

記述言語：英語掲載種別：研究論文（学術雑誌）

Feline herpesvirus type 1 (FHV-1) causes a potentially fatal disease in cats. Through the use of virus inhibition and cytotoxicity assays, sinefungin, a nucleoside antibiotic, was assessed for its potential to inhibit the growth of FHV-1. Sinefungin inhibited in vitro growth of FHV-1 most significantly over other animal viruses, such as feline infectious peritonitis virus, equine herpesvirus, pseudorabies virus and feline calicivirus. Our results revealed that sinefungin specifically suppressed the replication of FHV-1 after its adsorption to the host feline kidney cells in a dose-dependent manner without obvious cytotoxicity to the host cells. This antibiotic can potentially offer a highly effective treatment for animals infected with FHV-1, providing alternative medication to currently available antiviral therapies.

DOI： 10.1038/s41429-019-0234-4

Redox-tuning of oxidizing disulfide oxidoreductase generates a potent disulfide isomerase. 査読国際誌

Shinya Sutoh, Yuko Uemura, Yuko Yamaguchi, Asako Kiyotou, Rena Sugihara, Makiko Nagayasu, Mihoko Kurokawa, Koreaki Ito, Naoki Tsunekawa, Michiko Nemoto, Kenji Inagaki, Takashi Tamura

Biochimica et biophysica acta. Proteins and proteomics 1867 ( 3 ) 194 - 201 2019年3月

記述言語：英語掲載種別：研究論文（学術雑誌）

Oxidative folding of extracellular proteins is pivotal for the biogenesis of bacterial virulence factors. Escherichia coli DsbA catalyzes disulfide bond formation in extracellular proteins and in multicomponent architectures on the cell surface. The present study assessed the significance of the redox properties of DsbA by exploiting the plaque-forming ability of bacteriophage M13, which specifically recognizes F-pili during infection of the host cell. A library of mutant dsbA genes was constructed by randomizing the dipeptide XX sequence in the active-site redox motif CXXC and then screened for mutants that altered plaque yield and appearance. In total, 24 dsbA mutant alleles produced substantially different degrees of complementation, and one mutant dsbA gene that encodes a CDIC sequence produced over 40-fold more clear plaques than wild type dsbA. The redox potential of purified DsbA [CDIC] was -172 mV, representing a less-oxidizing catalysis than the wild type DsbA (-122 mV), but one that is closer to yeast protein disulfide isomerase (-175 mV). DsbA [CDIC] exhibited a greater ability to refold fully denatured glutathionylated ribonuclease A than the wild type enzyme and a DsbA [CRIC] mutant, which has the same redox potential of -172 mV. Homology modeling and molecular dynamics simulation suggest that the CDIC mutant may have an enlarged substrate-binding cleft near the redox center, which confers kinetic advantages when acting on protein substrates.

DOI： 10.1016/j.bbapap.2018.12.005

Integrated transcriptomic and proteomic analyses of a molecular mechanism of radular teeth biomineralization in Cryptochiton stelleri. 査読国際誌

Michiko Nemoto, Dongni Ren, Steven Herrera, Songqin Pan, Takashi Tamura, Kenji Inagaki, David Kisailus

Scientific reports 9 ( 1 ) 856 - 856 2019年1月

担当区分：責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

Many species of chiton are known to deposit magnetite (Fe3O4) within the cusps of their heavily mineralized and ultrahard radular teeth. Recently, much attention has been paid to the ultrastructural design and superior mechanical properties of these radular teeth, providing a promising model for the development of novel abrasion resistant materials. Here, we constructed de novo assembled transcripts from the radular tissue of C. stelleri that were used for transcriptome and proteome analysis. Transcriptomic analysis revealed that the top 20 most highly expressed transcripts in the non-mineralized teeth region include the transcripts encoding ferritin, while those in the mineralized teeth region contain a high proportion of mitochondrial respiratory chain proteins. Proteomic analysis identified 22 proteins that were specifically expressed in the mineralized cusp. These specific proteins include a novel protein that we term radular teeth matrix protein1 (RTMP1), globins, peroxidasins, antioxidant enzymes and a ferroxidase protein. This study reports the first de novo transcriptome assembly from C. stelleri, providing a broad overview of radular teeth mineralization. This new transcriptomic resource and the proteomic profiles of mineralized cusp are valuable for further investigation of the molecular mechanisms of radular teeth mineralization in chitons.

DOI： 10.1038/s41598-018-37839-2

Novel Compound Heterozygous TYK2 Mutations in Primary Immunodeficiency with T-Cell Lymphopenia 査読

Hattori Hiroyoshi, Nemoto Michiko, Maeda Naoko, Akita Nobuhiro, Moritani Suzuko, Muramatsu Hideki, Kawasaki Tomonori, Maejima Masami, Ode Hirotaka, Hachiya Atsuko, Sugiura Wataru, Yokomaku Yoshiyuki, Iwatani Yasumasa, Horibe Keizo

PEDIATRIC BLOOD & CANCER 65 S45 2018年11月

Compound heterozygous TYK2 mutations underlie primary immunodeficiency with T-cell lymphopenia. 査読国際誌

Michiko Nemoto, Hiroyoshi Hattori, Naoko Maeda, Nobuhiro Akita, Hideki Muramatsu, Suzuko Moritani, Tomonori Kawasaki, Masami Maejima, Hirotaka Ode, Atsuko Hachiya, Wataru Sugiura, Yoshiyuki Yokomaku, Keizo Horibe, Yasumasa Iwatani

Scientific reports 8 ( 1 ) 6956 - 6956 2018年5月

記述言語：英語掲載種別：研究論文（学術雑誌）

Complete tyrosine kinase 2 (TYK2) deficiency has been previously described in patients with primary immunodeficiency diseases. The patients were infected with various pathogens, including mycobacteria and/or viruses, and one of the patients developed hyper-IgE syndrome. A detailed immunological investigation of these patients revealed impaired responses to type I IFN, IL-10, IL-12 and IL-23, which are associated with increased susceptibility to mycobacterial and/or viral infections. Herein, we report a recessive partial TYK2 deficiency in two siblings who presented with T-cell lymphopenia characterized by low naïve CD4+ T-cell counts and who developed Epstein-Barr virus (EBV)-associated B-cell lymphoma. Targeted exome-sequencing of the siblings' genomes demonstrated that both patients carried novel compound heterozygous mutations (c.209_212delGCTT/c.691C > T, p.Cys70Serfs*21/p.Arg231Trp) in the TYK2. The TYK2 protein levels were reduced by 35% in the T cells of the patient. Unlike the response under complete TYK2 deficiency, the patient's T cells responded normally to type I IFN, IL-6, IL-10 and IL-12, whereas the cells displayed an impaired response to IL-23. Furthermore, the level of STAT1 was low in the cells of the patient. These studies reveal a new clinical entity of a primary immunodeficiency with T-cell lymphopenia that is associated with compound heterozygous TYK2 mutations in the patients.

DOI： 10.1038/s41598-018-25260-8

An Internal Sequence Region Catalytically Essential for the Human Selenophosphate Synthetase 2 査読

Muneaki Takahata, Michiko Nemoto, Kenji Inagaki, Takashi Tamura

FREE RADICAL BIOLOGY AND MEDICINE 112 65 - 65 2017年11月

Gene cloning, recombinant expression, purification and characterization of l-methionine decarboxylase from Streptomyces sp. 590. 査読国際誌

Masaya Hayashi, Akane Okada, Kumiko Yamamoto, Tomomi Okugochi, Chika Kusaka, Daizou Kudou, Michiko Nemoto, Junko Inagaki, Yuu Hirose, Toshihide Okajima, Takashi Tamura, Kenji Soda, Kenji Inagaki

Journal of biochemistry 161 ( 4 ) 389 - 398 2017年4月

記述言語：英語掲載種別：研究論文（学術雑誌）

l-Methionine decarboxylase (MetDC) from Streptomyces sp. 590 depends on pyridoxal 5'-phosphate and catalyzes the non-oxidative decarboxylation of l-methionine to produce 3-methylthiopropylamine and carbon dioxide. MetDC gene (mdc) was determined to consist of 1,674 bp encoding 557 amino acids, and the amino acid sequence is similar to that of l-histidine decarboxylases and l-valine decarboxylases from Streptomyces sp. strains. The mdc gene was cloned and recombinant MetDC was heterologously expressed by Escherichia coli. The purification of recombinant MetDC was carried out by DEAE-Toyopearl and Ni-NTA agarose column chromatography. The recombinant enzyme was homodimeric with a molecular mass of 61,000 Da and showed optimal activity between 45 to 55 °C and at pH 6.6, and the stability below 30 °C and between pH 4.6 to 7.0. l-Methionine and l-norleucine were good substrates for MetDC. The Michaelis constants for l-methionine and l-norleucine were 30 and 73 mM, respectively. The recombinant MetDC (0.50 U/ml) severely inhibited growth of human tumour cells A431 (epidermoid ovarian carcinoma cell line) and MDA-MB-231 (breast cancer cell line), however showed relatively low cytotoxicity for human normal cell NHDF-Neo (dermal fibroblast cell line from neonatal foreskin). This study revealed the properties of the gene and the protein sequence of MetDC for the first time.

DOI： 10.1093/jb/mvw083

A non-radioactive assay for selenophosphate synthetase activity using recombinant pyruvate pyrophosphate dikinase from Thermus thermophilus HB8. 査読国際誌

Saho Kamada, Takahiro Okugochi, Kaori Asano, Ryuta Tobe, Hisaaki Mihara, Michiko Nemoto, Kenji Inagaki, Takashi Tamura

Bioscience, biotechnology, and biochemistry 80 ( 10 ) 1970 - 2 2016年10月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：TAYLOR & FRANCIS LTD

Biosynthesis of selenocysteine-containing proteins requires monoselenophosphate, a selenium-donor intermediate generated by selenophosphate synthetase (Sephs). A non-radioactive assay was developed as an alternative to the standard [8-(14)C] AMP-quantifying assay. The product, AMP, was measured using a recombinant pyruvate pyrophosphate dikinase from Thermus thermophilus HB8. The KM and kcat for Sephs2-Sec60Cys were determined to be 26 μM and 0.352 min(-1), respectively.

DOI： 10.1080/09168451.2016.1200458

Molecular evolution of gas cavity in [NiFeSe] hydrogenases resurrected in silico. 査読国際誌

Takashi Tamura, Naoki Tsunekawa, Michiko Nemoto, Kenji Inagaki, Toshiyuki Hirano, Fumitoshi Sato

Scientific reports 6 19742 - 19742 2016年1月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：NATURE PUBLISHING GROUP

Oxygen tolerance of selenium-containing [NiFeSe] hydrogenases (Hases) is attributable to the high reducing power of the selenocysteine residue, which sustains the bimetallic Ni-Fe catalytic center in the large subunit. Genes encoding [NiFeSe] Hases are inherited by few sulphate-reducing δ-proteobacteria globally distributed under various anoxic conditions. Ancestral sequences of [NiFeSe] Hases were elucidated and their three-dimensional structures were recreated in silico using homology modelling and molecular dynamic simulation, which suggested that deep gas channels gradually developed in [NiFeSe] Hases under absolute anaerobic conditions, whereas the enzyme remained as a sealed edifice under environmental conditions of a higher oxygen exposure risk. The development of a gas cavity appears to be driven by non-synonymous mutations, which cause subtle conformational changes locally and distantly, even including highly conserved sequence regions.

DOI： 10.1038/srep19742

Structural Insights into HIV-1 Vif-APOBEC3F Interaction. 査読国際誌

Masaaki Nakashima, Hirotaka Ode, Takashi Kawamura, Shingo Kitamura, Yuriko Naganawa, Hiroaki Awazu, Shinya Tsuzuki, Kazuhiro Matsuoka, Michiko Nemoto, Atsuko Hachiya, Wataru Sugiura, Yoshiyuki Yokomaku, Nobuhisa Watanabe, Yasumasa Iwatani

Journal of virology 90 ( 2 ) 1034 - 47 2016年1月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：AMER SOC MICROBIOLOGY

UNLABELLED: The HIV-1 Vif protein inactivates the cellular antiviral cytidine deaminase APOBEC3F (A3F) in virus-infected cells by specifically targeting it for proteasomal degradation. Several studies identified Vif sequence motifs involved in A3F interaction, whereas a Vif-binding A3F interface was proposed based on our analysis of highly similar APOBEC3C (A3C). However, the structural mechanism of specific Vif-A3F recognition is still poorly understood. Here we report structural features of interaction interfaces for both HIV-1 Vif and A3F molecules. Alanine-scanning analysis of Vif revealed that six residues located within the conserved Vif F1-, F2-, and F3-box motifs are essential for both A3C and A3F degradation, and an additional four residues are uniquely required for A3F degradation. Modeling of the Vif structure on an HIV-1 Vif crystal structure revealed that three discontinuous flexible loops of Vif F1-, F2-, and F3-box motifs sterically cluster to form a flexible A3F interaction interface, which represents hydrophobic and positively charged surfaces. We found that the basic Vif interface patch (R17, E171, and R173) involved in the interactions with A3C and A3F differs. Furthermore, our crystal structure determination and extensive mutational analysis of the A3F C-terminal domain demonstrated that the A3F interface includes a unique acidic stretch (L291, A292, R293, and E324) crucial for Vif interaction, suggesting additional electrostatic complementarity to the Vif interface compared with the A3C interface. Taken together, these findings provide structural insights into the A3F-Vif interaction mechanism, which will provide an important basis for development of novel anti-HIV-1 drugs using cellular cytidine deaminases. IMPORTANCE: HIV-1 Vif targets cellular antiviral APOBEC3F (A3F) enzyme for degradation. However, the details on the structural mechanism for specific A3F recognition remain unclear. This study reports structural features of interaction interfaces for both HIV-1 Vif and A3F molecules. Three discontinuous sequence motifs of Vif, F1, F2, and F3 boxes, assemble to form an A3F interaction interface. In addition, we determined a crystal structure of the wild-type A3F C-terminal domain responsible for the Vif interaction. These results demonstrated that both electrostatic and hydrophobic interactions are the key force driving Vif-A3F binding and that the Vif-A3F interfaces are larger than the Vif-A3C interfaces. These findings will allow us to determine the configurations of the Vif-A3F complex and to construct a structural model of the complex, which will provide an important basis for inhibitor development.

DOI： 10.1128/JVI.02369-15

Identification and characterization of the zosA gene involved in copper uptake in Bacillus subtilis 168. 査読国際誌

Takahiro Fukuhara, Kazuo Kobayashi, Yousuke Kanayama, Shu-ichi Enomoto, Taeko Kondo, Naoki Tsunekawa, Michiko Nemoto, Naotake Ogasawara, Kenji Inagaki, Takashi Tamura

Bioscience, biotechnology, and biochemistry 80 ( 3 ) 600 - 9 2016年

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：TAYLOR & FRANCIS LTD

DL-Penicillamine, a copper-specific metal chelator, remarkably suppressed the growth of Bacillus subtilis 168 when added to a synthetic medium under Cu(2+) limitation. DNA microarray and screening of 2,602 knockout mutants showed that the zosA gene was de-repressed in the presence of 0.1% dl-penicillamine, and that the zosA mutant was sensitive to dl-penicillamine medium. The zosA mutant delayed the growth under Cu-limitation even without the chelator, and the sensitivity to dl-penicillamine was reversed by induction using 0.3 mM IPTG and the Pspac promoter inserted directly upstream of the zosA gene. Furthermore, the zosA mutant showed elevated tolerance of excessive Cu(2+) but not of excessive Zn(2+) added to LB and synthetic media. Homology modeling of the ZosA protein suggested that the protein can fold itself into essential domains for constituting a metal transporting ATPase. Our study suggests that zosA is a candidate gene involved in copper uptake.

DOI： 10.1080/09168451.2015.1107462

Draft Genome Sequence of Streptomyces incarnatus NRRL8089, which Produces the Nucleoside Antibiotic Sinefungin. 査読国際誌

Kenshiro Oshima, Masahira Hattori, Hitomi Shimizu, Koji Fukuda, Michiko Nemoto, Kenji Inagaki, Takashi Tamura

Genome announcements 3 ( 4 ) 2015年7月

記述言語：英語掲載種別：研究論文（学術雑誌）

A draft genome sequence of Streptomyces incarnatus NRRL8089, which produces the nucleoside antibiotic sinefungin, is described here. The genome contains 8,897,465 bp in 76 contigs and 8,266 predicted genes. Interestingly, the genome encodes an open reading frame for selenocysteine-containing formate dehydrogenase-O and the selenoprotein biosynthetic gene cluster selABCD.

DOI： 10.1128/genomeA.00715-15

Oil accumulation by the oleaginous diatom Fistulifera solaris as revealed by the genome and transcriptome. 査読国際誌

Tsuyoshi Tanaka, Yoshiaki Maeda, Alaguraj Veluchamy, Michihiro Tanaka, Heni Abida, Eric Maréchal, Chris Bowler, Masaki Muto, Yoshihiko Sunaga, Masayoshi Tanaka, Tomoko Yoshino, Takeaki Taniguchi, Yorikane Fukuda, Michiko Nemoto, Mitsufumi Matsumoto, Pui Shan Wong, Sachiyo Aburatani, Wataru Fujibuchi

The Plant cell 27 ( 1 ) 162 - 76 2015年1月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：AMER SOC PLANT BIOLOGISTS

Oleaginous photosynthetic organisms such as microalgae are promising sources for biofuel production through the generation of carbon-neutral sustainable energy. However, the metabolic mechanisms driving high-rate lipid production in these oleaginous organisms remain unclear, thus impeding efforts to improve productivity through genetic modifications. We analyzed the genome and transcriptome of the oleaginous diatom Fistulifera solaris JPCC DA0580. Next-generation sequencing technology provided evidence of an allodiploid genome structure, suggesting unorthodox molecular evolutionary and genetic regulatory systems for reinforcing metabolic efficiencies. Although major metabolic pathways were shared with nonoleaginous diatoms, transcriptome analysis revealed unique expression patterns, such as concomitant upregulation of fatty acid/triacylglycerol biosynthesis and fatty acid degradation (β-oxidation) in concert with ATP production. This peculiar pattern of gene expression may account for the simultaneous growth and oil accumulation phenotype and may inspire novel biofuel production technology based on this oleaginous microalga.

DOI： 10.1105/tpc.114.135194

Morphological and molecular phylogenetic analysis of the high triglyceride-producing marine diatom, Fistulifera solaris sp nov (Bacillariophyceae) 査読

Mitsufumi Matsumoto, Shigeki Mayama, Michiko Nemoto, Yorikane Fukuda, Masaki Muto, Tomoko Yoshino, Tadashi Matsunaga, Tsuyoshi Tanaka

PHYCOLOGICAL RESEARCH 62 ( 4 ) 257 - 268 2014年10月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：WILEY-BLACKWELL

Fistulifera sp. strain JPCC DA0580, a marine pennate diatom, contains extremely high levels of intracellular triglyceride and has been suggested as a promising source of feedstock for biodiesel fuels. JPCC DA0580 was isolated from a mangrove swamp located in Sumiyo Bay below the mouths of the Sumiyo and Yakugachi Rivers in Amami-Ohshima, Kagoshima, Japan. In this study, the morphology and the 18S rDNA sequence of JPCC DA0580 were compared with those of other Fistulifera strains. JPCC DA0580 possesses morphological characters of the genus Fistulifera, namely lightly silicified frustules, a distinct median costa (raphe sternum), and a wart-like central pore (fistula). Morphometric analysis revealed that JPCC DA0580 differs from other Fistulifera species by the presence of a valve with coarser striation and coarser areolation. On the basis of 18S rDNA phylogeny, JPCC DA0580 formed a well-supported clade with other members of the Fistulifera species complex, although the number of nucleotide substitutions was highest in JPCC DA0580. Our results led us to propose the taxonomic name Fistulifera solaris sp. nov. for JPCC DA0580.

DOI： 10.1111/pre.12066

Identification of a frustule-associated protein of the marine pennate diatom Fistulifera sp. strain JPCC DA0580. 査読国際誌

Michiko Nemoto, Yoshiaki Maeda, Masaki Muto, Masayoshi Tanaka, Tomoko Yoshino, Shigeki Mayama, Tsuyoshi Tanaka

Marine genomics 16 39 - 44 2014年8月

記述言語：英語掲載種別：研究論文（学術雑誌）

Among the proteins localized on the cell wall (frustule) of diatoms (frustule-associated proteins), several proteins tightly associated with the cell wall have been implicated in frustule formation. These proteins include diatom-specific unique serine- and lysine-rich sequences represented by silaffins. Taking advantage of available genome information, we used a recently described bioinformatics approach to screen silaffin-like proteins rich in serine and lysine from the genome of the marine pennate diatom Fistulifera sp. strain JPCC DA0580 and identified 7 proteins. All of the proteins shared a sequence motif called the XGXG domain, which was also confirmed in a silaffin-like protein identified in other diatoms. In vivo localization analysis revealed that one of the identified proteins, G7408, occurs throughout the frustule with a slightly uneven distribution. This novel frustule-associated protein could be a useful tool to elucidate the mechanism of biosilica formation in diatoms and to functionalize this strain for future biotechnological applications.

DOI： 10.1016/j.margen.2014.01.006

2030年への挑戦"藻類を燃料に

田中剛, 根本理子, 吉野知子

太陽エネルギー 39 27 - 35 2014年1月

Proteomics analysis of oil body-associated proteins in the oleaginous diatom. 査読国際誌

Daisuke Nojima, Tomoko Yoshino, Yoshiaki Maeda, Masayoshi Tanaka, Michiko Nemoto, Tsuyoshi Tanaka

Journal of proteome research 12 ( 11 ) 5293 - 301 2013年11月

記述言語：英語掲載種別：研究論文（学術雑誌）

For biodiesel production from microalgae, it is desirable to understand the entire triacylglycerol (TAG) metabolism. TAG accumulation occurs in oil bodies, and although oil body-associated proteins could play important roles in TAG metabolism, only a few microalgal species have been studied by a comprehensive analysis. Diatoms are microalgae that are promising producers of biodiesel, on which such proteomics analysis has not been conducted to date. Herein, we identified oil body-associated proteins in the oleaginous diatom Fistulifera sp. strain JPCC DA0580. The oil body fraction was separated by cell disruption with beads beating and subsequent ultracentrifugation. Contaminating factors could be removed by comparing proteins from the oil body and the soluble fractions. This novel strategy successfully revealed 15 proteins as oil body-associated protein candidates. Among them, two proteins, which were parts of proteins predicted to have transmembrane domains, were indeed confirmed to specifically localize to the oil bodies in this strain by observation of GFP fusion proteins. One (predicted to be a potassium channel) was also detected from the ER, suggesting that oil bodies might originate from the ER. By utilizing this novel subtraction method, we succeeded in identifying the oil body-associated proteins in the diatom for the first time.

DOI： 10.1021/pr4004085

A process design and productivity evaluation for oil production by indoor mass cultivation of a marine diatom, Fistulifera sp. JPCC DA0580. 査読国際誌

Akira Satoh, Kyonosuke Ichii, Mitsufumi Matsumoto, Chihiro Kubota, Michiko Nemoto, Masayoshi Tanaka, Tomoko Yoshino, Tadashi Matsunaga, Tsuyoshi Tanaka

Bioresource technology 137 132 - 8 2013年6月

記述言語：英語掲載種別：研究論文（学術雑誌）

The present study involved the designing of a culture process and the evaluation of productivity of oil products from a highly oleaginous marine diatom, Fistulifera sp. JPCC DA0580, which had been cultured in a commercial-scale factory. The culture facility had a capacity of 48,000 L and held 96 flat-type 500-L photobioreactors (PBRs) equipped with artificial light, which secures a stable, perennial supply of the products. A 10 days culture that had reached a cell density of 6.5 g dry weight L(-1) possessing a cellular oil content of 48% (wt/wt) was found to provide the highest oil yield. On considering a production area of 1500 m(2), annual algal mass and oil productivity is 68.7 and 33.3 t ha(-1) year(-1), respectively. This study thus provides a reproducible prediction of a theoretical maximum oil yield from a highly oleaginous microalgal strain based on industrially practical production area.

DOI： 10.1016/j.biortech.2013.03.087

Phase Transformations and Structural Developments in the Radular Teeth of Cryptochiton Stelleri 査読

Qianqian Wang, Michiko Nemoto, Dongsheng Li, James C. Weaver, Brian Weden, John Stegemeier, Krassimir N. Bozhilov, Leslie R. Wood, Garrett W. Milliron, Christopher S. Kim, Elaine DiMasi, David Kisailus

ADVANCED FUNCTIONAL MATERIALS 23 ( 23 ) 2908 - 2917 2013年6月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：WILEY-V C H VERLAG GMBH

During mineralization, the hard outer magnetite-containing shell of the radular teeth of Cryptochiton stelleri undergoes four distinct stages of structural and phase transformations: (i) the formation of a crystalline -chitin organic matrix that forms the structural framework of the non-mineralized teeth, (ii) the templated synthesis of ferrihydrite crystal aggregates along these organic fibers, (iii) subsequent solid state phase transformation from ferrihydrite to magnetite, and (iv) progressive magnetite crystal growth to form continuous parallel rods within the mature teeth. The underlying -chitin organic matrix appears to influence magnetite crystal aggregate density and the diameter and curvature of the resulting rods, both of which likely play critical roles in determining the local mechanical properties of the mature radular teeth.

DOI： 10.1002/adfm.201202894

Molecular Bioengineering of Magnetosomes for Biotechnological Applications 査読

Atsushi Arakaki, Michiko Nemoto, Tadashi Matsunaga

Coordination Chemistry in Protein Cages: Principles, Design, and Applications 241 - 271 2013年4月

記述言語：英語掲載種別：論文集(書籍)内論文出版者・発行元：John Wiley and Sons

Organisms produce inorganic/organic composite materials, called biominerals, show amazing structures and exhibit excellent physical/chemical properties that often outperform artificial materials. From the basic studies on magnetotactic bacteria and their magnetosome formation mechanisms, methods for functional design of magnetosomes and magnetotactic bacterial cells were established through molecular bioengineering. This chapter introduces recent progress on the basic studies of magnetosome formation mechanism and the design of functional magnetic particles and their applications to biotechnology based on their unique properties. Moreover, the results obtained from these fundamental studies allow us to develop novel molecular constructs on the magnetosome surface. The constructed functional magnetosomes generated by the molecular bioengineering techniques are used for various biotechnological applications. © 2013 John Wiley &amp
Sons, Inc. All rights reserved.

DOI： 10.1002/9781118571811.ch10

Establishment of a genetic transformation system for the marine pennate diatom Fistulifera sp. strain JPCC DA0580--a high triglyceride producer. 査読国際誌

Masaki Muto, Yorikane Fukuda, Michiko Nemoto, Tomoko Yoshino, Tadashi Matsunaga, Tsuyoshi Tanaka

Marine biotechnology (New York, N.Y.) 15 ( 1 ) 48 - 55 2013年2月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：SPRINGER

A genetic transformation system for the marine pennate diatom, Fistulifera sp. JPCC DA0580, was established using microparticle bombardment methods. Strain JPCC DA0580 has been recently identified as the highest triglyceride (60 % w/w) producer from a culture collection of 1,393 strains of marine microalgae, and it is expected to be a feasible source of biodiesel fuel. The transformation conditions for strain JPCC DA0580 were optimised using the green fluorescent protein gene (gfp) and the gene encoding neomycin phosphotransferase II (nptII). The most efficient rate of transformation was attained when tungsten particles (0.6 μm in diameter) were used for microparticle bombardment. The effect of endogenous and exogenous promoters on the expression of nptII was examined. Endogenous promoters were more efficient for obtaining transformants compared with exogenous promoters. Southern hybridisation analysis suggested that nptII integrated into the nuclear genome. This genetic manipulation technique should allow us to understand the mechanisms of high triglyceride accumulation in this strain, thereby contributing to improving BDF production.

DOI： 10.1007/s10126-012-9457-0

Proteomic analysis from the mineralized radular teeth of the giant Pacific chiton, Cryptochiton stelleri (Mollusca). 査読国際誌

Michiko Nemoto, Qianqian Wang, Dongsheng Li, Songqin Pan, Tadashi Matsunaga, David Kisailus

Proteomics 12 ( 18 ) 2890 - 4 2012年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：WILEY-BLACKWELL

The biomineralized radular teeth of chitons are known to consist of iron-based magnetic crystals, associated with the maximum hardness and stiffness of any biomineral. Based on our transmission electron microscopy analysis of partially mineralized teeth, we suggest that the organic matrix within the teeth controls the iron oxide nucleation. Thus, we used Nano-LC-MS to perform a proteomic analysis of the organic matrix in radular teeth of the chiton Cryptochiton stelleri in order to identify the proteins involved in the biomineralization process. Since the genome sequence of C. stelleri is not available, cross-species similarity searching and de novo peptide sequencing were used to screen the proteins. Our results indicate that several proteins were dominant in the mineralized part of the radular teeth, amongst which, myoglobin and a highly acidic peptide were identified as possibly involved in the biomineralization process.

DOI： 10.1002/pmic.201100473

Assessment of the anti-biofouling potentials of a copper iodide-doped nylon mesh. 査読国際誌

Tetsuya Sato, Yoshie Fujimori, Tsuruo Nakayama, Yasuo Gotoh, Yoshihiko Sunaga, Michiko Nemoto, Tadashi Matsunaga, Tsuyoshi Tanaka

Applied microbiology and biotechnology 95 ( 4 ) 1043 - 50 2012年8月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：SPRINGER

We propose a copper iodide (CuI)-doped nylon mesh prepared using polyiodide ions as a precursor toward anti-biofouling polymer textile. The CuI-doped nylon mesh was subjected to the prevention of biofouling in marine environments. The attachment of the marine organisms was markedly inhibited on the CuI-doped nylon mesh surface until 249 days. Scanning electron microscopy-energy dispersive X-ray analysis indicated that copper compounds were maintained in the nylon mesh after the field experiment, although copper content in the nylon mesh was reduced. Therefore, the copper ions slowly dissolved from nylon mesh will contribute to the long-term prevention of biofouling. Furthermore, electron spin resonance analysis revealed the generation of reactive oxygen species (ROS) from CuI-doped nylon mesh after the field experiment. One of the possibilities for toxic action of copper ions will be the direct effect of Cu+ -induced ROS on biofilm forming on nylon mesh surface. The proposed polymer textile can be applied to fishing and aquafarming nets, mooring rope for ship, or silt fence to restrict polluted water in marine environments.

DOI： 10.1007/s00253-011-3720-6

Investigation of the antiviral properties of copper iodide nanoparticles against feline calicivirus. 査読

Nozomi Shionoiri, Tetsuya Sato, Yoshie Fujimori, Tsuruo Nakayama, Michiko Nemoto, Tadashi Matsunaga, Tsuyoshi Tanaka

Journal of bioscience and bioengineering 113 ( 5 ) 580 - 6 2012年5月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：SOC BIOSCIENCE BIOENGINEERING JAPAN

This study demonstrated the antiviral properties of copper iodide (CuI) nanoparticles against the non-enveloped virus feline calicivirus (FCV) as a surrogate for human norovirus. The effect of CuI nanoparticles on FCV infectivity to Crandell-Rees feline kidney (CRFK) cells was elucidated. The infectivity of FCV to CRFK cells was greatly reduced by 7 orders of magnitude at 1000μgml(-1) CuI nanoparticles. At the conditions, electron spin resonance (ESR) analysis proved hydroxyl radical production in CuI nanoparticle suspension. Furthermore, amino acid oxidation in the viral capsid protein of FCV was determined by nanoflow liquid chromatography-mass spectrometric (nano LC-MS) analysis. The use of CuI nanoparticles showed extremely high antiviral activity against FCV. The high antiviral property of CuI nanoparticles was attributed to Cu(+), followed by ROS generation and subsequent capsid protein oxidation. CuI nanoparticles could be proposed as useful sources of a continuous supply of Cu(+) ions for efficient virus inactivation. Furthermore, this study brings new insights into toxic actions of copper iodide nanoparticles against viruses.

DOI： 10.1016/j.jbiosc.2011.12.006

Prevention of marine biofouling on nylon mesh doped with silver iodide 査読

Tetsuya Sato, Yoshie Fujimori, Tsuruo Nakayama, Yasuo Gotoh, Michiko Nemoto, Tadashi Matsunaga, Tsuyoshi Tanaka

COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS 396 41 - 45 2012年2月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ELSEVIER SCIENCE BV

Many textiles have been often used in marine environments for a wide variety of purposes. Consequently, effective and clean methods to prevent biofouling in these textiles are needed. In this study, a nylon mesh doped with AgI was examined for its antifouling performance. The nylon mesh was iodinated with an iodine-potassium iodide aqueous solution and subsequently immersed in silver nitrate solution to form AgI particles in the fiber. SEM-EDX analysis indicated that the AgI crystals were highly incorporated into the nylon 6,6 polymer (173 wt% gain). The bactericidal activity of AgI-doped nylon mesh was more than 200 times higher than that of silver-coated nylon mesh. Furthermore, continuous prevention of biofouling in the coastal marine environment was attained for 437 days by using the AgI-doped nylon mesh. Since the concentration of the released silver ions from the nylon mesh was estimated to be less than 1 ppb, the proposed nylon mesh is useful as an effective and clean method for prevention of biofouling in polymer textiles. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.colsurfa.2011.12.037

次世代液体バイオ燃料開発に向けた海洋生物資源の活用

田中剛, 根本理子, 松永是

ケミカルエンジニアリング 56 ( 9 ) 713 - 718 2011年9月

Proteomic analysis of irregular, bullet-shaped magnetosomes in the sulphate-reducing magnetotactic bacterium Desulfovibrio magneticus RS-1. 査読国際誌

Tadashi Matsunaga, Michiko Nemoto, Atsushi Arakari, Masayoshi Tanaka

Proteomics 9 ( 12 ) 3341 - 52 2009年6月

記述言語：英語掲載種別：研究論文（学術雑誌）

Recent molecular studies on magnetotactic bacteria have identified a number of proteins associated with bacterial magnetites (magnetosomes) and elucidated their importance in magnetite biomineralisation. However, these analyses were limited to magnetotactic bacterial strains belonging to the alpha-subclass of Proteobacteria. We performed a proteomic analysis of magnetosome membrane proteins in Desulfovibrio magneticus strain RS-1, which is phylogenetically classified as a member of the delta-Proteobacteria. In the analysis, the identified proteins were classified based on their putative functions and compared with the proteins from the other magnetotactic bacteria, Magnetospirillum magneticum AMB-1 and M. gryphiswaldense MSR-1. Three magnetosome-specific proteins, MamA (Mms24), MamK, and MamM, were identified in strains RS-1, AMB-1, and MSR-1. Furthermore, genes encoding ten magnetosome membrane proteins, including novel proteins, were assigned to a putative magnetosome island that contains subsets of genes essential for magnetosome formation. The collagen-like protein and putative iron-binding proteins, which are considered to play key roles in magnetite crystal formation, were identified as specific proteins in strain RS-1. Furthermore, genes encoding two homologous proteins of Magnetococcus MC-1 were assigned to a cryptic plasmid of strain RS-1. The newly identified magnetosome membrane proteins might contribute to the formation of the unique irregular, bullet-shaped crystals in this microorganism.

DOI： 10.1002/pmic.200800881

Formation of magnetite by bacteria and its application. 査読国際誌

Atsushi Arakaki, Hidekazu Nakazawa, Michiko Nemoto, Tetsushi Mori, Tadashi Matsunaga

Journal of the Royal Society, Interface 5 ( 26 ) 977 - 99 2008年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ROYAL SOC

Magnetic particles offer high technological potential since they can be conveniently collected with an external magnetic field. Magnetotactic bacteria synthesize bacterial magnetic particles (BacMPs) with well-controlled size and morphology. BacMPs are individually covered with thin organic membrane, which confers high and even dispersion in aqueous solutions compared with artificial magnetites, making them ideal biotechnological materials. Recent molecular studies including genome sequence, mutagenesis, gene expression and proteome analyses indicated a number of genes and proteins which play important roles for BacMP biomineralization. Some of the genes and proteins identified from these studies have allowed us to express functional proteins efficiently onto BacMPs, through genetic engineering, permitting the preservation of the protein activity, leading to a simple preparation of functional protein-magnetic particle complexes. They were applicable to high-sensitivity immunoassay, drug screening and cell separation. Furthermore, fully automated single nucleotide polymorphism discrimination and DNA recovery systems have been developed to use these functionalized BacMPs. The nano-sized fine magnetic particles offer vast potential in new nano-techniques.

DOI： 10.1098/rsif.2008.0170

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