Biology subjects

Ogino, H.

Publications and source records attributed to Ogino, H..

14 recordsLinked to original sources

bioRxiv2026

Cold-induced hepatic metabolic change links gluconeogenesis, lipid remodeling, and redox regulation in Xenopus laevis

BackgroundEctothermic vertebrates exhibit substantial physiological plasticity in response to environmental temperature fluctuations. Among them, amphibians show particularly pronounced metabolic adjustments under cold conditions; however, the molecular mechanisms by which the liver adapts to low temperatures remain poorly understood. To address this gap, we investigated the hepatic transcriptional response to cold exposure in the African clawed frog (Xenopus laevis) using RNA sequencing (RNA-seq) and quantitative PCR. ResultsExposure to 5{degrees}C for five days in X. laevis resulted in pronounced hyperglycemia and extensive transcriptional reprogramming in the liver. RNA-seq analysis indicated that, relative to frogs maintained at 24{degrees}C, 2,392 genes were upregulated, whereas 2,031 genes were downregulated. Notably, genes associated with gluconeogenesis, such as foxo1, g6pc1, and pck1, exhibited significant upregulation, whereas genes related to glycolysis and glucose utilization, including gck, pfkm, and ldhb, were downregulated. Concurrently, cold exposure induced the expression of genes involved in fatty acid synthesis, desaturation, and cholesterol biosynthesis, such as srebf1, acaca, fasn, scd, fads2, srebf2, and hmgcr. Conversely, genes related to fatty acid {beta}-oxidation, including ppara, cpt1a, cpt1b, slc25a20, acadl, hadha, and hadhb, were significantly suppressed. In alignment with this pattern, multiple components of the mitochondrial electron transport chain and ATP synthesis machinery were also downregulated. Additionally, gene groups involved in antioxidant defenses, such as gpx4, gpx1, prdx2, prdx5, prdx6, and ferritin-related genes, were upregulated. Representative transcriptomic changes were validated using quantitative PCR analysis. ConclusionsExposure to cold temperatures induced coordinated metabolic reprogramming in the liver of X. laevis. This reprogramming was characterized by the activation of gluconeogenesis, suppression of glycolysis, fatty acid {beta}-oxidation, and oxidative phosphorylation, and induction of lipid and cholesterol biosynthetic pathways. These metabolic adjustments suggest that frogs acclimated to cold conditions adopt an energy-conserving metabolic strategy while sustaining glucose production and promoting lipid remodeling to adapt to low-temperature environments. These findings offer novel insights into the molecular mechanisms underlying cold adaptation in ectothermic vertebrates and underscore the pivotal role of the liver in managing transcriptional responses to cold stress.

physiology↗

bioRxiv2026

Divergent mechanics of inner ear morphogenesis are coupled to developmental tempo over vertebrate evolution

Vertebrate embryos vary in size and developmental tempo based on reproductive strategies; however, organs of ancient origin, such as the eye and inner ear, remain highly conserved in structure and function. How both diverse embryonic traits and conserved organ development occur remains unclear. Here, we identify divergent morphogenetic mechanics of inner ear development, particularly in vesicular primordium expansion, in 12 species representing the major vertebrate lineages. Differences in cell volume regulation determine tissue growth mechanics, which diversify the expansion process but yield a conserved morphological outcome. Heterochronic shifts in organogenesis allow this regulation to evolve in coordination with a prolonged developmental period. These findings suggest that alternative morphogenetic mechanics mitigate the effects of diversified embryonic traits, thereby ensuring consistent morphological outcomes for highly conserved organs.

evolutionary biology↗

bioRxiv2025

Comparative Genomic Analysis of Cyanobacteria as Amphibian Food Sources: Insights into High-Temperature Tolerance Potential

Hot-springs represent one of the most accessible yet extreme environments on the Earths surface. We isolated and characterized two novel cyanobacterial strains of the genus Leptolyngbya, L. sp. Akita and L. sp. Seranma from geothermal hot-springs in Japan. These strains showed distinct morphological features; L. sp. Akita exhibited linear filamentous structures and blue-green color when cultured under white light, whereas L. sp. Seranma exhibited loosely coiled structures and a brown color under the same conditions. Whole-genome sequencing and comprehensive genomic analyses of their genomes identified the acquisition of gene clusters related to metabolic processes, which may be associated with strain-specific phenotypes. In addition, intestinal metagenomic analysis of tadpoles (Buergeria buergeri and B. japonica) sympatrically living with these strains in the hot-springs suggested that the tadpoles utilized these Leptolyngbya as temporal or regular foods in high-temperature environments. These findings provide insights into the ecological significance of these cyanobacteria in extreme environments and their potential applications in biotechnology and the ecological conservation of primary consumers, including amphibians.

microbiology↗

bioRxiv2024

Improvement of D-lactic acid production from methanol by metabolically engineered Komagataella phaffii via ultra-violet mutagenesis

Methanol has attracted attention as an alternative carbon source to petroleum. Komagataella phaffii, a methanol-assimilating yeast, is a useful host for the chemical production from methanol. A previous study successfully constructed a metabolically engineered K. phaffii GS115/S8/Z3 strain capable of producing D-lactic acid from methanol. In this study, we aimed to develop a strain with improved D-lactic acid production by applying ultra-violet mutagenesis to the D-lactic acid-producing strain, GS115/S8/Z3. The resulting mutant strain DLac_Mut2_221 produced 5.38 g/L of D-lactic acid from methanol, a 1.52-fold increase compared to the parent strain GS115/S8/Z3. Transcriptome analysis revealed 167 differentially expressed genes in DLac_Mut2_221, comprising 104 upregulated and 63 downregulated genes. These results suggest that the improvement in D-lactic acid production from methanol in the mutant strain involves three important mechanisms: (1) avoiding excessive formaldehyde accumulation, (2) activating the glyoxylate pathway, and (3) reducing the expression of O-glycosylated proteins required for cell wall stability. Metabolic engineering strategies for K. phaffii based on the knowledge gained from this study will contribute to improving the productivity of various useful chemicals from methanol.

bioengineering↗

bioRxiv2024

Co-utilization of microalgae and heterotrophic microorganisms improves wastewater treatment efficiency

Wastewater treatment using co-culture systems of microalgae and heterotrophic microorganisms is expected to be useful under atmospheric dilute carbon dioxide conditions. In this study, we investigated the combination of microalgae and heterotrophic microorganisms to improve the efficiency of wastewater treatment. Furthermore, to elucidate the cause of the changes in wastewater treatment efficiency in the co-culture system, changes in gene expression were revealed through transcriptome analysis. Three types of microalgae and five heterotrophic microorganisms were used in combination for wastewater treatment. The combination of Chlamydomonas reinhardtii NIES-2238 and Saccharomyces cerevisiae SH-4 showed the highest wastewater treatment efficiency. Using this combination for artificial wastewater treatment, the removal rates of TOC (Total organic carbon), PO43-, and NH4+ reached 80%, 93%, and 63%, respectively, after 18 h of treatment. Transcriptome analysis revealed that the combined wastewater treatment altered the expression of 1371 and 692 genes in C. reinhardtii and S. cerevisiae, respectively. The genes upregulated in C. reinhardtii included those related to molecular and ion transport. Genes upregulated in S. cerevisiae included those related to cell protection from various types of damage and stress. To the best of our knowledge, this is the first study to show that a combination of green algae and yeast improves the efficiency of wastewater treatment. As both the green alga C. reinhardtii and the yeast S. cerevisiae are highly safe microorganisms, the establishment of their effective combination for wastewater treatment is highly significant.

bioengineering↗

bioRxiv2024

Compromised actin dynamics underlie the orofacial cleft in Baraitser-Winter Cerebrofrontofacial Syndrome with a variant in ACTB

Craniofacial anomalies encompassing the orofacial cleft are associated with >30% of systemic congenital malformations. Baraitser-Winter Cerebrofrontofacial syndrome (BWCFF) is a rare genetic disorder attributed to variants in the actin beta (ACTB) or actin gamma genes that are correlated with a range of craniofacial abnormalities, including cleft lip and/or palate. The underlying pathological mechanism of BWCFF remains elusive, and it is necessary to investigate the etiology of orofacial clefts in BWCFF. In this study, we identified a missense variant (c.1043C>T: p.S348L) in the ACTB gene from a patient with BWCFF and concomitant cleft lip and palate. Furthermore, we performed functional assessments of this variant using various disease models such as the MDCK cell line and Xenopus laevis. These models revealed a compromised capacity of mutated ACTB to localize at the epithelial junction, consequently affecting the behavior of epithelial cells. Additionally, we made the noteworthy discovery that mutated ACTB exhibited an impaired ability to bind PROFILIN1, a critical factor in actin polymerization. This defective ability may contribute to the molecular etiology of aberrant epithelial cell adhesion and migration, resulting in orofacial cleft formation in BWCFF. Author SummaryAdvances in clinical sequencing have rapidly elucidated the genetic basis of rare diseases affecting multiple organs. In this study, we investigate the role of a variant in the ACTB gene, which is fundamental to cell structure, in causing orofacial clefts in the Baraitser-Winter Cerebrofrontofacial Syndrome (BWCFF), known for its distinctive facial anomalies. Using epithelial cell lines and frog embryo models, we investigated the effects of the ACTB gene alteration on cellular functions. Our results indicate that this genetic change disrupts the normal adhesion and movement of epithelial cells, processes that are critical for facial development. This research underscores the importance of the ACTB gene in shaping the face and suggests new directions for future research, potentially informing the diagnosis and treatment of BWCFF and related conditions.

genetics↗

bioRxiv2024

Development of a metabolic engineering technology to simultaneously suppress the expression of multiple genes in yeast and application in carotenoid production

In yeast metabolic engineering, there is a need for technologies that simultaneously suppress and regulate the expression of multiple genes and improve the production of target chemicals. In this study, we aimed to develop a novel technology that simultaneously suppresses the expression of multiple genes by combining RNA interference with global metabolic engineering technology (GMES). Furthermore, using {beta}-carotene as the target chemical, we attempted to improve its production by using the technology. First, we developed a technology to suppress the expression of the target genes with various strengths using RNA interference. Using this technology, total carotenoid production was successfully improved by suppressing the expression of a single gene out of 10 candidate genes. Then, using this technology, RNA interference strain targeting 10 candidate genes for simultaneous suppression was constructed. The total carotenoid production of the constructed RNA interference strain was 1.7 times compared with the parental strain. In the constructed strain, the expression of eight out of the 10 candidate genes was suppressed. We developed a novel technology that can simultaneously suppress the expression of multiple genes at various intensities and succeeded in improving carotenoid production in yeast. Because this technology can suppress the expression of any gene, even essential genes, using only gene sequence information, it is considered a useful technology that can suppress the formation of by-products during the production of various target chemicals by yeast.

bioengineering↗

bioRxiv2023

Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens

T-cell-mediated immunotherapies are limited by the extent to which cancer-specific antigens are homogenously expressed throughout a tumor. We reasoned that recurrent splicing aberrations in cancer represent a potential source of tumor-wide and public neoantigens, and to test this possibility, we developed a novel pipeline for identifying neojunctions expressed uniformly within a tumor across diverse cancer types. Our analyses revealed multiple neojunctions that recur across patients and either exhibited intratumor heterogeneity or, in some cases, were tumor-wide. We identified CD8+ T-cell clones specific for neoantigens derived from tumor-wide and conserved neojunctions in GNAS and RPL22, respectively. TCR-engineered CD8+ T-cells targeting these mutations conferred neoantigen-specific tumor cell eradication. Furthermore, we revealed that cancer-specific dysregulation in splicing factor expression leads to recurrent neojunction expression. Together, these data reveal that a subset of neojunctions are both intratumorally conserved and public, providing the molecular basis for novel T-cell-based immunotherapies that address intratumoral heterogeneity.

cancer biology↗

bioRxiv2023

Improvement of cell growth in green algae Chlamydomonas reinhardtii through co-cultivation with yeast Saccharomyces cerevisiae

Biological fixation methods have attracted considerable attention because they can be applied for the fixation of dilute CO2 in the atmosphere. Co-cultivation of certain microalgae with heterotrophic microorganisms can increase the growth potential of microalgae under dilute CO2 conditions. The objective of this study was to determine the culture conditions under which the growth potential of green algae Chlamydomonas reinhardtii is enhanced by co-culturing with the yeast Saccharomyces cerevisiae, and to identify the cause of the enhanced growth potential using transcriptome analysis. When C. reinhardtii and S. cerevisiae were co-cultured with an initial green algae to yeast inoculum ratio of 1:3, the cell concentration of C. reinhardtii reached 133 x 105 cells/mL on day 18 of culture, which was 1.5 times higher than that of the monoculture. Transcriptome analysis revealed that the expression levels of 363 green algae and 815 yeast genes were altered through co-cultivation. These include genes responsible for ammonium transport and CO2 enrichment mechanism in green algae and the genes responsible for glycolysis and stress responses in yeast. In conclusion, we identified the culture condition suitable for the co-cultivation of C. reinhardtii and S. cerevisiae. In addition, we discuss the cause of the increased growth potential of C. reinhardtii based on transcriptome analysis data. Although further studies are needed to elucidate the full impact of microbial interactions in C. reinhardtii and S. cerevisiae co-cultures, the findings of this study represent an important first step toward achieving this goal.

bioengineering↗

bioRxiv2023

Glioma-neuronal circuit remodeling induces regional immunosuppression

Neuronal activity-driven mechanisms impact glioblastoma cell proliferation and invasion1-7, and glioblastoma remodels neuronal circuits8,9. Distinct intratumoral regions maintain functional connectivity via a subpopulation of malignant cells that mediate tumor-intrinsic neuronal connectivity and synaptogenesis through their transcriptional programs8. However, the effects of tumor-intrinsic neuronal activity on other cells, such as immune cells, remain unknown. Here we show that regions within glioblastomas with elevated connectivity are characterized by regional immunosuppression. This was accompanied by different cell compositions and inflammatory status of tumor-associated macrophages (TAMs) in the tumor microenvironment. In preclinical intracerebral syngeneic glioblastoma models, CRISPR/Cas9 gene knockout of Thrombospondin-1 (TSP-1/Thbs1), a synaptogenic factor critical for glioma-induced neuronal circuit remodeling, in glioblastoma cells suppressed synaptogenesis and glutamatergic neuronal hyperexcitability, while simultaneously restoring antigen-presentation and pro-inflammatory responses. Moreover, TSP-1 knockout prolonged survival of immunocompetent mice harboring intracerebral syngeneic glioblastoma, but not of immunocompromised mice, and promoted infiltrations of pro-inflammatory TAMs and CD8+ T-cells in the tumor microenvironment. Notably, pharmacological inhibition of glutamatergic excitatory signals redirected tumor-associated macrophages toward a less immunosuppressive phenotype, resulting in prolonged survival. Altogether, our results demonstrate previously unrecognized immunosuppression mechanisms resulting from glioma-neuronal circuit remodeling and suggest future strategies targeting glioma-neuron-immune crosstalk may open up new avenues for immunotherapy.

cancer biology↗

bioRxiv2022

The shh limb enhancer is activated in patterned limb regeneration but not in hypomorphic limb regeneration in Xenopus laevis

Xenopus young tadpoles regenerate a limb with the anteroposterior (AP) pattern, but metamorphosed froglets regenerate a hypomorphic limb after amputation. The key gene for AP patterning, shh, is expressed in a regenerating limb of the tadpole but not in that of the froglet. Genomic DNA in the shh limb-specific enhancer, MFCS1 (ZRS), is hypermethylated in froglets but hypomethylated in tadpoles: shh expression may be controlled by epigenetic regulation of MFCS1. Is MFCS1 specifically activated for regenerating the AP-patterned limb? We generated transgenic Xenopus laevis lines that visualize the MFCS1 enhancer activity with a GFP reporter. The transgenic tadpoles showed GFP expression in hoxd13- and shh-expressing domains of developing and regenerating limbs, whereas the froglets showed no GFP expression in the regenerating limbs despite having hoxd13 expression. Genome sequence analysis and co-transfection assays using cultured cells revealed that Hoxd13 can activate Xenopus MFCS1. These results suggest that MFCS1 activation correlates with regeneration of AP-patterned limbs and that re-activation of epigenetically inactivated MFCS1 would be crucial to confer the ability to non-regenerative animals for regenerating a properly patterned limb.

developmental biology↗

bioRxiv2022

Rapid and collective determination of the complete "hot-spring frog" mitochondrial genome containing long repeat regions using Nanopore sequencing

The mitochondrial genome (mt-genome) is one of the promising molecular markers for phylogenetics and population genetics. Recently, various mt-genomes have been determined rapidly by using massively parallel sequencers. However, the control region (CR, also called D-loop) in mt-genomes remain difficult to precisely determine due to the presence of repeat regions. Here, using Nanopore sequencing, we succeeded in rapid and collective determination of complete mt-genome of the hot-spring frog, Buergeria japonica, and found that its mt-genome size was 22,274 bp including CR (6,929 bp) with two types of tandem repeat motifs forming repeat regions. Comparison of assemble strategies revealed that the long- and short-read data combined together enabled efficient determination of the CR, but the short-read data alone did not. The B. japonica CR was longer than that of a congenic species inhabiting cooler climate areas, Buergeria buergeri, because of the long repeat regions in the former. During the thermal adaptation of B. japonica, the longer repeat regions in its CR may have accumulated within a short period after divergence from B. buergeri.

genomics↗

bioRxiv2022

Retinoic acid control of pax8 during renal specification of Xenopus pronephros involves hox and meis3

Development of the Xenopus pronephros relies on renal precursors grouped at neurula stage into a specific region of dorso-lateral mesoderm called the kidney field. Formation of the kidney field at early neurula stage is dependent on retinoic (RA) signaling acting upstream of renal master transcriptional regulators such as pax8 or lhx1. Although lhx1 might be a direct target of RA-mediated transcriptional activation in the kidney field, how RA controls the emergence of the kidney field remains poorly understood. In order to better understand RA control of renal specification of the kidney field, we have performed a transcriptomic profiling of genes affected by RA disruption in lateral mesoderm explants isolated prior to the emergence of the kidney field and cultured at different time points until early neurula stage. Besides genes directly involved in pronephric development (pax8, lhx1, osr2, mecom), hox (hoxa1, a3, b3, b4, c5 and d1) and the hox co-factor meis3 appear as a prominent group of genes encoding transcription factors (TFs) downstream of RA. Supporting the idea of a role of meis3 in the kidney field, we have observed that meis3 depletion results in a severe inhibition of pax8 expression in the kidney field. Meis3 depletion only marginally affects expression of lhx1 and aldh1a2 suggesting that meis3 principally acts upstream of pax8. Further arguing for a role of meis3 and hox in the control of pax8, expression of a combination of meis3, hoxb4 and pbx1 in animal caps induces pax8 expression, but not that of lhx1. The same combination of TFs is also able to transactivate a previously identified pax8 enhancer, Pax8-CNS1. Mutagenesis of potential PBX-Hox binding motifs present in Pax8-CNS1 further allows to identify two of them that are necessary for transactivation. Finally, we have tested deletions of regulatory sequences in reporter assays with a previously characterized transgene encompassing 36.5 kb of the X. tropicalis pax8 gene that allows expression of a truncated pax8-GFP fusion protein recapitulating endogenous pax8 expression. This transgene includes three conserved pax8 enhancers, Pax8-CNS1, Pax8-CNS2 and Pax8-CNS3. Deletion of Pax8-CNS1 alone does not affect reporter expression, but deletion of a 3.5kb region encompassing Pax8-CNS1 and Pax8-CNS2 results in a severe inhibition of reporter expression both in the otic placode and kidney field domains.

developmental biology↗

bioRxiv2020

Physiological significance of proteolytic processing of Reelin revealed by cleavage-resistant Reelin knock-in mice

Reelin is a secreted protein that plays versatile roles in neuronal development and function, and hypoactivity of Reelin is implicated in many neuropsychiatric disorders. The strength of Reelin signaling is regulated by proteolytic processing, but its importance in vivo is not yet fully understood. Here, we generated Reelin knock-in (PA-DV KI) mice in which the key cleavage site of Reelin was abolished by mutation. As expected, the cleavage of Reelin was severely abrogated in the cerebral cortex and hippocampus of PA-DV KI mice. The amount of Dab1, whose degradation is induced by Reelin signaling, decreased in these tissues, indicating that the signaling strength of Reelin was augmented. The brains of PA-DV KI mice were largely structurally normal, but unexpectedly, the hippocampal layer was disturbed. This phenotype was ameliorated in hemizygote PA-DV KI mice, indicating that excess Reelin signaling is detrimental to hippocampal layer formation. The neuronal dendrites of PA-DV KI mice had more branches and were elongated compared to wild-type mice. These results present the first direct evidence of the physiological importance of Reelin cleavage and suggest that inhibition of Reelin cleavage would counteract neuropsychiatric disorders without causing severe systemic side effects.

neuroscience↗