Biology subjects

Okubo, R.

Publications and source records attributed to Okubo, R..

4 recordsLinked to original sources

bioRxiv2025

Mycn Reactivates the Cell Cycle in Adult Cardiomyocytes and Promotes Cardioprotection in Myocardial Infarction

BackgroundAdult mammalian cardiomyocytes are terminally differentiated and possess minimal capacity for cell cycle re-entry. However, recent studies have shown that a rare population of cycling cardiomyocytes may confer cardioprotective effects following myocardial infarction (MI). The Myc family--Myc, Mycl, and Mycn--plays central roles in regulating cell cycle progression and cellular plasticity. This raises the possibility that specific Myc isoforms could reactivate the cardiomyocyte cell cycle and promote cardioprotective responses in the ischemic heart. This study aimed to systematically evaluate the effects of Myc, Mycl, and Mycn on cardiomyocyte cell cycle activation and cardiac outcomes following MI. MethodsCardiomyocyte-specific overexpression of Myc, Mycl, or Mycn was achieved in adult mice via adeno-associated virus 9 vectors driven by the cardiac troponin T promoter. Cardiomyocyte cell cycle activity, structural remodeling, and functional outcomes were assessed using RNA sequencing, immunohistochemistry, and transthoracic echocardiography. Cardioprotective effects were evaluated in MI model mice. ResultsWhile all three Myc family members activated cell cycle-related gene expression to varying degrees, Mycn elicited the most robust response. Mycn overexpression significantly enhanced cardiomyocyte cell cycle re-entry, as demonstrated by increased 5-bromo-2-deoxyuridine incorporation and phosphorylation of histone H3. Mycn also induced hypertrophic growth, reflected by increased cardiomyocyte size and heart mass. Transcriptomic analyses revealed that Mycn uniquely upregulated genes associated with extracellular matrix remodeling and paracrine signaling, typically enriched in neonatal cardiomyocytes and previously linked to cardioprotection. Functionally, Mycn expression preserved cardiac contractility after MI, reduced infarct size, and increased capillary density in peri-infarct regions. ConclusionsThese findings identify Mycn as a functionally distinct member of the Myc family in the adult heart, capable of reactivating the cardiomyocyte cell cycle and promoting cardiac protection after ischemic injury. The cardioprotective effects appear to be mediated, in part, by the induction of a neonatal-like gene expression program supporting a stress-adaptive cardiac microenvironment.

molecular biology↗

bioRxiv2025

Mixing features of transcription factors and genes enables accurate prediction of gene regulation relationships for unknown transcription factors

Identifying regulatory relationships between transcription factors (TFs) and genes is essential to understand diverse biological phenomena related to gene expression. Recently, deep learning-based models to predict TFs that bind to genes from nucleotide sequences of the target genes have been developed, yet these models are trained to predict known TFs only. In this study we developed a deep learning model, GReNIMJA (Gene Regulatory Network Inference by Mixing and Jointing features of Amino acid and nucleotide sequences), to predict gene regulation even by unknown TFs. Our model is designed to mix the features of the TF amino acid sequences and nucleotide sequences of the target genes using a 2D LSTM architecture and to perform binary classification with the aim of determining the presence or absence of a regulatory relationship. The accuracy of our model in predicting regulatory relationships was 84.4% for known TFs (higher than those of conventional models) and 68.5% for unknown TFs; the latter is an unsolved task for conventional deep learning-based models. We expect our model to advance identification of unknown gene regulatory networks and contribute to the understanding of diverse biological phenomena.

systems biology↗

bioRxiv2023

Diatom pyrenoids are encased in a protein shell that enables efficient CO2 fixation

Pyrenoids are subcompartments of algal chloroplasts that concentrate Rubisco enzymes and their CO2 substrate, thereby increasing the efficiency of carbon fixation. Diatoms perform up to 20% of global CO2 fixation, but their pyrenoids remain poorly characterized at a molecular level. Here, we used in vivo photo-crosslinking to catalogue components of diatom pyrenoids and identified a pyrenoid shell (PyShell) protein, which we localized to the pyrenoid periphery of both the pennate diatom, Pheaodactylum tricornutum, and the centric diatom, Thalassiosira pseudonana. In situ cryo-electron tomography (cryo-ET) revealed that the pyrenoids of both diatom species are encased in a lattice-like protein sheath. Disruption of PyShell expression in T. pseudonana resulted in the absence of this protein sheath, altered pyrenoid morphology, and a high-CO2 requiring phenotype, with impaired growth and reduced carbon fixation efficiency under standard atmospheric conditions. Pyrenoids in mutant cells were fragmented and lacked the thylakoid membranes that normally traverse the Rubisco matrix, demonstrating how the PyShell plays a guiding role in establishing pyrenoid architecture. Recombinant PyShell proteins self-assembled into helical tubes, enabling us to determine a 3.0 [A]-resolution PyShell structure. We then fit this in vitro structure into an in situ subtomogram average of the pyrenoids protein sheath, yielding a putative atomic model of the PyShell within diatom cells. The structure and function of the diatom PyShell provides a new molecular view of how CO2 is assimilated in the ocean, a crucial biome that is on the front lines of climate change.

cell biology↗

bioRxiv2019

The olfactory basis of orchid pollination by mosquitoes

Mosquitoes are important vectors of disease and require sources of carbohydrates for reproduction and survival. Unlike host-related behaviors of mosquitoes, comparatively less is understood about the mechanisms involved in nectar-feeding decisions, or how this sensory information is processed in the mosquito brain. Here we show that Aedes spp. mosquitoes, including Aedes aegypti, are effective pollinators of the Platanthera obtusata orchid, and demonstrate this mutualism is mediated by the orchids scent and the balance of excitation and inhibition in the mosquitos antennal lobe (AL). The P. obtusata orchid emits an attractive, nonanal-rich scent, whereas related Platanthera species - not visited by mosquitoes - emit scents dominated by lilac aldehyde. Calcium imaging experiments in the mosquito AL revealed that nonanal and lilac aldehyde each respectively activate the LC2 and AM2 glomerulus, and remarkably, the AM2 glomerulus is also sensitive to DEET, a mosquito repellent. Lateral inhibition between these two glomeruli reflects the level of attraction to the orchid scents: whereas the enriched nonanal scent of P. obtusata activates the LC2 and suppresses AM2, the high level of lilac aldehyde in the other orchid scents inverts this pattern of glomerular activity, and behavioral attraction is lost. These results demonstrate the ecological importance of mosquitoes beyond operating as disease vectors and open the door towards understanding the neural basis of mosquito nectar-seeking behaviors.\n\nSignificance StatementNectar-feeding by mosquitoes is important for survival and reproduction, and hence disease transmission. However, we know little about the sensory mechanisms that mediate mosquito attraction to sources of nectar, like those of flowers, or how this information is processed in the mosquito brain. Using a unique mutualism between Aedes mosquitoes and Platanthera obtusata orchids, we reveal that this mutualism is mediated by the orchids scent. Furthermore, lateral inhibition in the mosquitos antennal (olfactory) lobe - via the neurotransmitter GABA - is critical for the representation of the scent. These results have implications toward understanding the olfactory basis of mosquito-nectar-seeking behaviors.

neuroscience↗