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Furukawa, S.

Publications and source records attributed to Furukawa, S..

18 recordsLinked to original sources

Comparative analyses of tailbeat frequency and stride length reveal how regionally endothermic fishes cruise fast

Cruising speed is a key factor affecting prey-search efficiency and migration range in continuously swimming animals. Tunas and lamnid sharks (e.g., white sharks) have convergently evolved traits for high-speed cruising, including the ability to maintain slow-twitch, aerobic red muscle (RM) warmer than ambient water, known as RM endothermy. Despite their well-known high cruising speeds, kinematic features underlying their elevated speeds remain unclear. Swim speed is the product of tailbeat frequency (TBF; Hz) and stride length (SL, the absolute distance traveled per tailbeat; m). RM endothermy is expected to elevate TBF by enhancing muscle contraction performance. Furthermore, within RM-endothermic fishes, tunas and lamnid sharks may exhibit distinct kinematic features because of differences in caudal fin morphology and tailbeat amplitude. Here, we compiled kinematic parameters from 20 fish species, including five RM-endothermic species, measured in the wild using animal-borne sensors. Comparative analyses showed that, for a given body mass and water temperature, RM-endothermic fishes exhibited 1.9 times higher cruising speed and TBF than ectothermic fishes, while SL remained similar. Within RM-endothermic fishes, tunas exhibited 2.3 times higher TBF than similar-sized lamnid sharks, whereas lamnid sharks showed 1.7 times longer SL than similar-sized tunas. These results indicate that RM endothermy is generally associated with higher TBF, while significant kinematic differences remain between tunas and lamnid sharks. This divergence may be partly explained by the greater caudal fin area and tailbeat amplitude in lamnid sharks. It may also reflect contrasting skeletal types of teleosts and elasmobranchs, which potentially influence body stiffness and swimming kinematics.

animal behavior and cognition↗

Radiocesium Uptake in Two Fungal Bed-cultivated Edible Mushroom Species in Forests in Fukushima, Japan

In Japan, mushrooms have long been valued as food resources, but the Fukushima nuclear accident disrupted production and shipment due to radiocesium contamination. Limited knowledge has particularly hindered outdoor fungal bed cultivation. To address this, we conducted cultivation experiments with Lyophyllum decastes and Lepista nuda across 14 broad-leaved deciduous forest sites in Fukushima Prefecture. Air dose rates at 1 m height ranged from 0.04 to 0.89 {micro}Sv/h. Radiocesium concentrations (combined 137Cs and 134Cs, expressed as Bq/kg at 90% water content) in fruit bodies were 0.4-12 (mean 2.3) for Ly. decastes and 0.2-43 (mean 8.1) for Le. nuda. Both species remained below Japans food safety threshold of 100 Bq/kg, indicating that safe cultivation is feasible across broad areas. Uptake patterns differed: concentrations in Ly. decastes correlated with contamination in litter and multiple soil layers, whereas in Le. nuda it correlated only with litter contamination. These findings suggest that clean soil fills for Ly. decastes and clean litter covers for Le. nuda could serve as mitigation strategies tailored to each species. Aggregated transfer factors (2.76 x 10-5 m2/kg for Ly. decastes and 6.60 x 10-5 m2/kg for Le. nuda) were lower than those reported for wild mushrooms. Overall, this study provides new insights into reducing radiocesium assimilation by cultivated mushrooms and supports the revival of outdoor fungal bed cultivation in contaminated landscapes.

ecology↗

Siglec-7 and -15 recognize repeated clustered sulfo-sialo O-glycan motifs on select O-glycoproteins

Siglecs are key immunoreceptors in immune homeostasis and cancer immunosuppression. Diverse endogenous and exogenous sialoglycan ligands induce Siglec-mediated immunoregulation, but the nature of endogenous Siglec ligands and how seemingly ubiquitous sialoglycans achieve selectivity is unclear. Here, we employed a HEK293 cell-based array and glycoprotein reporters designed from human mucins and mucin-like proteins with O-glycans in natural clusters and repeat motifs to dissect specificities of Siglec-7 and -15. We first used precomplexed Siglec-Fc chimera to demonstrate that CHST1-mediated 6-O-sulfation markedly enhanced binding to select O-glycoproteins, namely MAdCAM1, CD43, and PSGL-1. Probing binding properties of Siglec-7 expressed exogenously on CHO cells or endogenously on human monocytes by reverse assays employing fluorophore-tagged O-glycoprotein reporters revealed specific binding to the sulfo-sialyl core1 O-glycoform of the same O-glycoproteins. Our study indicates that Siglec-7 on immune cells employs multivalent interactions with repeated motifs of clustered sulfo-sialyl O-glycans to drive selectivity in ligand interactions and Siglec-induced immunosuppression.

molecular biology↗

The integration mechanism of the four positional cues--anterior, posterior, dorsal, and ventral--in axolotl limb regeneration

Axolotls (Ambystoma mexicanum) exhibit a remarkable ability to regenerate limbs after amputation. Classical experiments have suggested that contact between cells derived from distinct orientations--dorsal, ventral, anterior, and posterior--within the regenerating blastema is necessary for accurate limb pattern formation. However, the molecular basis for this requirement has remained largely unknown. Here, we demonstrate that both dorsal and ventral tissues are required for limb formation via induction of Shh expression, which plays a crucial role in limb patterning. Using the accessory limb model (ALM), we induced position-specific blastemas lacking cells derived from a single orientation (anterior, posterior, dorsal, or ventral). Patterned limb formation occurred only in blastemas containing both dorsal- and ventral-derived cells. We further observed that Shh expression requires dorsoventral contact within a blastema, highlighting the necessity of dorsoventral contact for inducing Shh expression. In addition, we identified WNT10B and FGF2 as dorsal- and ventral-mediated signals, respectively, that create the inductive environment for Shh expression. Our findings clarify the role of dorsal and ventral cells in inducing Shh, a mechanism that has rarely been studied in the context of limb regeneration and pattern formation. This model provides new insights into how cells with different positional identities drive the regeneration process.

developmental biology↗

Microsaccade direction reveals the variation in auditory selective attention processes

Selective spatial attention plays a critical role in perception in the daily environment where multiple sensory stimuli exist. Even covertly directing attention to a specific location facilitates the brains information processing of stimuli at the attended location. Previous behavioral and neurophysiological studies have shown that microsaccades, tiny involuntary saccadic eye movements, reflect such a process in terms of visual space and can be a marker of spatial attention. However, it is unclear whether auditory spatial attention processes that are supposed to interact with visual attention processes influence microsaccades and vice versa. Here, we examine the relationship between microsaccade direction and auditory spatial attention during dichotic oddball sound detection tasks. The results showed that the microsaccade direction was generally biased contralateral to the ear to which the oddball sound was presented or that to which sustained auditory attention was directed. The post-oddball modulation of microsaccade direction was associated with the behavioral performance of the detection task. The results suggest that the inhibition of stimulus-directed microsaccade occurs to reduce erroneous orientation of ocular responses during selective detection tasks. We also found that the correlation between microsaccade direction and neural response to the tone originated from the auditory brainstem (frequency-following response: FFR). Overall, the present study suggests that microsaccades can be a marker of auditory spatial attention and that the auditory neural activity fluctuates over time with the states of attention and the oculomotor system, also involving the auditory subcortical processes. Significant statementMicrosaccades, tiny involuntary saccadic eye movements, reflect covert visual attention and influence neural activity in the visual pathway depending on the attention states. However, we lack convincing evidence of whether and how microsaccades reflect auditory spatial attention and/or neural activity along the auditory pathway. Intriguingly, we showed that the microsaccade direction exhibited systematic stimulus-related change and correlated with auditory brainstem frequency-following response (FFR) during the dichotic selective attention task. These results suggest that microsaccades are associated with general spatial attention processes, not restricted to the visual domain, and can be a good tool for accessing fluctuating neural activity that may covary with the attention states.

neuroscience↗

Single-cell analysis of human diversity in circulating immune cells

Lack of diversity and proportionate representation in genomics datasets and databases contributes to inequity in healthcare outcomes globally1,2. The relationships of human diversity with biological and biomedical phenotypes are pervasive3, yet remain understudied, particularly in a single-cell genomics context. Here we present the Asian Immune Diversity Atlas (AIDA), a multi-national single-cell RNA-sequencing (scRNA-seq) healthy reference atlas of human immune cells. AIDA comprises 1,265,624 circulating immune cells from 619 healthy donors and 6 controls, spanning 7 population groups across 5 countries. AIDA is one of the largest healthy blood datasets in terms of number of cells, and also the most diverse in terms of number of population groups. Though population groups are frequently compared at the continental level, we identified a pervasive impact of sub-continental diversity on cellular and molecular properties of immune cells. These included cell populations and genes implicated in disease risk and pathogenesis as well as those relevant for diagnostics. We detected single-cell signatures of human diversity not apparent at the level of cell types, as well as modulation of the effects of age and sex by self-reported ethnicity. We discovered functional genetic variants influencing cell type-specific gene expression, including context-dependent effects, which were under-represented in analyses of non-Asian population groups, and which helped contextualise disease-associated variants. We validated our findings using multiple independent datasets and cohorts. AIDA provides fundamental insights into the relationships of human diversity with immune cell phenotypes, enables analyses of multi-ancestry disease datasets, and facilitates the development of precision medicine efforts in Asia and beyond.

genomics↗

Astrocyte-specific inhibition of primary cilium functions improves cognitive impairment during neuroinflammation by suppressing A1 astrocyte differentiation.

A1 astrocytes play a neurotoxic role in various neurodegenerative diseases. While inhibiting the differentiation of A1 astrocytes can slow disease progression, the mechanisms controlling A1 astrocyte differentiation are largely unknown. The primary cilium is a cellular organelle that receives extracellular signals and regulates cell proliferation, differentiation, and maturation. To elucidate the physiological function of the primary cilium in A1 astrocytes, we utilized primary astrocytes and an inflammation mouse model. We found that the length of the primary cilium was increased in astrocytes, and the inhibition of primary cilium formation inhibited their differentiation into A1 astrocytes. Since mice with systemic ciliogenesis defects exhibit embryonic lethality, the function of the primary cilium in adults has remained largely unclear. Therefore, we established conditional knockout (cKO) mice that specifically inhibit primary cilium function in astrocytes upon drug stimulation. In a neuroinflammation mouse model in which lipopolysaccharide (LPS) was intraperitoneally injected into wild-type mice, increases in A1 astrocyte number and primary cilium length were observed in the brain. In contrast, cKO mice exhibited a reduction in the proportions of A1 astrocytes and apoptotic cells in the brain. Additionally, the novel object recognition (NOR) score observed in the cKO mice was higher than that observed in the neuroinflammation model mice. These results suggest that the primary cilium in astrocytes is essential for A1 astrocyte differentiation, which leads to a decline brain function. We propose that regulating astrocyte-specific primary cilium signalling may be a novel strategy for the suppression of neuroinflammation.

neuroscience↗

Reference genome sequences of Mythimna separata (Lepidoptera: Noctuidae)

Lepidopteran insects are an important group of animals, among which some are used as biochemical and physiological model species in the insect and silk industries, whereas others are major agricultural pests. Therefore, genome sequences of several lepidopteran insects have been reported thus far. The oriental armyworm, Mythimna separata, is an agricultural pest commonly used to study insect immune reactions and interactions with parasitoid wasps as hosts. To improve our understanding of these research topics, reference genome sequences were constructed in the present study. Using long-read and short-read sequence data, de novo assembly and polishing were performed, and haplotigs were purged. Subsequently, gene predictions and functional annotations were performed. To search for orthologs of the Toll and immune deficiency (IMD) pathways and C-type lectins, annotation data analysis, BLASTp, and Hummer scans were performed. The M. separata genome is 682 Mbp; its contig N50 was 2.7 Mbp with 21,970 genes and 24,452 coding sites predicted. All orthologs of the core components of the Toll and IMD pathways and 105 C-type lectins were identified. These results suggest that the genome data were of sufficient quality as reference genome data and could contribute to promoting M. separata and lepidopteran research at the molecular and genome levels. Simple SummaryThe oriental armyworm, Mythimna separata, an agricultural pest, is commonly used to study insect immune reactions and interactions with parasitoid wasps. To promote such studies, a reference genome was constructed. The M. separata genome is 682Mbp long--a size comparable to that of other lepidopteran insects. The contig N50 value of the genome is 2.7 Mb, which indicates sufficient quality to be used as reference genome data. Gene set data were constructed using genome and RNA-sequencing data; a total of 21,970 genes and 24,452 coding sites were predicted. Functional gene annotation was performed using the predicted amino acid sequences and reference gene set data of the model organism and other insect species as well as Unigene and Pfam datasets. Consequently, 45-80% of the amino acid sequences were annotated using these data sets. Using these data, most of the orthologs of core components in the Toll and immune deficiency (IMD) pathways were identified, suggesting the presence of these two pathways in M. separata. Additionally, 105 C-type lectins were identified in the M. separata genome, which were more numerous than those in other insect species, suggesting that these genes may be duplicated.

bioinformatics↗

Deodorize with Bugs: Inoculation with black soldier fly larvae alters the microbiome and volatile organic compound profile of decomposing food waste

The black soldier fly (BSF; Hermetia illucens) is used in sustainable processing of many types of organic waste. However, organic waste being decomposed by BSF produces strong odors, hindering more widespread application. The odor components and how they are produced have yet to be characterized. We found that digestion of food waste by BSF significantly alters the microbial flora, based on metagenomic analyses, and the odor components generated, as shown by thermal desorption gas chromatography mass spectrometry analysis. Inoculation with BSF significantly decreased production of volatile organic sulfur compounds (dimethyl disulfide and dimethyl trisulfide), which are known to be released during methionine and cysteine metabolism by Lactobacillus and Enterococcus bacteria. BSF inoculation significantly changed the abundance of Lactobacillus and Enterococcus and decreased microbial diversity overall. These findings may help in optimizing use of BSF for deodorization of composting food waste.

microbiology↗

Human-like Modulation SensitivityEmerging through Optimization to Natural Sound Recognition

Natural sounds contain rich patterns of amplitude modulation (AM), which is one of the essential sound dimensions for hearing perception. The sensitivity of human hearing to AM measured by psychophysics takes diverse forms, from low-pass to high-pass, depending on the experimental conditions. Here, we address with a single framework the questions of why such patterns of AM sensitivity have emerged in the human auditory system and how they are realized by our neural mechanisms. Assuming that optimization for natural sound recognition has taken place during human evolution and development, we examined its effect on the formation of AM sensitivity by optimizing a computational model, specifically, a multi-layer (or deep) neural network, for natural sound recognition and simulating psychophysical experiments in which the models AM sensitivity was measured. Relatively higher layers in the optimized model exhibited qualitatively and quantitatively similar AM sensitivity to that of humans, even though the model was not designed to reproduce human-like AM sensitivity. The similarity of the models AM sensitivity to humans correlated with its sound recognition accuracy. Optimization of the model to degraded sounds revealed the necessity of natural AM patterns for the emergence of human-like AM sensitivity. Consistent results were observed from optimizations to two different types of natural sound. Moreover, simulated neurophysiological experiments on the same model revealed a correspondence between the model layers and the auditory brain regions that is based on the similarity of their neural AM tunings. The layers in which human-like psychophysical AM sensitivity emerged exhibited substantial neurophysiological similarity with the auditory midbrain and higher regions. These results suggest that the behavioral AM sensitivity of human hearing has emerged as a result of optimization for natural-sound recognition in the course of our evolution and/or development and that it is based on a stimulus representation encoded in the neural firing rates in the auditory midbrain and higher regions.

neuroscience↗

An efficient early-pooling protocol for environmental DNA metabarcoding

Environmental DNA (eDNA) metabarcoding, a method that applies high-throughput sequencing and universal primer sets to eDNA analysis, has been a promising approach for efficient, comprehensive biodiversity monitoring. However, significant money-, labor-, and time-costs are still required for performing eDNA metabarcoding. In the present study, we assessed the performance of an "early-pooling" protocol (a protocol based on the 1st PCR indexing) to reduce the experimental costs of the library preparation for eDNA metabarcoding. Specifically, we performed three experiments to test the effects of 1st PCR and 2nd PCR indexing protocols on the community composition revealed by eDNA metabarcoding, of post-1st-PCR exonuclease purification on index-hopping, and of the number of PCR replicates and eDNA template volume on the number of detected OTUs. By analyzing 204 eDNA libraries from 3 natural aquatic ecosystems and 1 mock eDNA sample, we show that (i) the 1st PCR indexing does not cause clear biases in the outcomes of eDNA metabarcoding, (ii) post-1st-PCR exonuclease purification reduces the risk of index-hopping, and (iii) increasing the eDNA template volume can increase the number of detected OTUs and reduce the variations in detected community compositions, as can increasing the number of the 1st PCR replicates. Our results show that an early-pooling protocol with post-1st-PCR exonuclease purification and an increased amount of DNA template will reduce the risk of index-hopping, the costs for consumables and reagents, and the handling time in the library preparation, and that it produces comparable results to a 2nd-PCR-indexing protocol. Therefore, once a target metabarcoding region is determined and a set of indexed-1st-PCR primers is prepared, the early-pooling protocol provides a cost-, labor-, and time-efficient way to process a large number of samples.

ecology↗

Fluctuation of cellular differentiation in limb regeneration is regulated by Pde4b in urodele amphibians

Urodele amphibians, Pleurodeles waltl and Ambystoma mexicanum, have organ-level regeneration capability, such as limb regeneration. Multipotent cells are induced by an endogenous mechanism in amphibian limb regeneration. It is well known that dermal fibroblasts receive regenerative signals and turn into multipotent cells, called blastema cells. However, the induction mechanism of the blastema cells from matured dermal cells was unknown. We previously found that BMP2, FGF2, and FGF8 (B2FF) could play sufficient roles in blastema induction in urodele amphibians. Here, we show that B2FF treatment can induce dermis-derived cells that can participate in multiple cell lineage in limb regeneration. We first established a newt dermis-derived cell line and confirmed that B2FF treatment on the newt cells provided plasticity in cellular differentiation in limb regeneration. Interspecies comparative analysis clarified that Pde4b upregulation by B2FF specifically took place in the newt cells. Blocking PDE4B signaling by Rolipram suppressed dermis-to-cartilage transformation and the mosaic knockout animals showed consistent results. Our results are a valuable insight into how dermal fibroblasts acquire multipotency during the early phase of limb regeneration via an endogenous program in amphibian limb regeneration.

developmental biology↗

Novel multicellular prokaryote discovered next to an underground stream

The emergence of multicellularity is a key event in the evolution of life and is an attractive challenge among researchers, including those investigating the artificial design of cellular behavior1. Multicellular organisms are widely distributed on Earth, and retracing the specific conditions conducive for the initial transition from unicellularity to multicellularity is difficult. However, by examining organisms that inhabit unique (e.g., isolated) environmental niches, we may be able to get a glimpse into primitive multicellularity in the context of a given environment. Here we report the discovery of a new bacterium that displayed multicellular-like characteristics and behavior. The bacterium, which was isolated adjacent to an underground stream in a limestone cave, is to be named Jeongeupia sacculi sp. nov. HS-3. On a solid surface, HS-3 self-organizes its filamentous cells to form an appearance similar to the nematic phase of a liquid crystal2. Mature colonies produce and accommodate clusters of coccobacillus progeny, and release them upon contact with water. HS-3 demonstrated novel, spatiotemporally regulated multicellularity that can resolve the so-called competition-dispersal trade-off problem3. This study illustrates a hypothetical missing link on the emergence of multicellularity.

evolutionary biology↗

Impact of conscious awareness on pupillary response to faces

Pupillary response reflects not only ambient light changes but also top-down factors. Nevertheless, it remains inconclusive whether the conscious awareness modulates the pupillary response. We investigated pupillary responses to faces under different conscious conditions using continuous flash suppression (CFS). In Experiment 1 and 2, we used a breaking-CFS procedure in which participants had to detect the face from suppression. Results showed that the pupil constricted more to upright faces than to inverted faces before the face was detected, suggesting that pupillary responses reflect face processing entering consciousness. In Experiment 3 and 4, we used a fixed duration-CFS procedure with both objective performance and subjective reports. Different pupillary responses were observed only when the participant was aware of the face. These findings imply that the conscious awareness is critical for modulating autonomic neural circuits of the pupillary function. The corresponding pupillary responses may reflect dynamic processes underlying conscious awareness.

neuroscience↗

Aberrant claudin-6-adhesion signal promotes endometrial cancer progression via estrogen receptor α

Cell adhesion proteins not only maintain tissue integrity but also possess signaling abilities to organize diverse cellular events in physiological and pathological processes; however, the underlying mechanism remains obscure. Among cell adhesion molecules, the claudin (CLDN) family often possesses aberrant expression in various cancers, but the biological relevance and molecular basis have not yet been established. Here, we show that high CLDN6 expression promotes endometrial cancer progression and represents the poor prognostic marker. The second extracellular domain and Y196/200 of CLDN6 were required to recruit and activate Src-family kinases (SFKs) and to stimulate malignant phenotypes. Importantly, we demonstrate that the CLDN6/SFK/PI3K-dependent AKT and SGK (serum- and glucocorticoid-regulated kinase) signalings target Ser518 in the human estrogen receptor and ligand-independently activate target genes in endometrial cancer cells, resulting in cancer development. The identification of this machinery highlights regulation of the transcription factors by cell adhesion to advance tumor progression.

cancer biology↗

Rapid ocular responses are a robust marker for bottom-up driven auditory salience

Despite the prevalent use of alerting sounds in alarms and human-machine interface systems, we have only a rudimentary understanding of what determines auditory salience - the automatic attraction of attention by sound - and the brain mechanisms which underlie this process. A major roadblock to understanding has been the lack of a robust, objective means of quantifying sound-driven attentional capture. Here we demonstrate that microsaccade inhibition - an oculomotor response arising within 300ms of sound onset - is a robust marker for the salience of brief sounds. Specifically, we show that a crowd sourced (N=911) subjective salience ranking correlated robustly with the superior colliculus (SC) mediated ocular freezing response measured in naive, passively listening participants (replicated in two groups of N=15 each). More salient sounds evoked earlier microsaccadic inhibition, consistent with a faster orienting response. These results establish that microsaccade-indexed activity within the SC is a practical objective measure for auditory salience.\n\nSignificance statementMicrosaccades are small, rapid, fixational eye movements, measurable with sensitive eye-tracking equipment. We reveal a novel, robust link between microsaccade dynamics and the subjective salience of brief sounds (salience ranking obtained from a large number of participants in an online experiment): Within 300 ms of sound onset, the eyes of naive, passively listening participants demonstrate different microsaccade patterns as a function of the sounds perceptual salience. These results position the Superior Colliculus (the generator of microsaccades) as an important brain area to investigate in the context of a putative multi-modal salience-hub and establish a robust objective means for quantifying auditory salience, critical in the development of sound-based human machine interfaces.

neuroscience↗

Phasic norepinephrine is a neural interrupt signal for unexpected events in rapidly unfolding sensory sequences - evidence from pupillometry

The ability to track the statistics of our surroundings is a key computational challenge. A prominent theory (Dayan & Yu, 2006) proposes that the brain monitors for unexpected uncertainty - events which deviate substantially from model predictions, indicating model failure. Norepinephrine (NE) is thought to play a key role in this process by serving as an interrupt signal, initiating model-resetting. However, evidence is from paradigms where participants actively monitored stimulus statistics. To determine whether NE routinely reports the statistical structure of our surroundings, even when not behaviourally relevant, we used rapid tone-pip sequences that contained perceptually salient pattern-changes associated with abrupt structural violations vs. emergence of regular structure. Phasic pupil dilations (PDR) were monitored to assess NE. We reveal a remarkable specificity: When not behaviourally relevant, only abrupt structural violations evoked a PDR. The results demonstrate that NE tracks unexpected uncertainty on rapid time scales relevant to sensory signals.

neuroscience↗

Cascaded Processing of Amplitude Modulation for Natural Sound Recognition

Temporal variation of sound envelope, or amplitude modulation (AM), is essential for auditory perception of natural sounds. Neural representation of stimulus AM is successively transformed while processed by a cascade of brain regions in the auditory system. Here we sought the functional significance of such cascaded transformation of AM representation. We modelled the function of the auditory system with a deep neural network (DNN) optimized for natural sound recognition. Neurophysiological analysis of the DNN revealed that AM representation similar to the auditory system emerged during the optimization. The better-recognizing DNNs exhibited larger similarity to the auditory system. The control experiments suggest that the cascading architecture, the data structure, and the optimization objective may be essential factors for the lower, middle and higher regions, respectively. The results were consistently observed across independent datasets. These results suggest the emergence of AM representation in the auditory system during optimization for natural sound recognition.

neuroscience↗