Biology subjects

Shimada, T.

Publications and source records attributed to Shimada, T..

At least 19 recordsLinked to original sources

bioRxiv2026

In vivo brain temperature measurement using quantum dot imaging temperature sensors

Temperature regulation in the brain is essential for maintaining neuronal function and preventing thermally induced damage. Here, we report the development and in vivo application of quantum dots (QDs) to high-resolution thermometry in the mouse brain using two-photon excitation microscopy. These QDs, via the red-to-green photoluminescence (PL) intensity ratios, enabled stable temperature measurements in both normal and chronically hypo-perfused cerebral tissue. Our findings show that localized neuronal activity leads to transient heat generation, which is rapidly dissipated by cerebrovascular responses. In a chronic hypoperfusion model, impaired vascular function resulted in exaggerated and prolonged brain temperature elevations. This thermometry system provides unprecedented insight into the mechanisms of cerebral thermoregulation and highlights the importance of vascular cooling in protecting the brain from heat-induced stress, particularly in pathological conditions such as stroke.

bioengineering↗

bioRxiv2026

Arabidopsis hydathodes contain a dense and heterogeneous epithem for apoplastic fluid release

Hydathodes are specialized leaf tissues that mediate guttation, the release of liquid water droplets from vascular plants. They consist of xylem endings, water pores, and the epithem. The epithem comprises small cells whose cell types and functional properties remain poorly understood. While molecular genetic information on hydathodes has accumulated--particularly in the model plant Arabidopsis thaliana through recent RNA-seq analyses--high-resolution anatomical insights into their spatial organization remain limited. In this study, we aimed to characterize the specialized anatomy of Arabidopsis hydathodes using complementary imaging approaches. A fluorescent dye taken up from roots stained hydathodes, consistent with a connection between hydathodes and the vasculature. Microfocus-X-ray computed tomography revealed that the hydathodes protrude from the abaxial leaf surface and are more densely packed internally than surrounding tissues. Light microscopy showed that the epithem was heterogeneous, with elongated cells proximally and rounded cells distally. We found that the epithem was surrounded by cells (hereafter referred to as "boundary cells") with plastids that resembled those of mesophyll cells. Transmission electron microscopy showed that the organelles in epithem cells were immature, and the apoplast contained electron-dense material. Finally, using transgenic plants expressing a secreted fluorescent marker protein, we detected GFP in guttation droplets, indicating that the droplets can contain apoplastic material. Together, these findings reveal that Arabidopsis hydathodes possess a dense and spatially heterogeneous epithem associated with the release of apoplastic fluid.

plant biology↗

bioRxiv2025

Arabidopsis root lipid droplets are hubs for membrane homeostasis under heat stress, and triterpenoid synthesis and storage.

O_LIPlant lipid droplets (LDs) and their associated proteins have numerous subcellular and physiological functions. While considerable progress has been made for LDs in many tissues, the function and composition of LDs in roots remains largely unexplored. C_LIO_LIWe investigated the changes of the number of LDs and of the lipidome in heat-stressed Arabidopsis thaliana roots. Furthermore, we isolated root LDs from the Arabidopsis mutant trigalactosyldiacylglycerol 1-1 sugar dependent 1-4 and investigated their proteome and lipidome. C_LIO_LIHeat stress lead to a degradation of membrane lipids and an increase in TAGs and LDs. while, fatty acid SEs decreased, probably acting as precursors for acylated sterol glycosides. A variety of proteins were enriched in root LDs, which are thus far not described as LD proteins. Transient expression of these proteins in many cases confirmed their LD localization, for example of the triterpene biosynthetic enzymes thalianol synthase and marneral synthase. We could furthermore show that the educts and products of these enzymes are enriched in root LDs, too. C_LIO_LIWe conclude that root LDs simultaneously act as a sink and source during heat stress-induced membrane remodeling. Furthermore, root LDs play a pivotal role in triperpene synthesis and storage, thereby highlighting LDs as hubs in specialized metabolism. C_LI

plant biology↗

bioRxiv2025

A major update of the genome assembly of Eri silkmoth, Samia ricini.

Indian eri silkmoth, Samia ricini, is a wild silkmoth whose silk occupies a significant economic position. In addition to its importance as an economic animal, S. ricini is also useful as a model species of Saturniidae. National BioResource of Japan (NBRP) maintains a S. ricini strain brought to Japan during WWII via Taiwan. Since we have previously published a draft genome assembly of S. ricini, we have attempted to construct a chromosome-level genome assembly to facilitate genetic studies of S. ricini. We successfully constructed a chromosome-scale genome assembly by exploiting two long-read-based technologies, HiFi reads and optical genome mapping. Furthermore, we performed functional annotations of the genome assembly, i.e., repeat annotation, transcriptome-based gene prediction, ATAC-seq, and PIWI-interacting RNA (piRNA)-targeted small RNA-seq. The assembly harbours 16,226 protein-coding genes and 636 piRNA clusters across three tissues: ovaries, testis, and embryos. ATAC-seq data comprehensively detected open chromosome regions, which will benefit when CRISPR/Cas9-mediated genome editing is conducted.

genomics↗

bioRxiv2024

A nucleic acid prodrug activates mitochondrial respiration and extends lifespan

Mitochondrial dysfunction caused by aging leads to decreased energy metabolism, resulting in functional decline and increased frailty in multiple tissues. Strategies for protecting and activating mitochondria under stressful conditions are required to suppress aging and age-related diseases. However, it is challenging to develop drugs capable of boosting mitochondrial respiration and compensating for the reduced intracellular adenosine triphosphate (ATP) levels. In this study, we developed a prodrug that stimulates the metabolism of intracellular adenine nucleotides (AXP: adenosine monophosphate (AMP), adenosine diphosphate (ADP), and ATP). It enhances AMP-activated protein kinase activity, fatty acid oxidation, oxidative stress resistance, and mitochondrial respiration, thereby increasing the intracellular ATP levels. Furthermore, this prodrug markedly extended the lifespan of Caenorhabditis elegans. AXP-driven stimulation of cellular energy metabolism proposed herein represents a novel geroprotective strategy and paves the way for the development of bioenergetic-molecule therapeutics.

bioengineering↗

bioRxiv2024

Evolutionary acquisition of a primitive light-dependent nuclear relocation in Marchantia polymorpha

The terrestrialization of plants was accompanied by exposure to several environmental stresses. Adaptation to these stresses required numerous changes at the cellular and molecular level. One such adaptation in the leaves of Arabidopsis thaliana is the movement of cell nuclei to avoid UV damage. In the dark, the nuclei locate to the bottom walls of leaf cells to distance genetic material from external stresses, but in response to intense blue light (an indication of the presence of UV), they move to the side walls to escape UV-induced DNA damage1. The movement is driven by the photoreceptor phototropin and the actin cytoskeleton2. However, how this protective mechanism evolved in land plants remains unclear. Here, we show that in the liverwort Marchantia polymorpha, nuclei show a similar, but less stable movement in response to intense blue light. In the dark, M. polymorpha positioned nuclei on the upper walls of epidermal cells in young thalli, but in response to intense blue light, the nuclei immediately moved to the side walls, similar to A. thaliana. However, the movement was transient and the nuclei returned to the upper walls through both the actin and microtubule cytoskeletons. Unlike A. thaliana, M. polymorpha responded to prolonged (> 1 day) exposure to low light by moving nuclei from the upper to the side walls through both the actin and microtubule cytoskeletons and two photoreceptors (phototropin and phytochrome). However, no light-dependent nuclear relocation was observed in charophyte algae, suggesting that light-dependent nuclear relocation was initially established in the common ancestor of land plants as a result of terrestrialization and then diverged during land plant evolution.

plant biology↗

bioRxiv2024

Transposon fusion gave birth to Fem, Bombyx mori female determining gene

Fem is a W-linked piRNA precursor, and Fem piRNA is a master gene of female determination in Bombyx mori. Since Fem has significantly low similarity to any known sequences and the origin of Fem remains unclear, two hypotheses have been proposed for the origin of Fem. The first one is that Fem is an allele of Masc, while the second one is that Fem arose by transposition of Masc. To draw a solid conclusion, we determined the W chromosome sequences of B. mori and a closely relative bombycid species of Trilocha varians with a Fem-independent sex determination system. Comprehensive genome comparison led us to the "third" hypothesis: Fem is a chimeric sequence of transposons. Although we still cannot completely exclude the first hypothesis, at least a large portion of the parts other than the 44-bp Masc similarity region is derived from transposons, and even the 44-bp region could correspond to the boundary of the two transposons, gypsy and satellite DNA.

genetics↗

bioRxiv2023

The Arabidopsis katamari2 Mutant Exhibits a Hypersensitive Seedling Arrest Response at the Phase Transition from Heterotrophic to Autotrophic Growth

Young seedlings use nutrients stored in the seeds to grow and acquire photosynthetic potential. This process, called seedling establishment, involves a developmental phase transition from heterotrophic to autotrophic growth. Some membrane-trafficking mutants of Arabidopsis thaliana (Arabidopsis), such as the katamari2 (kam2) mutant, exhibit growth arrest during seedling development, with a portion of individuals failing to develop true leaves on sucrose-free solid medium. However, the reason for this seedling arrest is unclear. In this study, we show that seedling arrest is a temporal growth arrest response that occurs not only in kam2 but also in wild-type Arabidopsis; however, the threshold for this response is lower in kam2 than in the wild type. A subset of the arrested kam2 seedlings resumed growth after transfer to fresh sucrose-free medium. Growth arrest in kam2 on sucrose-free medium was restored by increasing the gel concentration of the medium or covering the surface of the medium with a perforated plastic sheet. Wild-type Arabidopsis seedlings were also arrested when the gel concentration of sucrose-free medium was reduced. RNA sequencing revealed that transcriptomic changes associated with the rate of seedling establishment were observed as early as 4 days after sowing. Our results suggest that the growth arrest of both kam2 and wild-type seedlings is an adaptive stress response and is not simply caused by the lack of a carbon source in the medium. This study provides a new perspective on an environmental stress response under unfavorable conditions during the phase transition from heterotrophic to autotrophic growth in Arabidopsis.

plant biology↗

bioRxiv2023

Propagation path of a flowering cherry (Cerasus x yedoensis) cultivar 'Somei-Yoshino' traced by somatic mutations

Flowering cherry cultivar Somei-Yoshino (Cerasus x yedoensis) has been clonally propagated and spread all around the world including Japan. Somei-Yoshino is thought to be an interspecific hybrid derived from C. spachiana and C. speciosa; however, its origin is unclear. Since somatic mutations are randomly induced in genomes and stably transmitted through generations, we aimed to identify somatic mutations in the genome of Somei-Yoshino to trace its propagation path. A total of 46 Somei-Yoshino clones were collected from all over Japan and subjected to whole-genome sequencing. The results revealed 684 single nucleotide variants, of which 71 were found in more than two clones. Clustering analysis of the 46 clones using these 71 variants revealed six groups, four of which contained 40 of the 46 clones. In addition, because each of the four clones closely planted in Ueno Park, Tokyo, Japan, clustered into the four different groups, we considered that these four clones could be the ancestors of the Somei-Yoshino clones found in Japan. Furthermore, based on the comparison of mutant alleles with the genomes of Cerasus species, one of the four trees was concluded as the closest to the origin. Here, we propose that the origin of Somei-Yoshino is a chimera derived from at least four somatic mutants.

plant biology↗

bioRxiv2023

Haploid-resolved and chromosome-scale genome assembly in Citrus unshiu and its parental species, C. nobilis and C. kinokuni

Citrus, a member of the Rutaceae family, is a widely cultivated crop with numerous cultivars. In Japan, citrus fruits account for a significant portion of agricultural production. Although several new citrus varieties have been developed through conventional breeding programs, satsuma mandarin remains the dominant cultivar. In this study, chromosome-scale and haploid-resolved reference genome sequences of satsuma mandarin (Citrus unshiu Marc) and its parental varaieties, kishu mandarin (C. kinokuni hort. ex Tanaka) and kunenbo mandarin (C. nobilis Lour. var. kunip Tanaka) were generated using long-read sequencing and Hi-C technologies. The comparison of haploid and unphased genomes revealed structural differences between them, indicating distinct regions in each haploid. In addition, genetic linkage maps were constructed, and genetic and physical distances were compared. The results showed variations in polymorphism density across different regions of the chromosomes. Together, the obtained results provide valuable insights into the genomic characteristics and structural variations of satsuma mandarin and related citrus varieties. These insights will lead to the further elucidation and improvement of citrus cultivars through genome breeding strategies.

genomics↗

bioRxiv2023

Comprehensive analysis of nasal IgA antibodies induced by intranasal administration of the SARS-CoV-2 spike protein

Intranasal vaccination is an attractive strategy for preventing COVID-19 disease as it stimulates the production of multimeric secretory immunoglobulin A (IgA), the predominant antibody isotype in the mucosal immune system, at the target site of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry. Currently, intranasal vaccine efficacy is evaluated based on the measurement of polyclonal antibody titers in nasal lavage fluid. However, how individual multimeric secretory IgA protects the mucosa from SARS-CoV-2 infection remains to be elucidated. To understand the precise contribution and molecular nature of multimeric secretory IgA induced by intranasal vaccines, we developed 99 monoclonal IgA clones from nasal mucosa and 114 monoclonal IgA or IgG clones from nonmucosal tissues of mice that were intranasally immunized with the SARS-CoV-2 spike protein. The nonmucosal IgA clones exhibited shared origins and common and unique somatic mutations with the related nasal IgA clones, indicating that the antigen-specific plasma cells in the nonmucosal tissues originated from B cells stimulated at the nasal mucosa. Comparing the spike protein binding reactivity, angiotensin-converting enzyme-2-blocking and in vitro SARS-CoV-2 virus neutralization of monomeric and multimeric secretory IgA pairs recognizing different epitopes showed that even non-neutralizing monomeric IgAs, which represents 70% of the nasal IgA repertoire, can protect against SARS-CoV-2 infection when expressed as multimeric secretory IgAs. We also demonstrated that the intranasal administration of multimeric secretory IgA delivered as prophylaxis in the hamster model reduced infection-induced weight loss. Our investigation is the first to demonstrate the function of nasal IgA at the monoclonal level, showing that nasal immunization can provide effective immunity against SARS-CoV-2 by inducing multimeric secretory IgAs at the target site of the virus infection.

immunology↗

bioRxiv2023

Neutralizing antibody levels and epidemiological information of patients with breakthrough COVID-19 infection in Toyama, Japan

Breakthrough infection (BI) after coronavirus disease 2019 (COVID-19) vaccination has exploded owing to the emergence of various SARS-CoV-2 variants and has become a major problem at present. In this study, we analyzed the epidemiological information and possession status of neutralizing antibodies in patients with BI using SARS-CoV-2 pseudotyped viruses (SARS-CoV-2pv). Analysis of 44 specimens diagnosed with COVID-19 after two or more vaccinations showed high inhibition of infection by 90% or more against the Wuhan strain and the Alpha and Delta variants of pseudotyped viruses in 40 specimens. In contrast, almost no neutralizing activity was observed against the Omicron BA.1 variant. Many cases without neutralizing activity or BI were immunosuppressed individuals. The results of this study show that BI occurs even when there are sufficient neutralizing antibodies in the blood due to exposure to close contacts at the time of infection. Thus, even after vaccination, sufficient precautions must be taken to prevent infection.

microbiology↗

bioRxiv2023

Evaluation of SARS-CoV-2 isolation in cell culture from nasal/nasopharyngeal swabs or saliva specimens of patients with COVID-19

It has been revealed that SARS-CoV-2 can be efficiently isolated from clinical specimens such as nasal/nasopharyngeal swabs or saliva in cultured cells. In this study, we examined the efficiency of viral isolation including SARS-CoV-2 mutant strains between nasal/nasopharyngeal swab or saliva specimens. Furthermore, we also examined the comparison of viral isolation rates by sample species using simulated specimens for COVID- 19. As a result, it was found that the isolation efficiency of SARS-CoV-2 in the saliva specimens was significantly lower than that in the nasal/nasopharyngeal swab specimens. In order to determine which component of saliva is responsible for the lower isolation rate of saliva specimens, we tested the abilities of lactoferrin, amylase, cathelicidin, and mucin, which are considered to be abundant in saliva, to inhibit the infection of SARS-CoV-2 pseudotyped viruses (SARS-CoV-2pv). Lactoferrin and amylase were found to inhibit SARS-CoV-2pv infection. In conclusion, even if the same number of viral genome copies was detected by the real-time RT-PCR test, infection of SARS-CoV-2 present in saliva is thought to be inhibited by inhibitory factors such as lactoferrin and amylase, compared to nasal/nasopharyngeal swab specimens.

microbiology↗

bioRxiv2022

Deleterious mutations in a heterozygous chromosome result in recessive lethality in silkworm semiconsomic strains

In this study, we found two embryonic lethal mutations, t04 lethal (l-t04) and m04 lethal (l-m04), in semiconsomic strains T04 and M04, respectively. In these semiconsomic strains, the entire diploid genome, except for one chromosome 4 of the wild silkworm Bombyx mandarina, is substituted with chromosomes of the domesticated silkworm B. mori, and l-t04 and l-m04 mutations are located on B. mandarina-derived chromosome 4. The mutations responsible for the l-t04 and l-m04 were identified as the Bombyx homolog of imaginal discs arrested (Bmida) and TATA Box Binding Protein-associated factor 5 (BmTaf5), respectively. These findings indicate that both mutations were independently introduced during or after the development of semiconsomic strains. We conclude that the recessive embryonic lethality in the T04 and M04 strains is due to deleterious mutations produced in B. mandarina-derived chromosome 4. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/521575v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1c59ea3org.highwire.dtl.DTLVardef@131fbf0org.highwire.dtl.DTLVardef@93515borg.highwire.dtl.DTLVardef@1c23afe_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2022

Comprehensive Analysis of Peptide-Coding Genes Identifies an LRR-only Microprotein That Regulates Reproductive Organs in Marchantia polymorpha

1In the past two decades, many plant peptides have been found to play crucial roles in various biological events by mediating cell-to-cell communications. However, a large number of small open reading frames (sORFs) or short genes capable of encoding peptides remain uncharacterized. In this study, we examined several candidate genes for peptides conserved between two model plants: Arabidopsis thaliana and Marchantia polymorpha. We examined the expression pattern in M. polymorpha and subcellular localization using a transient assay with Nicotiana benthamiana. We found that one candidate, MpSGF10B, was expressed in meristems, gemma cups, and male reproductive organs called antheridiophores. MpSGF10B has an N-terminal signal peptide followed by two leucine-rich repeat (LRR) domains and was secreted to the extracellular region in N. benthamiana and M. polymorpha. Compared with the wild type, two independent knockout mutants had an increased number of antheridiophores, which emerged from meristems. It was revealed in gene ontology enrichment analysis that MpSGF10B was significantly co-expressed with genes related to cell cycle and development. These results suggest that MpSGF10B may regulate the reproductive development in M. polymorpha. Our research should shed light on the unknown role of LRR-only proteins in land plants.

plant biology↗

bioRxiv2022

Activation of SARS-CoV-2 by trypsin-like proteases in the clinical specimens of patients with COVID-19

SARS-CoV-2 enters host cells through the angiotensin converting enzyme 2 (ACE2) receptor and/or transmembrane protease, serine 2 (TMPRSS2). Serine proteases, such as TMPRSS2 and trypsin, promote viral entry. In this study, we investigated whether proteases increased SARS-CoV-2 infectivity using pseudotyped viruses and clinical specimens from patients with COVID-19. First, we investigated how trypsin increased infectivity using the pseudotyped virus. Our findings revealed that trypsin increased infectivity after the virus was adsorbed on the cells, but no increase in infectivity was observed when the virus was treated with trypsin. We examined the effect of trypsin on SARS-CoV-2 infection in clinical specimens and found that the infectivity of the SARS-CoV-2 delta variant increased 36,000-fold after trypsin treatment. By contrast, the infectivity of SARS-CoV-2 omicron variant increased to less than 20-fold in the clinical specimens. Finally, infectivity of clinical specimens containing culture supernatants of Fusobacterium necrophorum was increased from several- to 10-fold. Because SARS-CoV-2 infectivity increases in the oral cavity, which may contain anaerobic bacteria, keeping the oral cavities clean may help prevent SARS-CoV-2 infection. ImportanceIn this study, we examined whether trypsin-like proteases increased the infectivity of SARS-CoV-2. We found that trypsin-like proteases increased the infectivity of both the pseudotyped viruses and the live virus in the clinical specimens. The increase in infectivity was significantly higher for the delta than the omicron variant. A large amount of protease in the oral cavity during SARS-CoV-2 infection is expected to increase infectivity. Therefore, keeping the oral cavity clean is important for preventing infection.

microbiology↗

bioRxiv2022

A transcription factor module regulating stomatal formation is co-opted for the development of setae in the astomatous liverwort Marchantia polymorpha

The evolution of special types of cells requires the acquisition of new gene regulatory networks controlled by transcription factors (TFs). In stomatous plants, a TF module formed by subfamilies Ia and IIIb basic helix-loop-helix TFs (Ia-IIIb bHLH) regulates stomatal formation; however, how this module evolved during land plant diversification remains unclear. Here, we show that, in the astomatous liverwort Marchantia polymorpha, a Ia-IIIb bHLH module regulates the development of a unique sporophyte tissue, the seta, which is found in mosses and liverworts. The sole Ia bHLH gene, MpSETA, and a IIIb bHLH gene, MpICE2, regulate the cell division and/or differentiation of seta lineage cells. MpSETA can partially replace the stomatal function of Ia bHLH TFs in Arabidopsis thaliana, suggesting that a common regulatory mechanism underlies the setal and stomatal formation. Our findings reveal the co-option of a Ia-IIIb bHLH TF module for regulating cell fate determination and/or cell division of distinct types of cells during land plant evolution.

plant biology↗

bioRxiv2022

A rapid and universal liquid chromatograph-mass spectrometry-based platform, refmAb-Q nSMOL, for monitoring monoclonal antibody therapeutics

Accurate quantitation of antibody is critical for development of monoclonal antibody therapeutics (mAbs). Therapeutic drug monitoring has been applied to measure levels of mAbs in clinics for dose adjustment for autoimmune disease. Trough levels of mAbs can be a biomarker for cancer immunotherapy. Thus, the deployment of a rapid and universal platform for mAb monitoring may benefit processes ranging from drug development to clinical practice for a wide spectrum of diseases. However, mAb monitoring often requires development and conduct of an individual ligand binding assay such as ELISA, which is impractical to scale. We streamlined quantitation of antibody therapeutics by a nano-surface and molecular-orientation limited (nSMOL) proteolysis assay using LC-MS with a universal reference antibody (refmAb-Q), for accurate multiplexed quantitation of unique signature peptides derived from mAbs. This innovative refmAb-Q nSMOL platform may provide a practical solution for quantitating an ever-increasing number of mAbs from developmental to clinical use settings.

immunology↗