Biology subjects

Iijima, Y.

Publications and source records attributed to Iijima, Y..

6 recordsLinked to original sources

bioRxiv2025

Oxylipin carbonyl compositions in the chloroplast compartments

Aldehydes and ketones derived from oxidized lipids (oxylipin carbonyls) accumulate in plants under stress conditions, acting as signaling molecules or cytotoxic agents through electrophilic modification of biomolecules. Because chloroplasts generate reactive oxygen species and contain lipids rich in unsaturated fatty acids, they are likely major sites of oxylipin carbonyl formation. To identify chloroplast-derived carbonyl species and their sub-organellar distribution, we analyzed carbonyls in spinach leaves, whole chloroplasts, thylakoids, envelopes and stroma. A total of 26 carbonyl species were detected, of which 13 were identified. Chloroplasts contained 14 species, including formaldehyde, propionaldehyde, acetaldehyde, acetone, butyraldehyde, (E)-2-pentenal, (Z)-3-hexenal, (E)-2-hexenal, n-hexanal and 4-hydroxy-(E)-2-hexenal. Phenylacetaldehyde and n-pentanal, which were abundant in leaves, were not associated with chloroplasts. Thylakoid membranes contained all chloroplast carbonyls except acetone, indicating that they are a major site of carbonyl formation. Formaldehyde was highly enriched in thylakoids and envelopes, providing evidence that it can be generated within chloroplasts, most likely from membrane lipids. Estimated concentrations of several carbonyls in membranes reached over 1 millimolar. This high-resolution mapping of oxylipin carbonyls within chloroplast compartments, achieved here for the first time, provides a spatial framework for understanding their formation and functional roles in plant stress responses.

plant biology↗

bioRxiv2024

Biochemical state in tissue can be detected through ultrasound signal

Three-dimensional (3D) cell cultures, such as spheroids, are indispensable models for investigating cellular behaviors and responses under conditions that closely resemble in vivo environments. Conventional imaging techniques, including optical microscopy, are often limited by penetration depth and phototoxicity, complicating the analysis of structural and biochemical changes within dense 3D systems. This study demonstrates the application of ultrasound imaging for the non-invasive evaluation of internal dynamics in cancer spheroids over a 15-day period. Scattering-based acoustic parameters revealed spatial variations in brightness and density, correlating with cellular proliferation, apoptosis, and necrosis. Brightness values in central regions progressively decreased after Day 3, approaching near-zero by Day 15, reflecting necrotic core formation. Artificial inhibition of myosin contractility significantly influenced these patterns, providing insights into biomechanical contributions to spheroid organization. The findings establish ultrasound imaging as a label-free, high-penetration technique capable of addressing critical challenges in 3D culture analysis, offering new opportunities for studying cellular dynamics and therapeutic responses in spheroids and organoid models.

bioengineering↗

bioRxiv2023

Activity-regulated micro-exon splicing programs underlie late-onset plasticity at the axon initial segment

The axon initial segment (AIS) is a specialized neuronal compartment located at the proximal end of axons and initiates action potentials. AIS undergoes plastic changes with aging, disease, and activity levels; however, the molecular mechanisms underlying their plasticity remain unclear. We discovered that depolarization induces diffuse elongation of the AIS in cerebellar granule cells over the span of days via the Ca2+-dependent ERK/MAP kinase pathway. These structural changes were accompanied by a decrease in voltage-gated Na+ channel density, resulting in a homeostatic attenuation in neuronal excitability. Notably, we found that the late-onset AIS plasticity is associated with depolarization-induced alternative splicing of smaller exons (<100 nt) of transcripts encoding AIS-enriched proteins. In addition, depolarization-induced the skipping of the 53-nt exon19 from the transcript of the splicing protein Rbfox1. CRISPR-mediated removal of exon 19 from Rbfox1 promoted its nuclear localization and sequentially induced a series of downstream micro-exon splicing changes in several AIS proteins, recapitulating cerebellar AIS plasticity. In a Rbfox1-independent mechanism, depolarization-induced insertion of the developmentally regulated micro-exon 34 into the key AIS scaffolding protein Ankyrin G (AnkG). The constitutive insertion of exon 34 into AnkG disrupted its interaction with the AIS cytoskeletal protein {beta}IV spectrin and induced plastic changes in the AIS. Our findings provide fundamental mechanistic insights into the activity-mediated late-onset plasticity of AIS, highlighting the power of micro-scale splicing events in the homeostatic regulation of axonal remodeling.

neuroscience↗

bioRxiv2023

SAM68-regulated ALE selection of Pcdh15 maintains proper synapse development and function

Thousands of mammalian genes encode alternatively spliced isoforms in their 3 untranslated region (3UTR). Alternative 3UTR diversity may contribute to several neurological processes in developing and adult brains. SAM68 is the key splicing regulator for the diversity of neuronal 3UTR isoforms through alternative last exon (ALE) selection. However, the mechanisms underlying the control of splicing at the 3 end and its function in the nervous system remain unclear. Here, we show that neuronal SAM68-dependent ALE splicing is regulated depending on its target transcripts. For example, the selection of the ALE of protocadherin-15 (Pcdh15), a gene implicated in Usher syndrome and several neuropsychiatric disorders, is largely dependent on the expression of SAM68, partially regulated via the CaMK pathway, but independent of the U1 small nuclear ribonucleoprotein. We found that the aberrant ALEs of Pcdh15 caused membrane-to-soluble isoform conversion of the produced protein and disrupted its localization into excitatory and inhibitory synapses. In addition, the neuronal expression of the soluble form of PCDH15 (sPCDH15) preferentially affected the number of inhibitory synapses. sPCDH15 further reduced neuroligin-2-induced inhibitory, but not excitatory, synapses in artificial synapse formation assays. Our findings provide insights into the role of alternative 3UTR isoform selections in synapse development.

neuroscience↗

bioRxiv2020

Diversification of the restriction modification system of Streptococcus pyogenes through its acquisition of mobile elements

Restriction-modification (RM) systems are typically regarded as "primitive immune systems" in bacteria. The roles of methylation in gene regulation, segregation, and mismatch repair are increasingly recognized. To analyze methyltransferase (MTase) diversity in Streptococcus pyogenes, we compared the RM system distribution in eight new complete genome sequences obtained here and in the database-deposited complete genome sequences of 51 strains. The MTase gene distribution showed that type I MTases often change DNA sequence specificity via switching target recognition domains between strains. The type II MTases in the included strains fell into two groups: a prophage-dominant one and a CRISPR-dominant one. Some highly variable type II MTases were found in the prophage region, suggesting that MTases acquired from phage DNA can generate methylome diversity. Additionally, to investigate the possible contribution of DNA methylation to phenotype, we compared the methylomes and transcriptomes from the four most closely related strains, the results of which suggest that phage-derived methylases possibly regulate the methylome, and, hence, regulate expression levels in S. pyogenes. Our findings will benefit further experimental work on the relationship between virulence genes and pathogenicity in S. pyogenes.

microbiology↗

bioRxiv2018

Development of the Brief Personal Values Inventory for sense of values in the Japanese general population

The Portrait Values Questionnaire (PVQ) is a widely used questionnaire for assessing sense of values; however, it has limitations, especially for children. Therefore, the present study aims to develop a questionnaire for sense of values, called the Brief Personal Values Inventory (BPVI), consisting of simple questions and a smaller number of items compared to the PVQ. We first created 12 items for the BPVI and then tested their validity and reliability in 167 Japanese general population (81 males, mean age (SD) [range]: 23.4 (8.2) [15-57] years). Each of these items was correlated with one or more values in the PVQ-57. The BPVI items covered all higher-order values in Schwartzs theory (Openness to Change, Self-Enhancement, Conservation, and Self-Transcendence). In sum, the BPVI has an acceptable criterion-related validity and corresponds to higher-order values in Schwartzs value theory. The BPVI is suitable for a reliable and direct comparison of sense of values between children and adults, which may be useful for elucidating the developmental pathway of personal sense of values.

scientific communication and education↗