Biology subjects

Kodama, Y.

Publications and source records attributed to Kodama, Y..

15 recordsLinked to original sources

bioRxiv2026

First molecular evidence that perialgal vacuole membrane maturation is temporally regulated during establishment of Chlorella variabilis photoendosymbiosis in Paramecium tritobursaria

Photoendosymbiosis between the ciliate Paramecium tritobursaria and the green alga Chlorella variabilis provides a model for understanding stable photoendosymbiosis. A defining feature of this association is the perialgal vacuole (PV) membrane, a host-derived membrane that encloses each alga and prevents its digestion. However, the timing of PV membrane maturation remains poorly understood because of the lack of molecular markers to distinguish between immature and mature PV membranes. Previous studies have shown that the establishment of symbiosis proceeds through multiple regulated steps following algal uptake; however, the molecular maturation of the PV membrane has not been directly examined. Here, we report a monoclonal antibody that specifically recognizes the PV membrane in symbiotic P. tritobursaria. Time-course immunofluorescence analysis showed that the PV membrane antigen was absent in the early stages after algal uptake, appeared at 48 h, and was detected in all PV membranes by 72 h. The antigen persisted before and after synchronous PV swelling, an experimentally inducible state associated with the loss of normal PV membrane function, but was absent from the membranes surrounding the digested algae. Our findings provide the first molecular evidence that PV membrane maturation is a temporally regulated checkpoint during the establishment of photoendosymbiosis.

cell biology↗

bioRxiv2026

Early detection of pancreatic ductal adenocarcinoma by single-molecule profiling of pancreatic enzyme activities

Pancreatic ductal adenocarcinoma (PDAC) remains a leading cause of cancer-related mortality, largely due to diagnosis at advanced stages. Early detection through minimally invasive liquid biopsy holds promise for improving patient outcomes. Here, we report a blood-based liquid biopsy platform based on single-molecule enzyme activity profiling (SEAP), which detects proteoform-level alterations in circulating pancreatic enzymes at single-molecule resolution. Using a tissue-centric biomarker discovery strategy, we identified activity signatures of pancreas-specific digestive enzymes associated with PDAC. A combinatorial classifier detected PDAC (stage I-IV) with 95.5% specificity and 75.0% sensitivity (74.2% for stage I-II) across 690 blood samples collected from multiple hospitals and biobanks. Performance was further validated in an independent cohort enriched for early-stage disease, where 54.2% (13/24) of stage IA, 64.3% (9/14) of stage IB, and 21.4% (3/14) of stage 0 lesions were classified as positive. These findings support the clinical potential of SEAP for early detection of PDAC.

biochemistry↗

bioRxiv2026

Inflammasome activation drives gasdermin-independent plasma membrane rupture by clustering ninjurin-1 in macrophages

Inflammasome assembly rapidly triggers caspase-1 activation to initiate pyroptosis, an inflammatory cell death characterized by the release of cytosolic contents, including interleukin (IL)-1{beta}/. Here, we report that inflammasome activation drives necrotic cell death independent of gasdermin D (GSDMD) and GSDME, which are essential executors of pyroptosis by forming a pore on the plasma membrane and increasing membrane permeability. NLRP3 inflammasome activation induced necrotic cell death, coupled with IL-1{beta}/ release in Gsdmd-/-Gsdme-/- macrophages. Mechanistically, the oligomerization of ninjurin-1 (NINJ1) was caused by inflammasome activation even in the absence of GSDMD and GSDME. Concordantly, glycine, an inhibitor of NINJ1, blocked plasma membrane permeabilization triggered by inflammasome activation in Gsdmd-/-Gsdme-/- macrophages, but not in WT macrophages. The dimerizer-mediated ASC oligomerization promoted NINJ1-mNeonGreen cluster formation in the absence of GSDMD and GSDME. Moreover, NINJ1 deficiency prevented membrane permeabilization initiated by ASC oligomerization in Gsdmd-/-Gsdme-/- immortalized bone marrow-derived macrophages (iBMDM). Blocking of phosphatidylserine (PtdSer) exposure, a feature of inflammasome-driven necrotic cell death, by Xkr8 deficiency inhibited plasma membrane permeabilization in Gsdmd-/-Gsdme-/- iBMDM. These results suggest that inflammasome-triggered activation of caspase-1 itself drives inflammatory necrotic cell death independent of gasdermins.

cell biology↗

bioRxiv2026

Two-step polar plastid migration via F-actin and microtubules ensures unequal inheritance during asymmetric division of Arabidopsis zygote

The zygote is the origin of development, and in most angiosperms, it divides asymmetrically to establish the apical-basal axis. In Arabidopsis thaliana, various organelles in the zygote undergo polar migration along actin filaments (F-actin), resulting in unequal inheritance, but the behavior of plastids, essential precursors of chloroplasts, has remained unclear. Here, using quantitative live-cell imaging, we reveal that plastids undergo two-step polar migration: they first move apically together with the nucleus along F-actin, and when nuclear migration slows, they switch to microtubule (MT)-dependent migration to move further apically. This results in unequal plastid inheritance by the apical cell. Although these plastids are amyloplasts containing starch granules, starch is dispensable for migration, unlike the gravity response. Instead, a fertilization-activated MAP kinase pathway is required for polar plastid migration. Our results demonstrate that the zygote possesses a spatiotemporal regulatory mechanism that ensures unequal plastid inheritance at the onset of plant ontogeny.

plant biology↗

bioRxiv2025

Wounding activates the HSFA1 transcription factors to promote cellular reprogramming in Arabidopsis

Mechanical injury is a primary trigger for cellular reprogramming during organ regeneration, yet the molecular mechanisms that link wounding to reprogramming remain poorly understood. In this study we identify the Arabidopsis HEAT SHOCK FACTOR A1 (HSFA1) class of transcription factors, being key regulators of the heat stress response, as central players in wound-induced callus formation and shoot regeneration. Loss of HSFA1 function in the hsfa1abd triple mutants severely impairs cellular reprogramming, reducing callus formation from wounded hypocotyls, as well as shoot regeneration from explants. Conversely, overexpression of the HSFA1d gain-of-function variant markedly enhances regeneration. Time-series RNA-seq and ChIP-seq analyses revealed that HSFA1s directly activate the key reprogramming regulators WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1), PLETHORA 3 (PLT3) and ZINC FINGER OF ARABIDOPSIS THALIANA 6 (ZAT6). Furthermore, we demonstrate that HSFA1d activity is attenuated by SIZ1-mediated SUMOylation, linking post-translational modification to the regulation of wound responses. Our findings establish HSFA1s as an early transcriptional hub that integrates wound signals with the activation of a broad gene network that drives cellular reprogramming, thereby providing a mechanistic framework for understanding how stress-responsive transcription factors control regeneration.

plant biology↗

bioRxiv2025

Cultivated Beef Meat Has the Potential to Maintain Original Characteristics of Beef Meat with Customizable Features

Cultivated meat (CM) is currently attracting much attention because of its promise to become a solution to issues of environmental sustainability, animal welfare, and decarbonization. While the fabrication process and materials are still the main focus, it is not yet clear what the characteristics of the constructed CMs are and how they take on the original characteristics of beef meat. In this study, the biological, physicochemical and sensory characteristics of three types of beef (Wagyu, Crossbreed and Holstein) meat were systematically analyzed and compared to muscle and fat fibers constructed by three-dimensional printing using satellite and adipose-derived stem cells isolated from these beef meats. The different characteristics of each beef meat were largely taken on by the CM fibers composed of bSC and bADSC of each meat. In addition, some differing properties from those of the respective beef meat were observed in CM fibers such as one of the omega-3 fatty acids, docosahexaenoic acid (DHA; Wagyu fat fibers showed the highest amount). Furthermore, we also found the important possibility to increase the composition of oleic acid to over 80% in monounsaturated fatty acid (Wagyu has around 50% oleic acid). This study revealed the importance of using cells isolated from each beef meat to provide CM that closely resemble the original texture and taste of each meat, and further the possibility of more carefully arranging their properties.

bioengineering↗

bioRxiv2025

Cell-based multisensor array for detecting cancer biomarkers in human urine

Detecting volatile urinary biomarkers offers a compelling strategy for noninvasive diagnosis of diseases such as cancer. Biohybrid sensors employing sensor cells that express olfactory receptors--with finely tuned molecular recognition capabilities--are garnering increasing attention. However, their application to physiological samples remains challenging due to variability in sensor cell responsiveness and limited signal intensity. Here, we report a volatile biomarker detection platform based on a multisensor array in which insect olfactory receptor- expressing cells are encapsulated in hydrogel and housed within microwells featuring vertical slits. This structural design enables dense three-dimensional cell immobilization and rapid, uniform exposure to target molecules, enhancing the sensitivity of fluorescence responses and minimizing signal variability. Multiple types of sensor cells on a single array enabled the selective and simultaneous detection of potential cancer-related target molecules--acetophenone, phenol, and 6-methyl-5-hepten-2-one. Furthermore, through hexane extraction combined with gas-phase delivery, we reliably detected acetophenone introduced into human urine at micromolar concentrations. This platform offers a compact, reproducible, and scalable solution for volatile biomarker detection using cell-based sensors.

bioengineering↗

bioRxiv2021

Ultra-small cells and DPANN genome unveiled inside an extinct vent chimney

Chemosynthetic organisms flourish around deep-sea hydrothermal vents where energy-rich fluids are emitted from metal sulfide chimneys. In contrast to actively venting chimneys, the nature of microbial life in extinct chimneys without fluid venting remains largely unknown. Here, the occurrence of ultra-small cells in silica-filled grain boundaries inside an extinct chimney is demonstrated by high-resolution bio-signature mapping. The ultra-small cells are associated with extracellularly precipitated Cu2O nanocrystals. Single-gene analysis shows that the chimney interior is dominated by a member of Pacearchaeota known as a major phylum of DPANN. Genome-resolved metagenomic analysis reveals that the chimney Pacearchaeota member is equipped with a nearly full set of genes for fermentation-based energy generation from nucleic acids, in contrast to previously characterized Pacearchaeota members lacking many genes for nucleic acid fermentation. We infer that the ultra-small cells associated with silica and extracellular Cu2O nanocrystals in the grain boundaries are Pacearchaeota, on the basis of the experimentally demonstrated capability of silica to concentrate nucleic acids from seawater and the presence of Cu-exporting genes in a reconstructed Pacearchaeota genome. Given the existence of ~3-billion-year-old submarine hydrothermally deposited silica, proliferation of microbial life using silica-bound nucleic acids might be relevant to the primitive vent biosphere.

microbiology↗

bioRxiv2020

SNF1-related protein kinase 2 directly regulate group C Raf-like protein kinases in abscisic acid signaling

ABSTRUCTA phytohormone abscisic acid (ABA) has a major role in abiotic stress responses in plants, and subclass III SNF1-related protein kinase 2 (SnRK2) mediates ABA signaling. In this study, we identified Raf36, a group C Raf-like protein kinase in Arabidopsis, as an interacting protein with SnRK2. A series of reverse genetic and biochemical analyses revealed that Raf36 negatively regulates ABA responses and is directly phosphorylated by SnRK2s. In addition, we found that Raf22, another C-type Raf-like kinase, functions partially redundantly with Raf36 to regulate ABA responses. Comparative phosphoproteomic analysis using Arabidopsis wild-type and raf22raf36-1 plants identified proteins that are phosphorylated downstream of Raf36 and Raf22 in planta. Together, these results reveal a novel subsection of ABA-responsive phosphosignaling pathways branching from SnRK2.

plant 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

Nintedanib ameliorates experimental pulmonary arterial hypertension via inhibition of endothelial mesenchymal transition and smooth muscle cell proliferation

Neointimal lesion and medial wall thickness of pulmonary arteries (PAs) are common pathological findings in pulmonary arterial hypertension (PAH). Platelet-derived growth factor (PDGF) and fibroblast growth factor (FGF) signaling contribute to intimal and medial vascular remodeling in PAH. Nintedanib is a tyrosine kinase inhibitor whose targets include PDGF and FGF receptors. Although the beneficial effects of nintedanib were demonstrated for human idiopathic pulmonary fibrosis, its efficacy for PAH is still unclear. Thus, we hypothesized that nintedanib is a novel treatment for PAH to inhibit the progression of vascular remodeling in PAs. The inhibitory effects of nintedanib were evaluated both in endothelial mesenchymal transition (EndMT)-induced human pulmonary microvascular endothelial cells (HPMVECs) and human pulmonary arterial smooth muscle cells (HPASMCs) stimulated by growth factors. We also tested the effect of chronic nintedanib administration on a PAH rat model induced by Sugen5416 (a VEGF receptor inhibitor) combined with chronic hypoxia. Nintedanib was administered from weeks 3 to 5 after Sugen5416 injection, and pulmonary hemodynamics and PAs pathology were evaluated. Nintedanib attenuated the expression of mesenchymal markers in EndMT-induced HPMVECs and HPASMCs proliferation. Phosphorylation of PDGF and FGF receptors was augmented both in both intimal and medial lesions of PAs. Nintedanib blocked these phosphorylation, improved hemodynamics and reduced vascular remodeling involving neointimal lesions and medial wall thickening in PAs. Additionally, expressions Twist1, transcription factors associated with EndMT, in lung tissue was significantly reduced by nintedanib. These results suggest that nintedanib may be a novel treatment for PAH with anti-vascular remodeling effects.

physiology↗

bioRxiv2019

Chloroplast cold-avoidance response in Marchantia polymorpha occurs independently of changes in endogenous phototropin expression

When exposed to fluctuating light intensity, chloroplasts move towards weak light (accumulation response), and away from strong light (avoidance response). In addition, cold treatment (5{degrees}C) induces the avoidance response even under weak light conditions (cold-avoidance response). These three responses are mediated by the phototropin (phot), which is a blue-light photoreceptor and has also been found to act as a thermosensory protein that perceives temperature variation. Our previous report indicated that cold-induced changes in phot biochemical activity initiate the cold-avoidance response. In this study, we further explored the induction mechanism of the cold-avoidance response in the liverwort Marchantia polymorpha and examined the relationship between changes in the amount of phot and the induction of the cold-avoidance response. The switch between the accumulation and avoidance responses occurs at a so-called transitional light intensity. Our physiological experiments revealed that a cold-mediated decrease in the transitional light intensity leads to the induction of the cold-avoidance response. While artificial overexpression of phot decreased the transitional light intensity as much as cold treatment did, the amount of endogenous phot remained unchanged by cold treatment in wild-type M. polymorpha. Taken together, these findings show that the cold-avoidance response is initiated by a cold-mediated reduction of the transitional light intensity, independent of the amount of endogenous phot. This study provides a clue to understand the mechanism underlying the switch in direction of chloroplast relocation in response to light and temperature.

plant biology↗

bioRxiv2019

Prediction of prospective leaf morphology in lettuce based on intracellular chloroplast position

In the accumulation response, chloroplasts move toward weak blue light, staying at positions along the periclinal cell wall. By contrast, in the avoidance response, chloroplasts move away from strong blue light, escaping to positions along the anticlinal cell wall. The accumulation response maximizes light capture and the avoidance response reduces photodamage. The intracellular positioning of chloroplasts is important for optimizing photosynthesis and may have common signals with the regulators that determine leaf morphology, another factor that affects photosynthesis. Here, we propose that intracellular chloroplast position can be used to predict prospective leaf morphology in lettuce (Lactuca sativa). To test this, we induced the accumulation or avoidance response in lettuce cells through exposure to the appropriate strength of blue light and observed the growth of the plants. Our results indicated that leaf area increased in response to weak blue light inducing the accumulation response, and leaf thickness increased in response to strong blue light inducing the avoidance response.

plant biology↗

bioRxiv2018

Pirfenidone attenuates lung fibrotic fibroblast-mediated fibrotic responses to transforming growth factor-β1

Pirfenidone, an antifibrotic agent used for treatment of idiopathic pulmonary fibrosis (IPF), functions by inhibiting myofibroblast differentiation, which is involved in transforming growth factor (TGF)-{beta}1-induced IPF pathogenesis. However, unlike normal lung fibroblasts, the relationship between pirfenidone responses of TGF-{beta}1-induced human fibrotic lung fibroblasts and lung fibrosis is unknown. Here, we investigated the effect of pirfenidone on the functions of two new targets, collagen triple helix repeat containing protein 1 (CTHRC1) and four-and-a-half LIM domain protein 2 (FHL2), which included fibroblast activity, collagen gel contraction, and migration toward fibronectin. Compared to control lung fibroblasts, pirfenidone restored TGF-{beta}1-stimulated fibroblast-mediated collagen gel contraction, migration, and CTHRC1 release in lung fibrotic fibroblasts. Furthermore, pirfenidone attenuated TGF-{beta}1- and CTHRC1-induced fibroblast activity, bone morphogenic protein-4/Gremlin1 upregulation, and -smooth muscle actin, fibronectin, and FHL2 downregulation, similar to that observed post-CTHRC1 inhibition. In contrast, FHL2 inhibition suppressed migration and fibronectin expression but did not downregulate CTHRC1. Overall, pirfenidone suppressed fibrotic fibroblast-mediated fibrotic processes via inverse regulation of CTHRC1-induced lung fibroblast activity. Thus, CTHRC1 can be used for predicting pirfenidone response and developing new therapeutic target for lung fibrosis.\n\nSummary statementPirfenidone suppressed TGF-{beta}1-mediated fibrotic processes in fibrotic lung fibroblasts by attenuating CTHRC1 expression, suggesting that CTHRC1 may be a novel therapeutic target for treating patients with lung fibrosis.

cell biology↗

bioRxiv2018

Improved G-AgarTrap: A highly efficient transformation method for intact gemmalings of the liverwort Marchantia polymorpha

Liverworts are key species for studies of plant evolution, occupying a basal position among the land plants. Marchantia polymorpha has emerged as a highly studied model liverwort, and many relevant techniques, including genetic transformation, have been established for this species. Agrobacterium-mediated transformation is widely used in many plant species because of its low cost. Recently, we developed a simplified Agrobacterium-mediated method for transforming M. polymorpha, known as AgarTrap (agar-utilized transformation with pouring solutions). The AgarTrap procedure, which involves culturing the liverwort tissue in various solutions on a single solid medium, yields up to a hundred independent transformants. AgarTrap is a simple procedure, requiring minimal expertise, cost, and time.\n\nHere, we investigated four factors that influence AgarTrap transformation efficiency: (1) humidity, (2) surfactant in the transformation buffer, (3) Agrobacterium strain, and (4) light/dark condition. We adapted the AgarTrap protocol for transforming intact gemmalings, achieving an exceptionally high transformation efficiency of 97%. The improved AgarTrap method will enhance the molecular biological study of M. polymorpha. The present study also provides new possibilities for improving transformation techniques for a variety of plant species.

plant biology↗