Biology subjects

Kume, A.

Publications and source records attributed to Kume, A..

7 recordsLinked to original sources

bioRxiv2026

Effects of microgravity on the three-dimensional morphology of rhizoids in Physcomitrium patens

Rooting systems of plants perceive environmental stimuli and flexibly regulate their growth. Therefore, understanding stimulus perception and response mechanisms is essential for optimizing cultivation. During the transition from aquatic to terrestrial environments, land plants have acquired mechanisms to adapt to gravitational force on land. Thus, elucidating gravity responses of rhizoids in bryophytes, early diverging land plants, provides important insights into how gravity-response mechanisms were established during land plant evolution. Analyzing rhizoid morphology under microgravity, where gravitational effects are largely eliminated, provides an effective approach to examine the gravity-response mechanisms that evolved after terrestrialization. In this study, to elucidate microgravity effects on rhizoid growth of Physcomitrium patens, we analyzed 3D datasets obtained by refraction-contrast micro-CT using synchrotron radiation after fixation and embedding of samples from the Space Moss experiment conducted on the International Space Station. Because each CT volume contains numerous rhizoids, we optimized a WEKA-based machine-learning segmentation approach by improving preprocessing, training, and postprocessing steps, resulting in a significantly improved segmentation accuracy. Comparison of 3D morphological indices between manually segmented rhizoids and predicted results supported the validity of the proposed method for morphological analysis. Morphological analyses revealed that, compared with both ground and artificial 1 x g conditions, rhizoid elongation and gravitropic responses were suppressed under microgravity, leading to reduced vertical growth. These findings indicate that gravity plays a fundamental role in rhizoid morphogenesis, and their absence affects growth orientation and elongation. This study provides foundational data for research on the rooting systems of bryophytes in space.

plant biology↗

bioRxiv2024

Annual Variability in Diffuse Ratio and Spectral Characteristics of Solar Radiation: Cloud Effects in a Temperate Monsoon Region

Solar radiation (SR) dynamics have a profound effect on plant growth, development, and ecosystems, and they act as a primary energy source and important environmental signal that plants perceive through their photoreceptors, which primarily sense critical wavelength ratios (CWRs). The diffuse fraction of solar radiation (DF) is a key factor affecting the quality and distribution of light within the plant canopy. We analyzed one year of SR spectral observations measured by a ground-based rotating shadow-band spectroradiometer to evaluate the potential effects of DF and CWRs on plants in an outdoor environment in Fukuoka, Japan. The daily mean DF and all considered CWRs showed significant seasonal variations regardless of the solar meridian altitude. Cloudy or partly cloudy skies were prevalent throughout the year. The ratios of ultraviolet-A (UV-A)/UV-B, red (R)/blue (B), and R/green (G) increased during winter and decreased during summer. Conversely, the ratios of photosynthetically active radiation (PAR)/global solar radiation (GSI), UV/GSI, UV/PAR, B/G, R/far-red (FR), and UV-B/B increased during summer and decreased during winter. Specific CWRs correlated with air mass (AM) and vapor pressure (VP), and most of the CWR correlated with DF. AM, VP, and DF were also found to have a combined effect on specific CWRs that are important for plant light signals. This highlights the potential influence of AM, VP, and DF on plant light signals, thereby opening avenues for the development of innovative models of plant growth and ecological responses that incorporate plant photoreception.

ecology↗

bioRxiv2024

Prolonged exposure to hypergravity increases biomass and alters biomass allocation in Arabidopsis thaliana (L.) Heynh. with no apparent impact on element content in the shoot system

Previous studies have already shown that plants can complete their life cycle under microgravity. However, the effects of long-term exposure to altered gravity conditions, including microgravity, on most of the biological processes of a plants life cycle remain largely unexplored. Given the limited opportunities for space experiments, it is crucial to conduct ground-based experiments, such as hypergravity experiments. To investigate the longer-term effects of hypergravity, we have developed and utilized a custom-built hypergravity cultivation system using a centrifuge equipped with lighting, enabling the continuous growth of seed plants under hypergravity conditions. In this study, we examined the effects of 10 g hypergravity on the biomass of the shoot system (stems and rosette leaves) and the root system of vascular plants for the first time, covering the entire cultivation period from germination to 40 days. Our results showed that the dry mass of the stem per unit length was significantly higher under 10 g compared to the 1 g control, indicating a typical gravity resistance response of the stem. Moreover, the total dry mass of the stems, rosette leaves, and roots was higher under 10 g hypergravity compared to the 1 g control, suggesting an increase in biomass at the individual plant level. We also observed that the leaf mass per area of the rosette leaf was higher under hypergravity compared to the 1 g control, indicating enhanced photosynthesis rates in Arabidopsis and resulting in increased biomass of individual plants. In terms of biomass allocation, both root-shoot ratio and root mass fraction were significantly higher under hypergravity conditions compared to the 1 g control. Furthermore, we measured the content of mineral elements (Ca, Co, Cu, Fe, K, Mg, Mn, Mo, P, Zn) in the roots and rosette leaves using inductively coupled plasma optical emission spectrometry. Despite the increase in dry mass of the root system, we found no significant differences in the content of any of the ions analyzed between 10 g and 1 g conditions, indicating that mineral nutrient uptake homeostasis is maintained even under hypergravity conditions.

plant biology↗

bioRxiv2023

Prolonged exposure to hypergravity increases number and size of cells and enhances lignin deposition in the stem of Arabidopsis thaliana (L.) Heynh.

We have performed a lab-based hypergravity cultivation experiment using a centrifuge equipped with a lighting system and examined long-term effects of hypergravity on the development of the main axis (stem) of the Arabidopsis (Arabidopsis thaliana (L.) Heynh.) primary inflorescence. Plants grown under 1 x g (gravitational acceleration on Earth) conditions for 20-23 days and having the first visible flower bud were exposed to hypergravity at 8 x g for 10 days. We analyzed the effect of prolonged hypergravity conditions on growth, lignin deposition, and tissue anatomy of the main axis. As a result, the length of the main axis decreased and cross-sectional area, dry mass per unit length, cell number, lignin content of the main axis significantly increased under hypergravity. Lignin content in the rosette leaves also increased when they were exposed to hypergravity during their development. Except for interfascicular fibers, cross-sectional areas of the tissues composing the internode significantly increased under hypergravity in most type of the tissues in the basal part than the apical part of the main axis, indicating that the effect of hypergravity is more pronounced in the basal part than the apical part. The number of cells in fascicular cambium and xylem significantly increased under hypergravity both in the apical and basal internodes of the main axis, indicating a possibility that hypergravity stimulates procambium activity to produce xylem element more than phloem element. The main axis was suggested to be strengthened through changes in its morphological characteristics as well as lignin deposition under prolonged hypergravity conditions.

plant biology↗

bioRxiv2022

Efficient Gene Transduction in Pigs and Macaques with the Engineered AAV Vector AAV.GT5 for Hemophilia B Gene Therapy

Gene therapy for hemophilia using adeno-associated virus (AAV) vectors allows long-term coagulation factor expression. We examined the potential of a novel engineered liver-tropic AAV3B-based vector AAV.GT5 for hemophilia B gene therapy. In vitro transduction with AAV.GT5 in human hepatocytes was more than 100 times higher than with AAV-Spark100, while in vivo transduction efficacy into the liver and the increase in coagulation factor IX (FIX) antigen following intravenous injection of these vectors were similar in PXB mice (chimeric mice with a humanized liver) and macaques. The discrepancy was due to the low recovery and short half-life of AAV.GT5 in blood, depending on the positive charge of the heparin-binding site in the original AAV3B. The intra-hepatic vascular administration of AAV.GT5, but not AAV-Spark100, enhanced vector transduction into the liver and reduced vector distribution to the kidney in pigs. In macaques, the intra-hepatic artery injection of AAV.GT5 yielded a comparable increase in FIX antigen with a one-third dosage of peripheral venous administration. Two of four macaques who received AAV.GT5 intravenously did not develop neutralizing antibodies (NAbs) against AAV.GT5, while AAV-Spark100 induced serotype-specific NAbs in all four macaques. The NAb produced after the administration was relatively specific to the serotype and less responsive to the other serotype. As a result, the administration of AAV.GT5 successfully boosted FIX expression in one animal previously given AAV-Spark100. Thus, AAV.GT5 has different biodistribution and immunogenic characteristics compared with AAV-Spark100, and the intra-hepatic vascular administration may lessen the vector dose and avoid vector distribution to other organs. Key PointsO_LIThe AAV.GT5 vector has a strong transduction efficacy in human hepatocytes but has a faster clearance after systemic administration. C_LIO_LIIntra-hepatic vascular administration of the AAV.GT5 vector is an effective liver transduction method for hemophilia gene therapy. C_LI

genetics↗

bioRxiv2022

Three-dimensional visualization of moss rhizoid system by refraction-contrast X-ray micro-computed tomography

Land plants have two types of shoot-supporting systems, root system and rhizoid system, in vascular plants and bryophytes. However, since the evolutionary origin of the systems are different, how much they exploit common systems or distinct systems to architect their structures are largely unknown. To understand the regulatory mechanism how bryophytes architect rhizoid system responding to an environmental factor, such as gravity, and compare it with the root system of vascular plants, we have developed the methodology to visualize and quantitatively analyze the rhizoid system of the moss, Physcomitrium patens in 3D. The rhizoids having the diameter of 21.3 m on the average were visualized by refraction-contrast X-ray micro-CT using coherent X-ray optics available at synchrotron radiation facility SPring-8. Three types of shape (ring-shape, line, black circle) observed in tomographic slices of specimens embedded in paraffin were confirmed to be the rhizoids by optical and electron microscopy. Comprehensive automatic segmentation of the rhizoids which appeared in different three form types in tomograms was tested by a method using Canny edge detector or machine learning. Accuracy of output images was evaluated by comparing with the manually-segmented ground truth images using measures such as F1 score and IoU, revealing that the automatic segmentation using the machine learning was more effective than that using Canny edge detector. Thus, machine learning-based skeletonized 3D model revealed quite dense distribution of rhizoids, which was similar to root system architecture in vascular plants. We successfully visualized the moss rhizoid system in 3D for the first time.

plant biology↗

bioRxiv2022

Characterization of prefusion-F-specific antibodies elicited by natural infection with human metapneumovirus

Human metapneumovirus (hMPV) is a major cause of acute respiratory tract infections in infants and the elderly for which there are no approved vaccines or antibody therapies. The viral fusion (F) glycoprotein is required for entry and is the primary target of neutralizing antibodies, however, little is known about the humoral immune response generated by humans as a result of natural infection. Here, we use stabilized hMPV F proteins to interrogate memory B cells from two elderly donors. We obtained over 700 paired non-IgM antibody sequences representing 563 clonotypes, indicative of a highly polyclonal antibody response to hMPV F in these individuals. Characterization of 136 of these monoclonal antibodies revealed broad recognition of the hMPV F surface, with potent neutralizing antibodies targeting each antigenic site. Cryo-EM structures of two neutralizing antibodies reveal the molecular basis for recognition of two prefusion-specific epitopes at the membrane-distal apex of hMPV F. Collectively these results provide new insights into the humoral response to hMPV infection in the elderly and will guide development of novel vaccine antigens.

immunology↗