Biology subjects

Shimomura, K.

Publications and source records attributed to Shimomura, K..

13 recordsLinked to original sources

bioRxiv2025

Sex-specific doublesex regulation targeting the color-patterning gene h underlies the evolution of wing sexual dimorphism in the harlequin ladybug Harmonia axyridis

Organisms on Earth show various forms of sexual dimorphism, including ornaments, weapon traits, and pheromone glands, which has been acquired through sexual selection during evolution. Although the genetic basis of sexual trait has been investigated in diverse species, its evolutionary origin, evolutionary mode, and evolvability remain poorly understood. To address these issues, we investigated the strain-specific sexual dimorphism in elytral color patterns of the harlequin ladybug, Harmonia axyridis, a species with over 200 color morphs. The most basal Red-nSpots type color morph exhibits sexual dimorphism, whereas other derived color morphs have lost it. To investigate how this loss of sexual dimorphism is associated with the emergence of novel color morphs, we investigated the genetic basis of sexual dimorphism by focusing on the master sex differentiation gene, doublesex (dsx). We show that dsx regulates color pattern dimorphism by negatively modulating black spot size in males. This modulation is primarily mediated by the transcriptional regulation of the color patterning gene, h (Drosophila pannier ortholog). Intraspecific comparative ATAC-seq analysis of the pupal wings revealed that, at the h locus, not the absolute number of Dsx-binding motifs but the proportion of open chromatin regions containing Dsx-binding motifs relative to those lacking such motifs was reduced in strains that had lost sexual dimorphism and acquired novel color patterns, implying that sexual dimorphism evolves based on the balance between novel CREs and Dsx-binding motif density. The present study provides a fundamental molecular framework for understanding how a secondary sexual trait evolves within H. axyridis.

evolutionary biology↗

bioRxiv2025

CRISPR/Cas9-mediated genome editing reveals the involvement of a polyphenol oxidase in the shikonin-specific biosynthesis in Lithospermum erythrorhizon

Shikonin, a 1,4-naphthoquinone derivative produced by several Boraginaceae species, exhibits unique pharmacological properties and is used as a natural dye. The regulatory factors of shikonin production have been demonstrated using a cell culture system of Lithospermum erythrorhizon. Among these factors, copper is known to be the strongest enhancer of shikonin production. Although shikonin biosynthesis has been studied for over 40 years, the steps of naphthalene ring formation are still unknown, as is the reason for the effect of copper. In this study, we explored candidate genes associated with shikonin production using a PCR-select subtraction experiment. Polyphenol oxidase (PPO), a dicopper-dependent oxidoreductase, was highlighted because it showed synchronous expression with shikonin production. Transcriptome analysis of hairy roots and cultured cells of this plant revealed that, of the five PPO genes expressed in L. erythrorhizon, only PPO1 showed a strong correlation with shikonin production. Next, we generated genome-edited hairy roots of LePPO1 using CRISPR/Cas9-mediated mutagenesis to analyze its impact on shikonin derivative and other specialized metabolite production. The results showed that shikonin content was markedly reduced in all LePPO1-ge lines. Interestingly, the content of deoxyshikonofuran, a hydroquinone derivative and shunt product that branches after GHQ-3''-OH in the shikonin biosynthetic pathway, remained unaffected in the LePPO1-ge lines. These findings suggest that LePPO1 participates in naphthalene ring formation and explain why a copper ion is crucial for shikonin biosynthesis.

biochemistry↗

bioRxiv2024

β-adrenergic blockers increase cAMP and stimulate insulin secretion through a PKA/RYR2/TRPM5 pathway in pancreatic β-cells in vitro

{beta}-adrenergic blockers ({beta}-blockers) are extensively used to inhibit {beta}-adrenoceptor activation and subsequent cAMP production in many cell types. In this study, we characterized the effects of {beta}-blockers on mouse pancreatic {beta}-cells. Unexpectedly, high doses (100 M) of {beta}- blockers (propranolol and bisoprolol) led to a 5-10 fold increase in cAMP levels, enhanced intracellular influx, and stimulated a 2-4 fold increase in glucose-and glimepiride-induced insulin secretion in MIN6-K8 clonal {beta}-cells and isolated mouse pancreatic islets. These effects were observed despite minimal expression of {beta}-adrenoceptors in these cells. Mechanistically, cAMP increase led to ryanodine receptor 2 (RYR2) phosphorylation via protein kinase A (PKA), triggering Ca2+-induced Ca2+ release (CICR). CICR then activates transient receptor potential cation channel subfamily M member 5 (TRPM5), resulting in increased Ca2+ influx via voltage-dependent Ca2+ channels. These effects contradict the conventional understanding of the pharmacology of {beta}-blockers, highlighting the variability in {beta}-blocker actions depending on the experimental context. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/618403v3_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@c9ef31org.highwire.dtl.DTLVardef@176a67aorg.highwire.dtl.DTLVardef@abc69aorg.highwire.dtl.DTLVardef@17ba9d4_HPS_FORMAT_FIGEXP M_FIG C_FIG At high concentrations (> 10 M), the {beta}-adrenergic blocker propranolol paradoxically increased intracellular cAMP levels in pancreatic {beta}-cells. This leads to PKA-induced RYR2 phosphorylation and extracellular Ca2+ influx, leading to CICR from the ER. CICR activated TRPM5, which augmented {beta}-cell electrical activity, extracellular Ca2+ influx, and insulin secretion.

cell biology↗

bioRxiv2024

Pyruvate kinase modulates the link between β-cell fructose metabolism and insulin secretion

2Glucose triggers insulin secretion from pancreatic {beta}-cells through intracellular glucose metabolism, ATP production, and closure of ATP-sensitive K+ channels (KATP channels). Fructose also stimulates insulin secretion, but the underlying mechanisms remain unclear. This study investigated the contribution of phospholipase C (PLC) signaling and fructose metabolism to fructose-stimulated insulin secretion (FSIS) using MIN6-K8 clonal {beta}-cells and mouse islets. Fructose-induced PLC activation, assessed by inositol 1-phosphate accumulation, was reduced in fructose-unresponsive {beta}-cell models, such as diabetic mouse islets and KATP channel-deficient {beta}-cells, suggesting that {beta}-cell fructose responsiveness is primarily determined by PLC signaling. Although FSIS was dependent on KATP channels and Ca2+ influx, the ATP/ADP ratio was unexpectedly lowered by fructose, and suppression of intracellular fructose metabolism hardly affected FSIS. Metabolic flux analysis revealed that the accumulation of fructose 1-phosphate (F1P) suppressed pyruvate kinase (PK) activity, contributing to ATP depletion. Strikingly, a small-molecule PK activator, TEPP-46, antagonized F1P-mediated PK suppression, prevented the drop in the ATP/ADP ratio, and restored FSIS in MIN6-K8 cells, normal mouse islets, and fructose-unresponsive diabetic mouse islets. These findings revealed the metabolic effects of fructose in {beta}-cells and identified PK as a key regulator linking {beta}-cell fructose metabolism and FSIS, thereby providing new insights into the mechanisms of insulin secretion and potential therapeutic targets for fructose-associated metabolic diseases. 1 GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/608033v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@11ce1e9org.highwire.dtl.DTLVardef@1339f22org.highwire.dtl.DTLVardef@1493a5org.highwire.dtl.DTLVardef@e97026_HPS_FORMAT_FIGEXP M_FIG C_FIG Left: Fructose-stimulated insulin secretion (FSIS) is driven by sweet taste receptor (STR)-mediated PLC signaling in pancreatic {beta}-cells. Meanwhile, fructose metabolism does not promote FSIS because fructose causes accumulation of fructose 1-phosphate (F1P), which suppresses pyruvate kinase M2 (PKM2), lowering the ATP/ADP ratio. Right: A small-molecule PK activator counteracted F1P-mediated PKM2 inhibition, prevented ATP decrease, and substantially enhanced FSIS in normal and diabetic mouse {beta}-cells. Thus, PK has been identified as a key regulator linking {beta}-cell fructose metabolism and FSIS.

cell biology↗

bioRxiv2024

Genetic characterization of cucumber genetic resources in the NARO Genebank indicates their multiple dispersal trajectories to the East

The cucumber (Cucumis sativus) is an economically important vegetable crop cultivated and consumed worldwide. Despite its popularity, the manner in which cucumbers were dispersed from their origin in South Asia to the rest of the world, particularly to the east, remains a mystery due to the lack of written records. In this study, we performed genotyping-by-sequencing (GBS) on 723 worldwide cucumber accessions, mainly deposited in the Japanese National Agriculture and Food Research Organization (NARO) Genebank, to characterize their genetic diversity, relationships, and population structure. Analyses based on over 60,000 genome-wide single-nucleotide polymorphisms identified by GBS revealed clear genetic differentiation between Southeast and East Asian populations, suggesting that they reached their respective region independently, not progressively. A deeper investigation of the East Asian population identified two subpopulations with different fruit characteristics, supporting the traditional classification of East Asian cucumbers into two types thought to have been introduced by independent routes. Finally, we developed a core collection of 100 accessions representing at least 93.2% of the genetic diversity present in the entire collection. The genetic relationships and population structure, their associations with geographic distribution and phenotypic traits, and the core collection presented in this study are valuable resources for elucidating the dispersal history and promoting the efficient use and management of genetic resources for research and breeding in cucumber. Key messageGenotyping-by-sequencing of 723 worldwide cucumber genetic resources revealed that cucumbers were dispersed eastward via at least three distinct routes, one to Southeast Asia and two from different directions to East Asia.

plant biology↗

bioRxiv2024

Chromosome-level assembly of Cucumis sativus cv. 'Tokiwa' as a reference genome of Japanese cucumber

Cucumber is one of the most important vegetables in the Japanese market. To facilitate genomics-based breeding, there is a demand for reference genome of Japanese cucumber. However, although cucumber genome is relatively small, its assembly is a challenging issue because of tandem repeats comprising [~]30% ([~]100 Mbp) of the genome. To overcome, we deployed the Oxford nanopore sequencing that produces long reads with N50 length of >30 kbp. With this technology we achieved a chromosome-level assembly of cv Tokiwa, a founder line of Japanese cucumber represented with the elongated fruit shape and high-crisp texture. Compared to the existing cucumber genomes, the Tokiwa genome is 20% longer and annotated with 10% more genes. The assembly with nanopore long reads also resolved tandem repeats spanning >100 kbp, demonstrating its strength in overcoming repetitive sequences.

genomics↗

bioRxiv2024

Sildenafil amplifies calcium influx and insulin secretion in pancreatic β cells

Sildenafil, a phosphodiesterase-5 (PDE5) inhibitor, has been shown to improve insulin sensitivity in animal models and prediabetic patients. However, its other metabolic effects remain poorly investigated. This study examines the impact of sildenafil on insulin secretion in MIN6-K8 mouse clonal {beta} cells. Sildenafil is shown to amplify insulin secretion by enhancing Ca2+ influx, an effect that requires other depolarizing stimuli in MIN6-K8 cells but not in KATP channel-deficient {beta} cells, which are already depolarized. These results indicate that the action of sildenafil is dependent on depolarization and is independent of KATP channels. Furthermore, sildenafil-amplified insulin secretion is not inhibited by nifedipine or PDE5 knockdown. Thus, sildenafil stimulates Ca2+ influx independently of L-type voltage-dependent Ca2+ channels (VDCCs) and PDE5, a mechanism that differs from the known pharmacology of sildenafil and conventional insulin secretory pathways. Our results reposition sildenafil as an insulinotropic agent that can be used as a potential anti-diabetic medicine or a tool to elucidate the molecular mechanism of insulin secretion.

cell biology↗

bioRxiv2023

Chemogenetic activation of target neurons expressing insect Ionotropic Receptors in the mammalian central nervous system by systemic administration of ligand precursors

The IR-mediated neuronal activation (IRNA) technology allows stimulation of neurons in the brain that heterologously-express members of the insect chemosensory IR repertoire in response to their cognate ligands. In the current protocol, a ligand against the complex consisting of IR84a and IR8a subunits, phenylacetic acid (PhAc), is locally injected into a brain region, because of a low efficiency of PhAc for the delivery into the brain across the blood-brain barrier. To circumvent this invasive injection, here we developed a strategy for activation of target neurons in the brain through peripheral administration with a precursor of PhAc, methyl ester of PhAc (PhAcM), which is efficiently transferred into the brain and converted to the mature ligand by endogenous esterase activities. Peripheral administration of with PhAcM activated IR84a/IR8a-expressing neurons in the locus coeruleus of mice and increased the release of neurotransmitters in their nerve terminal regions. (S)-2-phenylpropionic acid ((S)-PhPr) was newly identified as a ligand for IR84a/IR8a, and peripheral administration with the methyl ester of PhPr with the S-configuration [(S)-PhPrM] caused similar effects on the target neurons. In addition, cell-type specific expression of IR84a/IR8a complex in the striatum of rats was unilaterally induced with a viral vector based on the Cre-loxP system. Peripheral administration with PhAcM or (S)-PhPrM stimulated the neurotransmitter release in the ipsilateral terminal regions of the vector-injected striatum, and PhAcM administration resulted in rotational behavior. Finally, we demonstrated that the metabolites of the peripherally administered-radiolabeled (S)-PhPrM accumulated in the IR84a/IR8a-expressing region in the striatum of the vector-injected rats. These results demonstrate that the systemic IRNA technique provides a powerful strategy for remote manipulation of diverse types of target neurons in the mammalian central nervous system.

neuroscience↗

bioRxiv2023

Identification of major quantitative trait loci for parthenocarpic ability in East Asian melon

Natural (genetic) parthenocarpy contributes to fruit yield and quality under unfavorable environmental conditions where there are no effective pollinators or fertile pollen grains. Several old melon cultivars and weedy melon in East Asia are known to have strong parthenocarpic ability, but there has been little progress in intentionally introducing this ability into current F1 hybrid cultivars. Here, we examined its inheritance and confirmed the selection accuracy of DNA markers linked to it. We conducted QTL analysis using three F2 populations derived from crosses between a non-parthenocarpic cultivar and three parthenocarpic accessions, and detected two major QTLs on chromosomes 2 (par2.1) and 3 (par3.1). The parthenocarpic parent allele at both QTLs enhanced parthenocarpic ability. Phenotypic segregation was well explained by par2.1 and par3.1 in two F2 populations derived from Japanese weedy melon and an old Korean cultivar and by par3.1 in one from an old Japanese cultivar. This difference suggests that the effects of par2.1 and par 3.1 depend on genetic background. Both QTL regions contain several phytohormone-related genes, so we randomly selected SNPs in auxin- and ethylene-related genes to confirm the accuracy of selection for parthenocarpic ability. These SNP markers proved sufficient, though not perfect, to select plants with strong parthenocarpic ability. These results provide new insights into the molecular mechanisms of parthenocarpic ability in melon and will contribute to the development of new cultivars with high parthenocarpic ability. Key messageSeveral oriental melons have strong parthenocarpic ability controlled by one or two loci. DNA markers linked to these loci can select individuals with this ability.

plant biology↗

bioRxiv2022

Opponent Learning with Different Representations in the Cortico-Basal Ganglia Pathways Can Develop Obsession-Compulsion Cycle

Obsessive-compulsive disorder (OCD) has been suggested to be associated with impairment of model-based behavioral control. Meanwhile, recent work suggested shorter memory trace for negative than positive prediction errors (PEs) in OCD. We explored relations between these two suggestions through computational modeling. Based on the properties of cortico-basal ganglia pathways, we modeled human as an agent having a combination of successor representation (SR)-based system that enables model-based-like control and individual representation (IR)-based system that only hosts model-free control, with the two systems potentially learning from positive and negative PEs in different rates. We simulated the agents behavior in the environmental model used in the recent work that describes potential development of obsession-compulsion cycle. We found that the dual-system agent could develop enhanced obsession-compulsion cycle, similarly to the agent having memory trace imbalance in the recent work, if the SR- and IR-based systems learned mainly from positive and negative PEs, respectively. We then simulated the behavior of such an opponent SR+IR agent in the two-stage decision task, in comparison with the agent having only SR-based control. Fitting of the agents behavior by the model weighing model-based and model-free control developed in the original two-stage task study resulted in smaller weights of model-based control for the opponent SR+IR agent than for the SR-only agent. These results reconcile the previous suggestions about OCD, i.e., impaired model-based control and memory trace imbalance, raising a novel possibility that opponent learning in model(SR)-based and model-free controllers underlies obsession-compulsion. Our model cannot explain the behavior of OCD patients in punishment, rather than reward, contexts, but it could be resolved if opponent SR+IR learning operates also in the recently revealed non-canonical cortico-basal ganglia-dopamine circuit for threat/aversiveness, rather than reward, reinforcement learning, and the aversive SR + appetitive IR agent could actually develop obsession-compulsion if the environment is modeled differently. Author summaryObsessive-compulsive disorder (OCD) is one of the major psychiatric disorders diagnosed in 2.5%-3% of the population, and is characterized as an enhanced cycle of obsessive thought, e.g., whether the door was locked, and compulsive action, e.g., checking door lock. It remains elusive why such an apparently maladaptive behavior could be enhanced. A prevailing theory proposes that humans use two control systems, flexible yet costly goal-directed system and inflexible yet costless habitual system, and impairment of the goal-directed system leads to OCD. On the other hand, recent work proposed a new theory that shorter memory trace for credit-assignment of negative, than positive, prediction errors can induce OCD. Relation between these two theories remains unclear. We show that opponent learning of particular type of goal-directed(-like) system, suggested to be implemented in the brain, and habitual system from positive versus negative prediction errors could exhibit an (apparent) overall decrease in goal-directed control and also develop enhanced obsession-compulsion cycle similar to the one developed by memory-trace imbalance, thereby bridging the two theories. Such an opponent learning of the two systems was actually suggested to be advantageous in certain dynamic environments, and could thus be evolutionarily selected at the cost of possible development of OCD.

neuroscience↗

bioRxiv2021

Combination of successor representation-based appetitive learning and individual representation-based aversive learning is a good strategy and can be implemented in the cortico-basal ganglia circuits

The direct and indirect pathways of the basal ganglia (BG) have been suggested to learn mainly from positive and negative feedbacks, respectively. Since these pathways unevenly receive inputs from different cortical neuron types and/or regions, they may preferentially use different state/action representations. We explored whether such combined use of different representations coupled with appetitive or aversive learning has computational benefits. We simulated reward learning tasks in dynamic environments, and examined the performance of animal modeled as an agent equipped with two learning systems, each of which used individual representation (IR) or successor representation (SR) of states. With varying the combination of IR or SR and also the learning rates from positive and negative reward prediction errors (RPEs) in each system, we found that combination of an SR-based system learning mainly from positive RPEs and an IR-based system learning mainly from negative RPEs could achieve good performance, as compared to other combinations, in many situations. The architecture of such a combination provides a novel coherent explanation for the functional significance and underlying mechanism of diverse findings about the cortico-BG circuits. These results suggest that combining different representations with appetitive and aversive learning is an effective learning strategy adopted by the brain.

neuroscience↗

bioRxiv2021

Excretion of triacylglycerol as a matrix lipid facilitating apoplastic accumulation of a lipophilic metabolite shikonin.

Plants produce a large variety of lipophilic metabolites, many of which are secreted by cells and accumulated in apoplasts. The mechanism of secretion remains largely unknown, because hydrophobic metabolites, which may form oil droplets or crystals in cytosol, inducing cell death, cannot be directly secreted by transporters. Moreover, some secondary metabolic lipids react with cytosolic components leading to their decomposition. Lipophilic metabolites should thus be solubilized by matrix lipids and compartmentalized by membrane lipids. The mechanism of lipophilic metabolite secretion was assessed using shikonin, a red naphthoquinone lipid, in Lithospermum erythrorhizon. Cell secretion of shikonin also involved the secretion of about 30% of triacylglycerol (TAG), composed predominantly of saturated fatty acids. Shikonin production was associated with the induction of large amounts of the membrane lipid phosphatidylcholine. Together with in vitro reconstitution, these findings suggest a novel role for TAG as a matrix lipid for the secretion of lipophilic metabolites.

plant biology↗

bioRxiv2020

Difficulty in Cessation of Undesired Habits: Goal-Based Reduced Successor Representation and Reward Prediction Errors

Difficulty in cessation of drinking, smoking, or gambling has been widely recognized. Conventional theories proposed relative dominance of habitual over goal-directed control, but human studies have not convincingly supported them. Referring to the recently suggested "successor representation" of states that enables partially goal-directed control, we propose a dopamine-related mechanism potentially underlying the difficulty in resisting habitual reward-seeking, common to substance and non-substance reward. Consider that a person has long been taking a series of actions leading to a certain reward without resisting temptation. Given the suggestions of the successor representation and the dimension reduction in the brain, we assumed that the person has acquired a dimension-reduced successor representation of states based on the goal state under the established non-resistant policy. Then, we show that if the person changes the policy to resist temptation, a large positive reward prediction error (RPE) becomes generated upon eventually reaching the goal, and it sustains given that the acquired state representation is so rigid that it does not change. Inspired by the anatomically suggested spiral striatum-midbrain circuit and the theoretically proposed spiraling accumulation of RPE bias in addiction, we further simulated the influence of RPEs generated in the goal-based representation system on another system representing individual actions. We then found that such an influence could potentially enhance the propensity of non-resistant choice. These results suggest that the inaccurate value estimation in the reduced successor representation system and its influence through the spiral striatum-midbrain circuit might contribute to the difficulty in cessation of habitual reward-seeking.

neuroscience↗