Biology subjects

Numata, K.

Publications and source records attributed to Numata, K..

12 recordsLinked to original sources

bioRxiv2026

Thermal Conductivity of Artificial Materials Engineered from Plant and Bacterial Cells

Bio-based materials are known for their excellent biodegradability and, in some cases, their potential to fix carbon dioxide. Owing to these properties, they are increasingly being utilized as environmentally friendly alternatives across various applications. In this study, we focused on using living cells themselves as material components, aiming to evaluate their potential as substitutes for conventional plastic-based thermal insulators. We selected two types of cells, photosynthetic purple non-sulfur bacterium Rhodovulum sulfidophilum and tobacco BY-2 plant suspension cells. After optimizing solidification conditions through the addition of pectin and cellulose nanofibers, we measured the thermal conductivity of the solidified cells under atmospheric pressure. The results showed that R. sulfidophilum exhibited 0.0553 W/m{middle dot}K, while BY-2 exhibited a thermal conductivity of 0.043 W/m{middle dot}K. Both values indicate relatively low thermal conductivity compared to existing bio-based materials, suggesting high insulation performance. Among the solidified cells, the solidified BY-2 cells showed minimal variation in thermal insulation performance under pressure changes, and had a low thermal emissivity as revealed by FT-IR analysis. Based on these findings, we propose that cell-derived materials can serve as potentially biodegradable bio-based thermal insulation materials.

bioengineering↗

bioRxiv2025

Low-salinity medium for large-scale biomass production of the marine purple photosynthetic bacterium Rhodovulum sulfidophilum

Marine purple non-sulfur bacteria such as Rhodovulum sulfidophilum are versatile due to their diverse applications in bioremediation, biotechnological production of useful materials, industrial production of value-added compounds, and agricultural fertilizers. Our previous study demonstrated the potential of its lysed and dried biomass as a nitrogen fertilizer for plant production. However, large-scale fertilizer production requires scaling up the culture to larger volumes, which is not cost-effective with currently available options for growth media. In this study, we tested a seawater-based, cost-effective alternative to the commonly used nutrient-rich culture medium for the growth of this bacterium. We found that reducing salinity from 3% to 1.2% had no adverse effects on its heterotrophic growth, dry cell yield, nitrogen content, and total amino acid composition. The nitrogen content and the weight percent of free lysine, aspartic acid, and glutamate increased in the biomass obtained from cultures grown at 1.2% salinity. Under autotrophic conditions, decreasing salinity to 1.2% did not affect cell growth, final dry cell yields, and total carbon assimilation, but N assimilation tended to be higher. Reducing salinity to 1.2% proved to be cost-effective and feasible for the cultivation of R. sulfidophilum without increasing the risk of contamination, providing a viable alternative for its large-scale cultivation and application as a plant nitrogen fertilizer.

microbiology↗

bioRxiv2025

High throughput protein serial crystallography using a grease matrix and a large-area support film

Serial femtosecond crystallography (SFX) using ultrashort pulses from X-ray free- electron lasers (XFELs) enables the determination of crystal structures at room temperature while minimizing radiation damage to the samples. This method involves irradiating numerous crystals one by one with XFEL pulses, allowing even the capture snapshots of dynamical structures in biological macromolecules. To achieve this, an efficient sample delivery system is essential for acquiring a large number of diffraction patterns. The most common approach uses a highly viscous grease matrix containing sample crystals, injected into the XFEL path from a narrow nozzle. However, the injection often suffers from clogging issues inside the injector nozzle, resulting in additional challenges such as the need for suitably sized crystals, increased sample consumption and unstable flow rates. Alternatively, a fixed-target approach, which scans a two-dimensional substrate with dispersed samples, can circumvent these issues. However, it must ensure the integrity of biological samples and provide sufficient surface area for efficient data collection. We here present an approach that utilizes a grease matrix and a large-area support film specially designed to address these requirements. This system offers a fast and reliable solution for protein SFX, enabling high-quality structure determination while significantly reducing sample consumption.

molecular biology↗

bioRxiv2022

Composition of minor ampullate silk makes its properties different from those of major ampullate silk

Spiders minor ampullate silk, or MI-silk, exhibits distinct mechanical properties and water resistance compared to its major ampullate counterpart (MA-silk). The principal protein constituent of MI-silk is known as minor ampullate spidroin, or MiSp, and while its sequence has been deciphered and is thought to underlie the differences in properties with MA-silk, the composition of MI-silk and the relationship between its composition and properties remain elusive. In this study, we set out to investigate the mechanical properties, water resistance, and proteome of MA-silk and MI-silk from Araneus ventricosus and Trichonephila clavata. We also synthesized artificial fibers from major ampullate spidroin, MaSp1 and 2, and MiSp to compare their properties. Our proteomic analysis reveals that the MI-silk of both araneids is composed of MiSp, MaSp1, and spidroin constituting elements (SpiCEs). The absence of MaSp2 in the MI-silk proteome and the comparison of the water resistance of artificial fibers suggest that the presence of MaSp2 is the reason for the disparity in water resistance between MI-silk and MA-silk.

molecular biology↗

bioRxiv2021

Darwin's bark spider shares a spidroin repertoire with Caerostris extrusa but achieves extraordinary silk toughness through gene expression

Spider silk is a protein-based material whose toughness suggests possible novel applications. A particularly fascinating example of silk toughness is provided by Darwins bark spider (Caerostris darwini) found in Madagascar. This spider produces extraordinarily tough silk, with an average toughness of 350 MJ/m and over 50% extensibility, and can build river-bridging webs with a size of 2.8 m2. Recent studies have suggested that specific spidroins expressed in C. darwini are responsible for the mechanical properties of its silk. Therefore, a more comprehensive investigation of spidroin sequences, silk thread protein contents, and phylogenetic conservation among closely related species is required. Here, we conducted genomic, transcriptomic, and proteomic analyses of C. darwini and its close relative Caerostris extrusa. A variety of spidroins and low-molecular-weight proteins were found in the dragline silk of these species; all of the genes encoding these proteins were conserved in both genomes, but their genes were more expressed in C. darwini. The potential to produce very tough silk is common in the genus Caerostris, and our results may suggest the existence of plasticity allowing silk mechanical properties to be changed by optimizing related gene expression in response to the environment.

molecular biology↗

bioRxiv2021

Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk

Dragline silk of golden orb-weaver spiders (Nephilinae) is noted for its unsurpassed toughness, combining extraordinary extensibility and tensile strength, suggesting industrial application as a sustainable biopolymer material. To pinpoint the molecular composition of dragline silk and the roles of its constituents in achieving its mechanical properties, we report a multiomics approach combining high-quality genome sequencing and assembly, silk gland transcriptomics, and dragline silk proteomics of four Nephilinae spiders. We observed the consistent presence of the MaSp3B spidroin unique to this subfamily, as well as several non-spidroin SpiCE proteins. Artificial synthesis and combination of these components in vitro showed that the multicomponent nature of dragline silk, including MaSp3B and SpiCE, along with MaSp1 and MaSp2, is essential to realize the mechanical properties of spider dragline silk.

molecular biology↗

bioRxiv2019

Synthetic peptide-induced internalization of biomolecules into various plant and algal cells via micropinocytosis

Efficient intracellular delivery of biomolecules is important for many different biological and biotechnological applications in living organisms, and is a prerequisite for certain types of fundamental and applied research. One major challenge is the delivery of unmodified, functional cargoes in a simple, time-efficient, and high-throughput manner. Herein, we present an efficient strategy that uses fusion peptides containing cell penetrating peptide, endosomal escape domain, and a sarcosine linker to introduce biomolecules, namely fluorescent protein and dextran, via macropinocytosis into the cells of various land plants and microalgae. Our peptide-mediated delivery system allows for high-throughput delivery of functional biomolecules within a few minutes to a few hours as well as open new possibilities for biology and biotechnology using difficult-to-transfect cell types.

plant biology↗

bioRxiv2019

Native protein delivery into rice callus using ionic complexes of protein and cell-penetrating peptides

Direct protein delivery into intact plants remains a challenge for the agricultural and plant science fields. Cell-penetrating peptide (CPP)-mediated protein delivery requires the binding of CPPs to a protein to carry the protein into the cell through the cell wall and lipid bilayer. Thus, we prepared ionic complexes of a CPP-containing carrier peptide and a cargo protein, namely, Citrine yellow fluorescent protein, and subsequently studied their physicochemical properties. Two types of carrier peptides, BP100(KH)9 and BP100CH7, were investigated for delivery efficiency into rice callus. Both BP100(KH)9 and BP100CH7 successfully introduced Citrine protein into rice callus cells under pressure and vacuum treatment. Moreover, delivery efficiency varied at different growth stages of rice callus; 5-day rice callus was a more efficient recipient for Citrine than 21-day callus.

plant biology↗

bioRxiv2019

Efficient callus induction and completion of regeneration in kenaf Hibiscus cannabinus

Kenaf, Hibiscus cannabinus, is a fiber-enriched plant belonging to Malvaceae and is an important fiber crop. The features of kenaf of being fast-growing and fiber-enriched suggest the potential for the use of kenaf in biomass and materials; however, the complete regeneration procedure, which is essential for genetic modification, is lacking. Here, we report the complete regeneration of kenaf from cotyledon explants achieved by callus induction on an improved callus-inducing medium and shoot induction on a shoot-inducing medium and by seed setting under a regulated growth condition in a chamber. Our complete regeneration method will enable the production of stably transformed kenaf that can improve the properties of kenaf as a material.

plant biology↗

bioRxiv2019

Optimal iron concentrations for growth-associated polyhydroxyalkanoate biosynthesis in the marine photosynthetic purple bacterium Rhodovulum sulfidophilum

Polyhydroxyalkanoates (PHAs) are a group of natural biopolyesters that resemble petroleum-derived plastics in terms of physical properties but are less harmful biologically to the environment and humans. Most of the current PHA producers are heterotrophs, which require expensive feeding materials and thus contribute to the high price of PHAs. Marine photosynthetic bacteria are promising alternative microbial cell factories for cost-effective, carbon neutral and sustainable production of PHAs. In this study, Rhodovulum sulfidophilum, a marine photosynthetic purple nonsulfur bacterium with a high metabolic versatility, was evaluated for cell growth and PHA production under the influence of various media components found in previous studies. We evaluated iron, using ferric citrate, as another essential factor for cell growth and efficient PHA production and confirmed that PHA production in R. sulfidophilum was growth-associated under microaerobic and photoheterotrophic conditions. In fact, a subtle amount of iron (1 to 2 M) was sufficient to promote rapid cell growth and biomass accumulation, as well as a high PHA yield during the logarithmic phase. However, an excess amount of iron did not enhance the growth rate or PHA productivity. Thus, we successfully confirmed that an optimum concentration of iron, an essential nutrient, promotes cell growth in R. sulfidophilum and also enhances PHA utilization.

microbiology↗

bioRxiv2017

Atomic resolution structure of serine protease proteinase K at ambient temperature

Atomic resolution structures (beyond 1.20 [A]) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 [A] resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value of B-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites.

biochemistry↗

bioRxiv2016

Metabolomic and proteomic analyses of a quiescent Escherichia coli cell factory reveal the mechanisms behind its production efficiency

1Quiescent (Q-Cell) Escherichia coli cultures can be created by using the signalling molecule indole to halt cell division of an hns mutant strain. This uncouples metabolism from cell growth and allows for more efficient use of carbon feedstocks. However, the reason for the increased productivity of cells in this state was previously unknown. We show here that Q-cells can maintain metabolic activity in the absence of growth for up to 24 h, leading to four times greater per-cell productivity of a model metabolite, 3-hydroxybutyrate (3HB), than a control. Metabolomic data show that by disrupting the proton-motive force, indole interrupts the tricarboxylic acid cycle, leading to the accumulation of metabolites in the glycolysis pathway that are excellent starting points for high-value chemical production. By comparing protein expression patterns between wild-type and Q-cell cultures we show that Q-cells overexpress stress response proteins, which prime them to tolerate the metabolic imbalances incurred through indole addition. Quiescent cultures produced half the cell biomass of control cultures lacking indole, but were still able to produce 39.4 g.L-1 of 3HB compared to 18.6 g.L-1 in the control. Therefore, Q-cells have high potential as a platform technology for the efficient production of a wide range of commodity and high value chemicals.

microbiology↗