Biology subjects

Abe, N.

Publications and source records attributed to Abe, N..

9 recordsLinked to original sources

bioRxiv2026

N-terminal intrinsically disordered region mediates self-catalytic interfacial nucleation of Aspergillus oryzae hydrophobin RolA

Hydrophobins are biosurfactant proteins that coat the cell surfaces of filamentous fungi. On the conidial surface, hydrophobins self-assemble into rodlets, forming a dense hydrophobic film that promotes air-dispersibility. Although rodlet formation is closely associated with the physiology of filamentous fungi, its underlying molecular mechanisms remain largely unknown. Previously, we revealed that RolA, a hydrophobin derived from Aspergillus oryzae, forms rodlets at the air-water interface. In this study, we focused on the flexible N-terminal region of RolA, which lacks a well-defined tertiary structure, and hypothesized that this intrinsically disordered region regulates rodlet formation. To investigate its role, we used RolA mutants with reduced charges in the N-terminal region and analyzed the rodlet formation process on the surface of a water-in-air sessile droplet using atomic force microscopy. In addition, we quantitatively characterized rodlet formation at the air-water interface by applying a kinetic perspective to the interfacial tension change profiles obtained from dynamic surface tension measurements. The results suggested that RolA first forms a monolayer at the air-water interface, then rodlet formation proceeds through the continuous supply of free RolA monomers from the bulk phase to the interfacial RolA film. Our molecular dynamics simulations of RolA at the interface supported a model in which RolA molecules within the interfacial film interact with free monomers in the bulk phase through their N-terminal regions. These results reveal a previously unidentified role of the N-terminal region in rodlet formation and provide a more comprehensive framework for understanding the molecular mechanism underlying RolA rodlet formation.

biophysics↗

bioRxiv2026

Identity-state expression and switching in co-conscious dissociative identity disorder: a non-traumatic proof-of-concept fMRI study

Dissociative identity disorder (DID) remains debated because identity-state phenomena are privately experienced and may be attributed to suggestion, simulation or role enactment. Most neuroimaging studies rely on symptom provocation or traumatic recall, which complicates interpretation and is poorly suited to co-conscious presentations where simultaneous awareness should make state differences hardest to detect. We applied Identity-State Characterization and Analysis (ID-SCAN), a non-traumatic, identity-cued functional magnetic resonance imaging protocol, to a DSM-5-diagnosed woman with persistent co-consciousness between Adult and Adolescent identity-states. One task used identical insect images that evoked opposite preferences across identity-states; the other used trait judgments about self, the other identity-state and a shared intimate other. Analyses combined Bayesian single-case general linear modelling, generalized psychophysiological interaction connectivity and searchlight representational similarity analysis. Identity-instruction cue epochs were pooled across tasks to assess switch direction. The same insect stimuli engaged different valuation-related configurations across identity-states: Adolescent-selective effects centred on striato-thalamic regions, whereas Adult-selective effects extended to amygdala and orbitofrontal/medial prefrontal cortex, with distinct task-evoked coupling. Adult-as-self and Adolescent-as-self occupied separable positions within canonical self-referential regions. Cue-locked activity differed by switch direction across tasks, with larger reconfiguration when switching to Adult (mean between-cluster beta separation 4.30 versus 0.85; permutation p = 0.0001). Cross-task overlap localized a limited shared task-related substrate mainly to posterior visual and dorsal parietal cortex. Even under persistent co-consciousness and without trauma provocation, identity-state expression and switching showed convergent within-person neural signatures. The findings support non-traumatic mechanistic phenotyping of dissociative presentations and motivate cohort and longitudinal studies, including treatment-tracking work.

neuroscience↗

bioRxiv2026

How the brain represents a romantic partner: dissociable roles of the nucleus accumbens and anterior insula

Humans form selective and enduring pair bonds with romantic partners, a principal feature of human sociality. Neuroimaging studies have shown that romantic partners are differentially represented from other individuals in the nucleus accumbens (NAcc) and anterior insula (aINS), and that the specificity of partner representations in the NAcc diminishes as relationships mature. However, it remains unclear whether such differentiation reflects partner-specific coding or mere differences in familiarity with others, and whether these regions play different roles in romantic bonding. To address these questions, we applied multiple regression representational similarity analysis to fMRI data from 51 heterosexual male participants in early romantic relationships. The data were acquired during a social incentive delay task, in which participants anticipated social approval from their female romantic partner, a female friend, or an unfamiliar female individual. This approach allowed us to dissociate partner-specific representations from familiarity-related effects in the NAcc and aINS. We found that both regions exhibited partner-specific representations that could not be explained by familiarity. Consistent with previous findings, partner specificity in the NAcc was negatively associated with relationship duration, indicating that partner-specific coding in this region is established early in romantic relationships and diminishes as relationships progress. Moreover, greater partner specificity in the aINS was associated with more frequent intrusive thoughts about the partner. Together, these findings demonstrate that romantic partners are represented in the NAcc and aINS in a qualitatively distinct manner from other individuals, and that these regions support dissociable aspects of romantic bonding. Key PointsO_LIMultiple regression representational similarity analysis revealed partner-specific representations in the nucleus accumbens and anterior insula that cannot be explained by familiarity. C_LIO_LIIndividuals in longer relationships showed reduced partner specificity in the nucleus accumbens, consistent with prior findings. C_LIO_LIIndividuals exhibiting greater partner specificity in the anterior insula reported more frequent intrusive thoughts about their partner, indicating dissociable psychological functions across regions. C_LI

neuroscience↗

bioRxiv2024

Multi-objective computational optimization of human 5' UTR sequences

The computational design of mRNA sequences is a critical technology for both scientific research and industrial applications. Recent advances in prediction and optimization models have enabled the automatic scoring and optimization of 5' UTR sequences, key upstream elements of mRNA. However, fully automated design of 5' UTR sequences with more than two objective scores has not yet been explored. In this study, we present a computational pipeline that optimizes human 5' UTR sequences in a multi-objective framework, addressing up to four distinct and conflicting objectives. Our work represents an important advancement in the multi-objective computational design of mRNA sequences, paving the way for more sophisticated mRNA engineering.

bioinformatics↗

bioRxiv2023

Wistar rats raised in an affectionate environment display lifesaving-like behaviors while distinguishing life from death

It is generally believed that humans are the only species that values life. However, it is not well understood whether animals have a nature that values life. In this study, we attempted to determine whether male Wistar rats have this nature. Normally-reared rats did not show lifesaving-like actions towards anesthesia-induced comatose rats, although they seemed to distinguish life from death. Considering the possibility that different rearing conditions may foster a life-valuing nature, male Wistar rat pups were reared in several ways: normal rearing, loving rearing (LR; rats reared as if they were cute pets), rearing in an enriched environment, reared with gentle stroking of the back, and normal rearing of offspring of rats raised under LR conditions. When placed in an anxiety-producing environment, only LR rats escaped into the hands of the person who reared them, indicating attachment. Only the LR rats displayed lifesaving-like actions towards unknown comatose rats or drowning pups. LR rats also stopped attacks by biting ICR mice that were attacking C57BL/6 mice. Thus, rearing in an affectionate environment may foster a life-valuing nature, even in rats, suggesting that the valuing of life may be neither innate nor human-specific.

animal behavior and cognition↗

bioRxiv2022

Microbial mat compositions and localization patterns explain the virulence of black band disease in corals

Black band disease (BBD) in corals is characterized by a distinctive, band-like microbial mat, which spreads across the tissues and often kills infected colonies. The microbial mat is dominated by cyanobacteria but also commonly contains sulfide-oxidizing bacteria (SOB), sulfate-reducing bacteria (SRB), and other microbes. The migration rate in BBD varies across different environmental conditions including temperature, light, and pH. However, whether variations in the migration rates reflect differences in the microbial consortium within the BBD mat remains unknown. Here, we show that the micro-scale surface structure, bacterial composition, and spatial distribution differed across BBD lesions with different migration rates. The migration rate was positively correlated with the relative abundance of potential SOBs belonging to Arcobacteraceae localized in the middle layer within the mat and negatively correlated with the relative abundance of other potential SOBs belonging to Rhodobacteraceae. Our study highlights the microbial composition in BBD as an important determinant of virulence.

microbiology↗

bioRxiv2022

Enhanced Mirror Neuron Network Activity and Effective Connectivity during Live Interaction

Facial expressions are indispensable in daily human communication. Previous neuroimaging studies investigating facial expression processing have presented pre-recorded stimuli and lacked live face-to-face interaction. Our paradigm alternated between presentations of real-time model performance and pre-recorded videos of dynamic facial expressions to participants. Simultaneous functional magnetic resonance imaging (fMRI) and facial electromyography activity recordings, as well as post-scan valence and arousal ratings were acquired from 44 female participants. Live facial expressions enhanced the subjective valence and arousal ratings as well as facial muscular responses. Live performances showed greater engagement of the right posterior superior temporal sulcus (pSTS), right inferior frontal gyrus (IFG), right amygdala and right fusiform gyrus, and modulated the effective connectivity within the right mirror neuron system (IFG, pSTS, and right inferior parietal lobule). A support vector machine algorithm could classify multivoxel activation patterns in brain regions involved in dynamic facial expression processing in the mentalizing networks (anterior and posterior cingulate cortex). These results indicate that live social interaction modulates the activity and connectivity of the right mirror neuron system and enhances spontaneous mimicry, further facilitating emotional contagion. HighlightsO_LIWe alternately presented real-time and pre-recorded dynamic facial expressions. C_LIO_LILive facial expressions enhanced emotion contagion and spontaneous facial mimicry. C_LIO_LILive conditions modulated mirror neuron system activity and effective connectivity. C_LIO_LIThe mentalizing network showed distinctive multivoxel patterns in live conditions. C_LIO_LIThe results support the validity of second-person design in social neuroscience. C_LI

neuroscience↗

bioRxiv2020

Dense encoding of developmental regulatory information may constrain evolvability

Gene regulatory changes underlie much of phenotypic evolution. However, the evolutionary potential of regulatory evolution is unknown, because most evidence comes from either natural variation or limited experimental perturbations. Surveying an unbiased mutation library for a developmental enhancer in Drosophila melanogaster using an automated robotics pipeline, we found that most mutations alter gene expression. Our results suggest that regulatory information is distributed throughout most of a developmental enhancer and that parameters of gene expression--levels, location, and state--are convolved. The widespread pleiotropic effects of most mutations and the codependency of outputs may constrain the evolvability of developmental enhancers. Consistent with these observations, comparisons of diverse drosophilids reveal mainly stasis and apparent biases in the phenotypes influenced by this enhancer. Developmental enhancers may encode a much higher density of regulatory information than has been appreciated previously, which may impose constraints on regulatory evolution. Quote"Rock, robot rock Rock, robot rock Rock, robot rock" Daft Punk (2005)

evolutionary biology↗

bioRxiv2019

Context-dependent gene regulation by transcription factor complexes

Eukaryotic transcription factors (TFs) form complexes with various partner proteins to recognize their genomic target sites. Yet, how the DNA sequence determines which TF complex forms at any given site is poorly understood. Here we demonstrate that high-throughput in vitro binding assays coupled with unbiased computational analysis provides unprecedented insight into how complexes of homeodomain proteins adapt their stoichiometry and configuration to the bound DNA. Using inferred knowledge about minor groove width readout, we design targeted protein mutations that destabilize homeodomain binding in a complex-specific manner. By performing parallel SELEX-seq, ChIP-seq, RNA-seq and Hi-C assays, we not only reveal complex-specific functions, but also show that TF binding sites that lack a canonical sequence motif emerge as a consequence of direct interaction with functionally bound sites.

genomics↗