Biology subjects

Takeda, K.

Publications and source records attributed to Takeda, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Effects of periodic group housing opportunities on reproductive performance and welfare in sows

ObjectiveStall housing of pregnant sows raises welfare concerns, whereas conventional group housing systems often reduce space efficiency. This study evaluated the effects of periodic group housing (PG) on reproductive performance and welfare compared with continuous stall housing (CS). MethodsSows in the CS group (n = 15) were continuously housed in stalls. In the PG group (n = 15), sows were housed in groups of three and allocated 1 day of group housing and 6 days of stall housing per week over 10 weeks. During group housing sessions, the sows had access to a group housing area containing sawdust. Behavioral observations and salivary cortisol measurements were conducted on the first day of the stall housing session in weeks 1, 6, and 10. Behavioral indices were expressed as proportions based on 90 sampling points recorded at 1-min intervals. ResultsThe number of stillbirths was significantly lower in the PG group than in the CS group (0.63 vs. 1.49 piglets per litter). whereas other reproductive outcomes, including total litter size and average birth weight, did not differ. In older parity sows, the PG treatment markedly increased the proportion of time spent lying, suggesting reduced discomfort associated with restricted movement. Furthermore, the proportion of exploratory behavior decreased markedly, and drinking behavior showed a decreasing trend across parity levels in the PG group, suggesting partial satisfaction of motivations for environmental exploration and oral manipulation. The proportion of oral abnormal behavior showed a pronounced interaction between housing treatment and experimental week, increasing from week 1 to week 6 in the PG group. Salivary cortisol concentrations did not differ between the groups. ConclusionPG may improve reproductive performance and partially satisfy the behavioral motivations restricted under continuous stall housing. This system may represent a practical alternative for improving animal welfare while minimizing economic losses.

animal behavior and cognition↗

bioRxiv2026

Structural basis for loss of covalent flavinylation in the H158Y mutant of pyranose oxidase

Pyranose oxidase from Phanerochaete chrysosporium (PcPOx) is a flavoprotein that forms a covalent 8-N3-histidyl-FAD linkage at His158. Here, we determined the crystal structure of the PcPOx H158Y variant at 1.69 [A] resolution and investigated its FAD occupancy and catalytic activity. Tyr158 adopts a rotamer conformation incompatible with covalent flavinylation, placing its phenolic O atom 8.7 [A] away from the FAD C8 atom. This conformation is stabilized through a Tyr158-Lys79 hydrogen bond. The additional mutation K79A abolishes this hydrogen bond, potentially freeing the Tyr158 residue for other conformations, but does not restore covalent flavin attachment. The H158Y variant retains substantial FAD occupancy and tetrameric assembly but shows markedly reduced oxidase and dehydrogenase turnover rates (less than 13% of WT). These results provide a structural explanation for the failure of tyrosine substitution to support covalent flavinylation in PcPOx and offer insights into requirements for engineering alternative covalent flavin linkages.

biochemistry↗

bioRxiv2026

Cytoplasmic mRNA granules regulate cell fate decisions during PINK1/Parkin mitophagy

Mitophagy is generally considered to promote cell survival by removing damaged mitochondria in response to mitochondrial stress, whereas apoptosis occurs during prolonged stress. However, the mechanisms that determine cell survival and cell death under these stress conditions remain poorly understood. Here, we showed that cytoplasmic mRNA granules, designated as mitophagy-induced mRNA granules (mitoRGs), were formed transiently and played an important role in cell fate decisions during PINK1/Parkin-dependent mitophagy. Although some components, such as G3BP1, were shared with stress granules (SGs), mitoRGs were distinct from SGs because mitoRG assembly required the mitochondrial protein phosphatase PGAM5. In response to mitochondrial stress, PGAM5 was released into the cytosol from mitochondria and incorporated into mitoRGs, but was then released back into the cytosol during mitoRG disassembly following prolonged mitochondrial stress, corresponding with the induction of apoptosis. Impairment of mitoRG assembly through G3BP1 depletion sensitized cells to apoptosis during mitophagy in a PGAM5-dependent manner. These results suggest that mitoRGs regulate cell fate decisions by spatiotemporally controlling PGAM5 and its pro-apoptotic activity during PINK1/Parkin mitophagy.

cell biology↗

bioRxiv2025

The RUMIGEN EpiChip: a versatile, medium density DNA methylation Beadchip for large scale population studies in cattle

BackgroundDNA methylation contributes to the elaboration of phenotypes and is hypothesized to account for interindividual variations in farm animals. Currently, methodologies available to investigate DNA methylation in cattle rely on high throughput sequencing, which cannot be applied to large cohorts. To enable large scale DNA methylation analysis, we developed the RUMIGEN EpiChip, the first DNA methylation array specifically designed for cattle. ResultsManufactured by Illumina, the EpiChip contains 43,317 CpG markers allowing analysis of phenotypes of agronomical interest as well as the study of regulatory processes. The assay design drew on data from numerous studies achieved by the scientific community, and includes CpGs where methylation varies with health status, physiological stage, fertility, and environmental challenges, as well as CpGs located in functional genomic elements (promoters, CTCF binding sites, expression quantitative trait loci). The technical performances of the EpiChip were tested on several semen and blood DNA samples and in two laboratories, showing excellent repeatability, accuracy and interoperability. Methylation values were also concordant with those obtained by reduced representation bisulfite sequencing. The EpiChip has demonstrated a good ability to explore biological processes such as genomic imprinting and differences between cell types, opening the possibility of inferring blood cell composition. Finally, analysis of longitudinal ear biopsies allowed accurate age prediction, suggesting the potential of the array to refine epigenetic clocks. ConclusionsThe RUMIGEN EpiChip is a cost-effective and versatile resource that opens new opportunities for the study of regulatory mechanisms underlying phenotypic variation and for large-scale association analyses in cattle.

genomics↗

bioRxiv2025

Nonlinear hippocampal coding of the pair-bonded partner in prairie voles

Neural representation of specific opposite-sex partners remains largely unexplored. Using monogamous prairie voles, we demonstrated that partner preference required the ventral hippocampus, in which 3-4 Hz oscillations were enhanced following partner interaction. We identified ventral hippocampal neurons responding selectively to the pair-bonded partner and stranger, which encoded identity-related information in a nonlinear manner, shedding light upon how mammalian brains create distinct neural representations of romantic opposite-sex partners.

neuroscience↗

bioRxiv2025

Genome sequence data and integrative RNA-Seq data of Black Soldier Fly (Hermetia illucens) (A Japanese strain)

The black soldier fly, Hermetia illucens, is a dipteran insect with a distinctive black body in the adult stage. The larvae of this species possess biological features which can be used for industrial applications. We established an H. illucens field-collected strain to develop an industrial system for recycling organic waste. We constructed whole-genome sequences of the strain of H. illucens and prepared a gene set and its functional annotation data to promote research on the social implementation of H. illucens and genetically characterise this strain. In addition, time-course transcriptome data of the larvae and transcriptome expression data of multiple tissues from 6th instar larvae and male and female adults were prepared. The genome size and its N50 value were approximately 1.05 Gbp and 191 bp, respectively. The results of the validation analyses of the genome and transcriptome expression data showed that these data were reliable as reference data, suggesting that they can be used in research on the industrial usage of evolutionary H. illucens or evolutionary or comparative biology.

genomics↗

bioRxiv2025

Flexible fitting to infer atomistic-precision models of large-amplitude conformational dynamics in biomolecules from high-speed atomic force microscopy imaging

High-speed atomic force microscopy (HS-AFM) experiments allow direct observation of biomolecular dynamics at the single-molecule level, acquiring a large amount of topographic imaging data that visualizes changes of the molecular surface during functional activity over an extended period of time. Since images have no atomistic resolution, a major challenge has been to develop post-experimental computational methods to infer atomistic information from measurements. The recently developed NMFF-AFM flexible fitting method provides a computationally efficient approach promising to infer atomistic-precision models of conformational dynamics from resolution-limited AFM imaging data. We report the software integration of this method into the well-established BioAFMviewer platform and demonstrate first applications to experimental HS-AFM imaging data. To facilitate applications, we developed a direct workflow from raw experimental AFM data to visualization and analysis of fitting results. The presented applications to experimental data of a single protein domain, a protein complex, and a megadalton size protein filament demonstrate versatility of NMFF-AFM modelling to reproduce large-amplitude conformational motions of biomolecular dynamics from HS-AFM imaging. As a first step towards automated large-scale analysis of AFM imaging data, we furthermore demonstrate reconstruction of an atomistic molecular movie of protein dynamics, involving large-amplitude conformational transitions, from a measured HS-AFM movie sequence. Implementation of flexible fitting within the standalone user-friendly interactive BioAFMviewer software opens the opportunity for broad range applications to facilitate the understanding of resolution-limited HS-AFM measurements.

biophysics↗

bioRxiv2025

Theanine boosts frontal theta and hippocampal beta and gamma oscillations for familiarity in object recognition

Theanine, a non-proteinogenic amino acid derivative from green tea leaves, enhances object recognition memory in rats through facilitated neurogenesis. In this sense, the cellular mechanism for the theanine-enhanced object recognition memory has been elucidated to some extent, but physiological evidence still remains unclear. To tackle this issue, we chronically fed mice with theanine (or tap water) for three weeks, implanted electrodes into the hippocampus and frontal cortex, both of which are responsible for object recognition memory. We then recorded the local field potentials from the two regions during the novel object recognition task, evaluated the task performance, and broke down the neural signals in the hippocampus and frontal cortex into delta, theta, beta, low gamma, and high gamma frequency bands. The discrimination ratio of theanine-treated mice was higher than that of vehicle-treated mice. We also found that theta oscillations in the frontal cortex and beta and low gamma oscillations in the hippocampus in theanine-treated mice were simultaneously enhanced for familiar objects. These results shed light on the new physiological underpinnings of object recognition memory enhanced by exogenous substances.

pharmacology and toxicology↗

bioRxiv2025

Comprehensive Molecular Docking on the AlphaFold-Predicted Protein Structure Proteome: Identifying Target Protein Candidates for Puberulic Acid, a Suspected Lethal Nephrotoxin

This study presents a novel in silico screening method for identifying potential protein-ligand interactions within the complete structural proteome, as predicted by AlphaFold2, using puberulic acid as a test case. The methodology utilizes molecular docking simulations to predict interactions based on structural compatibility and binding affinity estimations. This approach highlights proteins, such as sodium/myo-inositol cotransporters, which exhibit theoretical high affinity for puberulic acid, suggesting possible competitive inhibition or mimetic interactions that could disrupt osmoregulation. It is important to clarify that these simulations provide a hypothetical framework for understanding potential interactions. The high docking scores do not directly translate to biological effects but serve as a basis for further experimental validation. This cautious interpretation acknowledges the inherent limitations of predictive modeling while maintaining confidence in the robustness of the computational process. Moreover, the exploratory nature of this study is supported by the fact that binding affinity predictions are not influenced by protein amino acid length or the predictive accuracy (pLDDT scores) provided by AlphaFold2. This independence from structural prediction metrics suggests that the docking results offer a reliable exploration of potential interactions across a wide array of proteins, making this approach a valuable asset in the fields of drug discovery and toxicological research. The ability to comprehensively identify candidate proteins with potential affinity to chemical compounds enhances the predictive capacity of toxicological assessments and supports the strategic development of safer pharmaceutical agents.

bioinformatics↗

bioRxiv2024

Unsupervised alignment reveals structural commonalities and differences in neural representations of natural scenes across individuals and brain areas

Neuroscience research has extensively explored the commonality of neural representations of sensory stimuli across individuals to uncover universal neural mechanisms in the encoding of sensory information. To compare neural representations across different brains, Representational Similarity Analysis (RSA) has been used, which focuses on the similarity structures of neural representations for different stimuli. Despite the broad applicability and utility of RSA, one limitation is that its conventional framework assumes that neural representations of particular stimuli correspond directly to those of the same stimuli in different brains. This assumption excludes the possibility that neural representations correspond differently and limits the exploration of finer structural similarities. To overcome this limitation, we propose to use an unsupervised alignment framework based on Gromov-Wasserstein Optimal Transport (GWOT) to compare similarity structures without presupposing stimulus correspondences. This method allows for the identification of optimal correspondence between neural representations of stimuli based solely on internal neural representation relationships, and thereby provides a more detailed comparison of neural similarity structures across individuals. We applied this unsupervised alignment to investigate the commonality of representational similarity structures of natural scenes, using large datasets of Neuropixels recordings in mice and fMRI recordings in humans. We found that the similarity structure of neural representations in the same visual cortical areas can be well aligned across individuals in an unsupervised manner in both mice and humans. In contrast, we found that the degree of alignment across different brain areas cannot be fully explained by proximity in the visual processing hierarchy alone, but also found some reasonable alignment results, such that the similarity structures of higher-order visual areas can be well aligned with each other but not with lower-order visual areas. We expect that our unsupervised approach will be useful for revealing more detailed structural commonalities or differences that may not be captured by the conventional supervised approach.

neuroscience↗

bioRxiv2024

Corticocortical and Corticomuscular Connectivity Dynamicsin Standing Posture: Electroencephalography Study

Cortical involvements, including those in the sensorimotor, frontal, and occipitoparietal regions, are important mechanisms of neural control in human standing. Previous research has shown that cortical activity and corticospinal excitability vary flexibly in response to postural demand. However, it is unclear how corticocortical and corticomuscular connectivity is dynamically modulated during standing balance and over time. This study investigated the dynamics of this connectivity using electroencephalography (EEG) and electromyography (EMG). The EEG and EMG were measured in different 4 positions: sitting (ST), normal quiet standing (QS), one-leg standing (ON), and standing on a piece of wood (WD). For corticomuscular connectivity, we concentrated on sway-varying connectivity in the timing of peak velocity of postural sway in the anteroposterior direction. For the corticocortical connectivity, the time-varying connectivity was quantified, particularly in the {theta}-band connectivity which is linked to error identification, using a sliding-window approach. The study found that corticomuscular connectivity from the brain to the lower-limb muscle was strengthened during the sway peak in the {gamma}- and {beta}-frequency bands, while the connectivity strength from the muscle to the brain was decreased in the {theta}- and -band. For the time-varying connectivity, the {theta}-connectivity in all time-epoch was divided into 7 states including both posture-relevant and -irrelevant clusters. In one of the 7 states, the strong connectivity pairs were concentrated in the mid-central region and the proportion of epochs from the ON and WD conditions was significantly higher, indicating a functional role for posture balance. These findings shed light on electrodynamic connectivity which varies in response to postural demand. Those dynamics, particularly in the {theta}-band connectivity, can be used for ongoing monitoring and/or intervention for postural disability.

neuroscience↗

bioRxiv2024

OrgaMeas: A pipeline that integrates all the processes of organelle image analysis

Although image analysis has emerged as a key technology in the study of organelle dynamics, the commonly used image-processing methods, such as threshold-based segmentation and manual setting of regions of interests (ROIs), are error-prone and laborious. Here, we present a highly accurate high-throughput image analysis pipeline called OrgaMeas for measuring the morphology and dynamics of organelles. This pipeline mainly consists of two deep learning-based tools: OrgaSegNet and DIC2Cells. OrgaSegNet quantifies many aspects of different organelles by precisely segmenting them. To further process the segmented data at a single-cell level, DIC2Cells automates ROI settings through accurate segmentation of individual cells in differential interference contrast (DIC) images. This pipeline was designed to be low cost and require less coding, to provide an easy-to-use platform. Thus, we believe that OrgaMeas has potential to be readily applied to basic biomedical research, and hopefully to other practical uses such as drug discovery.

cell biology↗

bioRxiv2024

Endothelial PHD2 deficiency induces apoptosis resistance and inflammation via AKT activation and AIP1 loss independent of HIF2α

BACKGROUNDIn hypoxic and pseudohypoxic rodent models of pulmonary arterial hypertension (PAH), hypoxia-inducible factor (HIF) inhibition reduces disease severity. However, HIF activation alone, due to genetic alterations or use of inhibitors of prolyl hydroxylase domain (PHD) enzymes, has not been definitively shown to cause PAH in humans, indicating the involvement of other mechanisms. METHODSPseudohypoxia was investigated in primary human lung endothelial cells by silencing PHD2, and in Tie2-Cre/Phd2 knockout mice, a rodent model of PAH. Lung vascular endothelial cells from PAH patients, and lung tissue from both SU5416/hypoxia PAH rats and PAH patients, were examined for validation. RESULTSPHD2 silencing or inhibition, while activating HIF2, induces apoptosis-resistance, hypo-proliferation, and IFN/STAT activation in endothelial cells, independent of HIF signaling. Mechanistically, PHD2 deficiency activates AKT and ERK, inhibits JNK, and reduces AIP1 (ASK1-interacting protein 1), all independent of HIF2. Like PHD2, AIP1 silencing affects these same kinase pathways and produces a similar dysfunctional endothelial cell phenotype, which can be partially reversed by AKT inhibition. These findings are corroborated in lung tissues of rodent PAH models and pulmonary vascular endothelial cells and tissues from PAH patients. CONCLUSIONSPHD2 deficiency in lung vascular endothelial cells induces an apoptosis-resistant, inflammatory, and hypo-proliferative phenotype. AKT activation and AIP1 loss, but not HIF signaling, drive these aberrant phenotypic changes. Our study suggests that HIF blockade alone may not suffice for PAH therapy; targeting PHD2, AKT, and AIP1 has the potential for developing more effective treatment. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/578286v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1fd0a0borg.highwire.dtl.DTLVardef@19e6ba9org.highwire.dtl.DTLVardef@1ae2827org.highwire.dtl.DTLVardef@ce31ec_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPHD2 silencing in human lung vascular endothelial cells suppresses apoptosis, inhibits proliferation, and activates STAT signaling, effects that persist despite HIF2 inhibition or knockdown. C_LIO_LIPHD2 silencing activates AKT and ERK, inhibits JNK, and decreases AIP1, all independently of HIF2 C_LIO_LILike PHD2, AIP1 silencing led to similar alterations in kinase signaling and endothelial cell phenotypes, which are partially reversed by ATK inhibition. C_LIO_LIThese in vitro findings align with observations in lung vascular endothelial cells and tissues from rodent models of PAH as well as PAH patients. C_LI

cell biology↗

bioRxiv2023

Analysis of chronic host-aspergilloma interactions using a novel mouse model

An aspergilloma is a fungus ball caused by chronic infection of Aspergillus species in a pre- existing cavity, such as a destroyed lung or the sinuses. Patients with pulmonary aspergilloma are at risk of sudden life-threatening hemoptysis. Antifungal therapy is administered to aspergilloma patients who are ineligible for surgery, but its efficacy is limited. Understanding the pathophysiology of aspergilloma is crucial for developing further treatment strategies. The mechanism behind the long-term host response to aspergilloma is poorly understood. We created a novel mouse model to analyze the host response to aspergilloma by implanting a fungus ball of Aspergillus fumigatus into an air-filled subcutaneous cavity. Our findings indicate that a live fungus ball led to tissue invasion, even in immunized mice. When a fungus ball consisting of dead hyphae was implanted, it persisted for over three months and induced pathological findings simulating human aspergilloma, including an inflammatory cell infiltration into the fungus ball and angiogenesis in the cavity wall. Dead fungus ball induced Th1 and Th17 inflammatory cytokines and vascular endothelial growth factor. Neutrophils infiltrated the inside of the fungus ball immediately after implantation, and macrophages surrounded it after a one-week delay. The macrophages around the fungus ball were swollen with phagocytosed fragments of dead hyphae and transformed into foam cells containing fat droplets. We also confirmed in vitro that macrophages were damaged and transformed into foam cells by direct contact with dead hyphae. This model holds promise to provide new insights into the fungal-host interaction during aspergillomas. NOTATION OF PRIOR ABSTRACT PUBLICATION/PRESENTATIONNone IMPORTANCEChronic aspergillosis, which affects over 3 million people worldwide with a 5-year survival rate of 50%, is understudied compared to other forms. Our study focuses on aspergilloma, a key aspect of chronic aspergillosis, using a groundbreaking mouse model that mirrors clinical features over three months. By studying host-fungal interactions within aspergillomas, we discovered Th1 and Th17 inflammatory responses to dead fungal hyphae. Initially, neutrophils dominate, later giving way to macrophages with a lipid-accumulating foamy phenotype. This transition may impede aspergilloma clearance. In addition, even dead hyphae induce vascular endothelial growth factor and promote angiogenesis. Our findings, which are critical for the prevention of fatal hemoptysis, highlight the need for innovative treatments that target fungal clearance and challenge the limited efficacy of antifungal agents against dead fungal bodies. This research represents a significant step forward in the understanding of chronic aspergillosis.

microbiology↗

bioRxiv2023

Toolbox for Gromov-Wasserstein optimal transport: Application to unsupervised alignment in neuroscience

BackgroundUnderstanding how sensory stimuli are represented across different brains, species, and artificial neural networks is a critical topic in neuroscience. Traditional methods for comparing these representations typically rely on supervised alignment, which assumes direct correspondence between stimuli representations across brains or models. However, it has limitations when this assumption is not valid, or when validating the assumption itself is the goal of the research. New methodTo address the limitations of supervised alignment, we propose an unsupervised alignment method based on Gromov-Wasserstein optimal transport (GWOT). GWOT optimally identifies correspondences between representations by leveraging internal relationships without external labels, revealing intricate structural correspondences such as one-to-one, group-to-group, and shifted mappings. ResultsWe provide a comprehensive methodological guide and introduce a toolbox called GWTune for using GWOT in neuroscience. Our results show that GWOT can reveal detailed structural distinctions that supervised methods may overlook. We also demonstrate successful unsupervised alignment in key data domains, including behavioral data, neural activity recordings, and artificial neural network models, demonstrating its flexibility and broad applicability. Comparison with existing methodsUnlike traditional supervised alignment methods such as Representational Similarity Analysis, which assume direct correspondence between stimuli, GWOT provides a nuanced approach that can handle different types of structural correspondence, including fine-grained and coarse correspondences. Our method would provide richer insights into the similarity or difference of representations by revealing finer structural differences. ConclusionWe anticipate that our work will significantly broaden the accessibility and application of unsupervised alignment in neuroscience, offering novel perspectives on complex representational structures. By providing a user-friendly toolbox and a detailed tutorial, we aim to facilitate the adoption of unsupervised alignment techniques, enabling researchers to achieve a deeper understanding of cross-brain and cross-species representation analysis.

neuroscience↗

bioRxiv2023

Genome-wide neighbor effects predict genotype pairs that reduce herbivory in mixed planting

Genetically diverse populations can increase plant resistance to natural enemies. Yet, beneficial genotype pairs remain elusive due to the occurrence of both positive and negative effects of mixed planting on plant resistance, called associational resistance and susceptibility. We used genome-wide polymorphisms of the plant species Arabidopsis thaliana to identify genotype pairs that enhance associational resistance to herbivory. By quantifying neighbor interactions among 199 genotypes grown in a randomized block design, we predicted that 823 of the 19,701 candidate pairs could reduce herbivory through associational resistance. We planted such pairs with predicted associational resistance in mixtures and monocultures and found a significant reduction in herbivore damage in the mixtures. Our study highlights the potential application to assemble genotype mixtures with positive biodiversity effects.

ecology↗

bioRxiv2023

Subchronic Toxicity Assessment of Perfluoroalkyl Substances by Mixed Exposure of Nine Substances at Daily Intake Relevant Concentration

Per- and poly-fluoroalkyl substances (PFAS) have been utilized extensively for various applications owing to their distinctive chemical properties. They exhibit high persistence in the environment and accumulate within the human body, necessitating toxicity assessments. However, the consequences of prolonged, low-level exposure to PFAS and concurrent exposure to multiple PFAS have not been explored. In this study, male C57BL/6J mice (aged 8 weeks) were exposed to a composite of nine PFAS, which include long-chain PFAS (e.g. perfluorooctanoic acid and perfluorooctanesulfonic acid) and short-chain PFAS (e.g. perfluorobutanoic acid and perfluorobutanesulfonic acid) at concentrations equivalent to the estimated daily human intake in the composition reported (1 {micro}g/L [sum of the nine compounds], the maximum reported exposure concentration) via drinking water. Histological examination revealed vacuolization of hepatocytes and irregular arrangement of hepatocyte cords, suggesting that exposure to low levels of the PFAS mixture causes morphological changes in liver tissues. Transcriptome analysis revealed that PFAS exposure mainly altered a group of genes related to metabolism and chemical carcinogenesis. Machine learning analysis of the liver metabolome showed a typical concentration-independent alteration upon PFAS exposure, and in addition to known substances such as glutathione, a compound with unknown biological function; 2,5-dihydro-2,4-dimethyloxazole was found. This study demonstrates that daily exposure to PFAS leads to morphological changes in liver tissues and alters the expression of metabolism-and cancer-related genes as well as phospholipid metabolism. Future studies are required to evaluate the chronic toxicity of prolonged, low-level exposure to PFAS mixtures and to investigate the health effects of PFAS.

pharmacology and toxicology↗

bioRxiv2022

Structural dynamics of E6AP E3 ligase HECT domain and involvement of flexible hinge loop in ubiquitin chain synthesis mechanism

Ubiquitin (Ub) ligases E3 are an important factor in selecting target proteins for ubiquitination and determining the type of polyubiquitin chains on the target proteins. In the HECT (homologous to E6AP C-terminus)-type E3 ligases, the HECT domain is composed of an N-lobe containing the E2-binding site and a C-lobe containing the catalytic Cys residue that forms a thioester bond with Ub. These two lobes are connected by a flexible hinge loop. The large conformational rearrangement of the HECT domain via the flexible hinge loop is essential for HECT-type E3-mediated Ub transfer from E2 to a target protein. However, detailed insights into the structural dynamics of this type of E3 ligases remain unclear. Here, we provide the first direct demonstration of structural dynamics of the E6AP HECT domain using high-speed atomic force microscopy. We also investigated structural dynamics of hinge loop flexibility restricted HECT domain, and we found that flexibility of the E6AP hinge loop has a great impact not only on its structural dynamics but also on the formation of free Ub chains mediated by E3-E3 interactions.

biophysics↗