Biology subjects

Maeda, K.

Publications and source records attributed to Maeda, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Neural populations in the dorsal and ventral cervical spinal cord share temporal dynamics during reach

Neural population dynamics provide a popular framework for studying motor cortex function. However, whether such dynamics reflect stage-specific computations or are shared across the input and output stages of a sensorimotor circuit is unknown. In the spinal cord, afferent inputs and motor outputs are segregated by anatomical depth. Here we developed depth-resolved Neuropixels recordings from the rat cervical spinal cord during targeted reaching behavior. Across our recordings, population activity was low-dimensional and organized into transient, rotational and target-specific dynamical motifs. Despite differences in single-neuron activity by depth, dorsal and ventral populations expressed nearly identical dynamics across targets and animals. The dominant target-invariant component was strikingly synchronized across depths, whereas other components, including the target-specific component, showed condition-dependent ventral-to-dorsal delays with timing consistent with movement-related feedback. Thus, cervical spinal population dynamics span sensory and motor territories, and may reflect shared coordination of activity rather than purely state-specific local processing.

neuroscience↗

bioRxiv2026

An evolvable and functionally partitioned network underlies developmental remodelling in teleosts

Comparative embryology has revealed that early animal development is based on highly conserved genetic programs. Beyond embryogenesis however, animals undergo remarkably diverse post-embryonic developmental transitions such as metamorphosis. Whether these transitions are also organised into conserved genetic programs remains largely unexplored. To identify conserved genetic programs underlying post-embryonic development, we examine metamorphic remodelling in five teleost fishes, spanning 200 million years of evolution. By integrating comparative co-expression networks, evolutionary genomics, phylogenetic modelling, and functional data in zebrafish, we uncovered a conserved post-embryonic developmental network. This conserved network comprises components involved in core cellular processes, and involved in development and physiology, both of which are under the control of thyroid hormone during metamorphosis. Despite evolutionary conservation at the coding sequence level, this network exhibits significant turnover in gene family copy number following the teleost-specific whole-genome duplication as well as lineage-specific expansions and contractions. The variation in gene copy numbers is associated with macroevolutionary variation in a number of ecological and morphological traits, including swimming performance, and trophic level. Cross-species tissue expression, zebrafish single-cell transcriptomics, and zebrafish perturbation phenotypes placed the implicated genes in biological contexts relevant to these traits. Together, our results provide evidence of an ancient, functionally partitioned post-embryonic developmental network that has diversified throughout teleost evolution. The heterochronic variation in network function, changes in endocrine activity, and gene-family turnover provide potential routes through which a shared developmental architecture contributed to the evolution of phenotypic diversity in teleosts.

evolutionary biology↗

bioRxiv2026

Computer experimentation on E. coli ammonium transport and assimilation reveals mechanisms for energy coupling, balanced futile cycling, and robust growth

Nitrogen is essential for all life forms, and microorganisms prefer ammonium as a nitrogen source. Due to the low affinity of glutamine synthetase (GS) for ammonium, E. coli must maintain high intracellular ammonium (NH4+) concentrations to sustain its rapid growth. Under ammonium limitation, E. coli imports ammonium through the transporter AmtB and incorporates it into glutamine by using GS. On the basis of structural and mutagenesis information, mechanisms have been proposed for the transport of ammonia (NH3) and protons by AmtB through spatially (partly) separate routes. These mechanisms do not explain the required coupling between proton and ammonia transports. How does the membrane potential push the ammonia inward so as to attain high concentrations near GS? We here compare six candidate kinetic models of E. coli ammonium transport and assimilation in terms of how they reproduce experimental data from the literature: three variants of the electro-binding model in which the membrane potential affects AmtB-NH4+ binding, and three variants of the electro-flipping model in which it influences the conformational flip of the transporter. The computer simulations decide that the electro-binding models are 28 times more plausible than the electro-flipping models and suggest that the transmembrane electric potential affects AmtB-NH4+ binding from the cytoplasmic side. The addition of kinetic and thermodynamic features to existing structural information plus our requirement of an explanation of the coupling, suggest a new spatiotemporal mechanism of coupling of ammonia and proton flows in AmtB. Further simulations show that GS and AmtB regulation is coordinated via both the uridylyltransferase/uridylyl-removing enzyme (UTase) and 2-oxoglutarate binding, allowing the cell to minimize futile cycling while maintaining rapid growth. The free energy cost of transport-related futile cycling exceeded that of the GS reaction itself. Moreover, AmtB enabled robust growth under varying ammonium concentrations and pH levels, albeit at a cost of futile cycling that became substantial at low ammonium. These findings highlight the crucial roles of GS and AmtB in E. colis adaptations and provide new insights into the trade-off mechanism between nutrient acquisition and energy efficiency.

systems biology↗

bioRxiv2026

A surrogate marker of protection confirms the efficacy of an AddaS03-adjuvanted West Nile virus subunit vaccine

West Nile virus (WNV) is the causative agent of fatal West Nile encephalitis. To date, no human vaccine against WNV has been approved. Adjuvants are important for developing effective and affordable vaccines that enhance the immunogenicity and decrease the required antigen doses. In this study, we assessed the efficacy of AddaS03, a synthetic adjuvant analogous to AS03, in a WNV subunit vaccine composed of soluble recombinant envelope protein (sEnv). Using a passive immunization mouse model, we defined the neutralizing antibody titer threshold required for protection against lethal WNV infections and applied this threshold as a surrogate marker to evaluate adjuvant efficacy. AddaS03-adjuvanted formulations elicited markedly higher neutralizing antibody titers compared to Alhydrogel adjuvant 2% (Alhydrogel), even at suboptimal antigen doses, and consistently exceeded the defined protective threshold titer. Moreover, in a sequential challenge mouse model, AddaS03-adjuvanted vaccines completely protected mice from symptomatic WNV infections, whereas Alhydrogel-adjuvanted vaccines failed to confer full protection. Collectively, these findings demonstrate that AddaS03 is a promising adjuvant for WNV subunit vaccine development and highlights the utility of a passive immunization model for defining protective antibody thresholds as a surrogate marker for vaccine evaluation.

microbiology↗

bioRxiv2026

Extracellular vesicles from antigen-activated B cells stimulate oncogenic herpesvirus lytic gene expression

B cell-derived extracellular vesicles (B-EVs) have been associated with immunomodulatory functions like antigen presentation, cytokine signaling, and T cell activation. However, little is known about the general composition of B-EVs or how the state of the donor cells affects the B-EV composition or functions. We performed integrated proteomic, lipidomic, and transcriptomic analyses of EVs secreted by B cells in resting conditions or upon 30 min of B cell receptor (BCR) activation. Antigen-driven BCR stimulation led to acute remodeling of the protein and lipid composition, and RNA cargo of the B-EVs, which also translated into differential responses in recipient B cells. Remarkably, EVs from activated B cells stimulated lytic gene expression of latent oncogenic {gamma}-herpesviruses Epstein-Barr virus (EBV) and Kaposi sarcoma-associated herpesvirus (KSHV). These findings suggest a novel mechanism for the potentially oncogenic reactivation of these lifelong-persisting latent herpesviruses, residing in B cells. Our results support a mechanism in which, upon immune activation, B-EVs from antigen-specific B cells induce viral reactivation in bystander B cells in a paracrine manner, providing molecular insights that bridge immune activation and the pathogenesis of {gamma}-herpesvirus infections.

immunology↗

bioRxiv2025

Molecular signature of COVID-19 prior to its exacerbation by multi-omics survey

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic due to its high transmissibility and ability to evade innate immune responses. Comprehensive characterization of the disease is essential for elucidating its pathophysiology and clinical progression. In this study, we performed multi-omics analyses of plasma samples collected from SARS-CoV-2-positive patients prior to clinical deterioration of coronavirus disease 2019 (COVID-19). These samples revealed the potential of previously reported clinical parameters, including CRP and neutrophil level, to predict COVID-19 exacerbation in the early stage. Our analysis identified a novel panel of molecules that precede the clinical manifestations associated with COVID-19 progression. These candidate biomarkers exhibited strong correlations with previously reported clinical and immunological parameters. Notably, several inflammation-related markers showed inverse associations with specific interferon subtypes, including IFN-6 and IFN-8, potentially reflecting mechanisms of SARS-CoV-2-mediated immune evasion. Our findings contribute to the understanding of virus-induced acute exacerbation and offer a valuable foundation for future pandemic research.

microbiology↗

bioRxiv2025

Transfer of the synechan biosynthesis and regulatory pathway enables sulfated polysaccharide production in Synechococcus elongatus PCC 7942

Many sulfated polysaccharides (SPSs) possess useful physicochemical properties and biological activities and are widely used in industry. Currently, major SPSs are derived from livestock and marine organisms. To contribute both to addressing global environmental challenges and to the development of diverse SPSs, microbial production systems are therefore required. Nevertheless, bacteria capable of producing SPSs are limited. In contrast, many cyanobacteria synthesize diverse SPSs, making them promising hosts to produce valuable SPSs, sources for novel SPSs, and genetic resources for SPS biosynthesis. However, no study has introduced an entire heterologous SPS biosynthetic system into cyanobacteria to produce a heterologous SPS. We recently identified a novel SPS, synechan, and elucidated the genetic basis for the biosynthesis and regulation of cyanobacterial SPSs. Here, we heterologously expressed the gene set responsible for synechan biosynthesis and its regulation in the non-SPS-producing cyanobacterium Synechococcus elongatus PCC 7942 and successfully induced the production of an SPS. This work provides a foundation for engineering cyanobacteria to produce useful SPSs and, to our knowledge, the first functional heterologous reconstitution in cyanobacteria of a large gene cluster encoding a complex membrane-associated biosynthetic system and thus an important step in synthetic-biology-based engineering of cyanobacteria.

synthetic biology↗

bioRxiv2025

GDA-Pred: Generative AI-Driven Data Augmentation for Improved Prediction of IL-6 and IL-13 Inducing Peptides

The identification of interleukin-6 (IL-6) and interleukin-13 (IL-13) inducing peptides is crucial for accelerating drug discovery targeting cancer, immune disorders, and infectious diseases. However, experimental screening methods remain time-consuming and costly. To address these limitations, various machine learning and deep learning models have been developed, yet their performance is still constrained by the limited availability of experimentally validated data. In this study, we propose a generative AI-driven data augmentation (GDA) framework and predictor, GDA-Pred, to improve the prediction performance of state-of-the-art (SOTA) classifiers for identifying IL-6 and IL-13 inducing peptides. GDA expands the training dataset by generating novel peptide sequences using three types of generative AI models: generative adversarial networks (GANs), diffusion models (DMs), and variational autoencoders (VAEs). The GDA framework is defined by four key parameters: the type of generative model, the sequence identity cutoff, the probability threshold (PT) for selecting generated peptides, and the augmentation ratio (AR) between generated and real peptides. Since optimizing these parameters is challenging with small datasets, we adopt a case study-oriented proof-of-concept approach using a moderately sized dataset of anti-inflammatory peptides (AIPs) to derive interpretable optimal settings. The performance of the optimized GDA was evaluated using stratified 5-fold cross-validation with cluster-based partitioning and a hold-out test on benchmark datasets. The optimized GDA was then applied to SOTA classifiers, collectively termed GDA-Pred, to identify IL-6 and IL-13 inducing peptides, both of which are limited by small dataset sizes. GDA-Pred substantially improved the prediction performance for both cytokine-inducing peptide tasks, demonstrating the feasibility of GDA-Pred as a robust and generalizable framework.

bioinformatics↗

bioRxiv2025

Identification of a novel small molecule facilitating HIV elimination by the "Shock-and-Kill" approach

The development of antiretroviral therapy (ART) has significantly improved the prognosis of people living with HIV (PLWH). However, reservoirs of latent viruses represent a major barrier to achieving a complete cure of HIV infection. To overcome the burden of viral latency, the "Shock-and-Kill" strategy employs latency-reversing agents (LRAs) to reactivate the virus and thus render it susceptible to elimination. Existing LRAs are not optimal and there is an unmet need for improvement. By screening a small molecule library, we identified the novel LRA candidate 2-HSB (2-hydrido-2,2-spirobi(1,3,2-benzodioxaphosphole)) which not only reactivates latent HIV provirus but also induces specific cytopathic effects in both monocytic and T lymphocytic latent HIV reservoirs. Thus, this novel compound represents a dual "shock and kill" agent, unlike known LRAs which are limited to the "shock". The probable involvement of HIV-1 tat protein may account for its selectivity. Although both shock and kill effects seemed to be regulated by spleen tyrosine kinase, they were independent of each other, indicating that neither activation-induced cell death nor cell death-induced reactivation was occurring. Crucially, 2-HSB induced viral transcription in ART-suppressed PLWH samples in vitro. Our findings present 2-HSB as a promising dual-action compound for the "Shock and Kill" strategy, demonstrating efficacy in both transformed cell lines and clinically-relevant primary samples. These results raise the possibility of distinguishing the mode of action of the two effects, potentially leading to the development of a single agent causing both HIV-1 reactivation and elimination and contributing to the improvement of treatment.

microbiology↗

bioRxiv2025

Transcriptomic insights into the tripartite plant-pathogen-mycoparasite interaction reveal novel mechanisms involving fungal secretomes and plant amino acid metabolism

O_LIThe tomato-Cladosporium fulvum (syn. Fulvia fulva) pathosystem has served as a model for the gene-for-gene concept of effectors and resistance proteins, but this binary framework does not include the potential influence of other microbial participants. Here we describe the dramatic changes in gene expression of all members of the tritrophic interaction among tomato, C. fulvum, and mycoparasitic fungus Hansfordia pulvinata. C_LIO_LITranscriptomic analyses of the mycoparasite H. pulvinata during parasitism of C. fulvum on tomato on planta and in vitro revealed a dramatic upregulation of genes encoding small secreted proteins during mycoparasitism, notably, a Nep1-like protein (HpNlp1) lacked typical necrosis-inducing activity but induced the accumulation of antifungal compounds inhibiting spore germination of C. fulvum. C_LIO_LISimilarly, in C. fulvum parasitized by H. pulvinata, effector genes were highly expressed. Strikingly, effector protein Ecp2 was found to share structural similarity with pathogen killer toxin 4 proteins and had broad-spectrum antifungal activity, indicating a dual function in fungal competition and Cf-ECP2-mediated plant resistance. C_LIO_LIIn tomato plants infected by C. fulvum parasitized by H. pulvinata, primary metabolism and defense-related genes were exclusively activated. These results suggest that in the tritrophic interaction, the mycoparasite simultaneously suppressed the pathogen and induced plant resistance. This study uncovers a multilayered molecular network in which the mycoparasite coordinates pathogen suppression and plant defense within the tritrophic interaction. C_LI

microbiology↗

bioRxiv2025

Spinal interneuronal populations encode static hindlimb posture in the cat

Proprioceptive signals from primary afferents reflect changes in single-joint angles, whereas neuronal population in the cerebral cortex represent whole-limb postures. Where and how this transformation emerges along the somatosensory axis from peripheral proprioceptive receptors remains unclear. We simultaneously recorded many lumbosacral spinal neurons in two decerebrate, immobilized cats while a robotic device held the hindlimb at 16 static endpoint positions spanning hip-knee configurations. Using high-density multielectrode recordings, we asked how spinal populations encode static limb state. At the single-neuronal level, activities in a majority of neurons covaried with a single joints angle (hip or knee), a smaller subset showed combined modulation by both joints, and a distinct subset ( single-endpoint neurons) fired selectively at one unique hip-knee configuration near the sampled joint-range limits and was quiescent in adjacent postures. Population analyses revealed a low-dimensional structure: the first two principal components tracked knee and hip angles, respectively, whereas a third component isolated a boundary-aligned, posture-specific pattern, with loadings peaking at the same extreme configurations preferred by single-endpoint neurons. Decoders trained on ensemble activity reconstructed both joint angles and the limbs endpoint position in body-centered coordinates, indicating that the recorded spinal-interneuron populations contain sufficient information to reconstruct whole-limb kinematics. Together, these findings are consistent with a hierarchical organization whereby joint-based representations within spinal-interneuron populations could contribute to the emergence of limb-centered representations in the ascending proprioceptive pathways. The boundary preference of single-endpoint neurons supports a possible categorical coding scheme at workspace limits that may provide spinal "landmarks" for switching control modes, enhancing stability near kinematic extremes, and supporting recalibration of proprioceptive population codes. Key PointsO_LIWe simultaneously recorded many lumbar spinal neurons in two decerebrate, immobilized cats while a robot held the hindlimb at 16 static positions to test how spinal populations encode posture. C_LIO_LIMany neurons varied with a single joint angle (hip or knee), a smaller subset showed combined hip-knee modulation, and a distinct subset was active only at one specific endpoint posture. C_LIO_LIPopulation analyses revealed a low-dimensional structure: the first two principal components tracked knee and hip angles, while a third captured a posture-specific pattern aligned with single-endpoint neurons. C_LIO_LIDecoders trained on ensemble activity reconstructed joint angles and the limbs endpoint, indicating that spinal interneuronal populations contain sufficient information for whole-limb kinematics. C_LIO_LIThese findings are consistent with a hierarchical organization whereby joint-based representations within spinal-interneuron populations could contribute to the emergence of limb-centered representations in the ascending proprioceptive pathways. C_LI

neuroscience↗

bioRxiv2025

VPS13C/PARK23 initiates lipid transfer and membrane remodeling for efficient lysosomal repair

Perturbations in lysosome integrity are tightly linked to neurological disorders and ageing, but the underlying pathogenic mechanisms are incompletely understood. Using an unbiased proteomic approach, we here identified the bridge-like lipid transport protein VPS13C/PARK23 as a key component of a global early response pathway to lysosome damage. VPS13C readily binds lysosomes under mechanical or osmotic tension in anticipation of membrane lesions. The latter trigger a conformational change in the proteins C-terminus, involving its ATG2C domain acting as sensor of damage-induced lipid packing defects. We show that ER-lysosome contacts formed by VPS13C provide critical binding platforms for OSBP/ORPs to enable efficient ER wrapping of damaged lysosomes. A chemical approach to assess directional ER-to-lysosome lipid transport revealed that VPS13C is essential for large-scale lipid delivery to acutely damaged lysosomes to facilitate their repair. Our findings offer new mechanistic insights into how loss-of-function mutations in VPS13C may enhance the risk of Parkinsons disease.

cell biology↗

bioRxiv2025

Lipid Landscape of human cells

Eukaryotic cells synthesise thousands of lipid species, yet the principles that organise them across compartments remain unclear. Here we introduce PAP-SL, parallel (immuno)affinity purification coupled to shotgun lipidomics, to map [~]300 lipid species across six compartments of human cells and uncover general rules of lipid organisation. Correlation analyses of stoichiometric lipid compositions resolved archetypal distribution trajectories. Biosynthetic origin set the baseline: mitochondrial and lysosomal pathways generated confined pools, whereas the ER acted as a dispatch hub shaping downstream membrane territories. The ER established the saturated plasma membrane through transfer of phosphatidylserine, sphingolipids, and cholesterol, together with species-level selection of more saturated glycerophospholipids across diverse headgroups, while less-saturated species moved unselectively into mitochondria. The ER also channelled ether-linked glycerophospholipids to lysosomes, forming a territory dominated by ether phosphatidylcholine that collapsed under ethanolamine-driven metabolic rewiring. PAP-SL defines a framework to resolve lipid organisation and its metabolic plasticity in health and disease.

systems biology↗

bioRxiv2025

Human aged astrocytes induce neurotoxicity in response to inflammatory stimuli

Astrocytes play a critical role in neuroinflammation and the pathogenesis of neurodegenerative diseases. Here we found that human induced pluripotent stem cell (iPSC)-derived astrocytes responded differently to inflammatory triggers compared to rodent astrocytes, showing increased neurotoxicity when exposed to TNF- and IFN-{gamma}. Furthermore, astrocytes with senescent features showed even higher levels of neurotoxicity in the presence of TNF- and IFN-{gamma}, suggesting a potential link between aging and neurodegenerative diseases. It was also demonstrated that LPS-activated neuron/astrocyte/microglia tri-culture produced TNF-, leading to neurotoxicity in the tri-culture when IFN-{gamma} was present. Through compound screening, we identified Janus kinase inhibitors capable of preventing neurotoxicity in astrocytes induced by TNF- and IFN-{gamma}, demonstrating the potential use of neurotoxic astrocytes as a platform for drug screening. These results provide insight into the complex relationship between aging, inflammation, and neurodegenerative diseases, emphasizing the potential of targeting astrocytes as a novel therapeutic approach for addressing neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Mutation or deletion of the Avr6 avirulence effector gene of Fulvia fulva leads to breakdown of the Cf-6 leaf mold resistance locus in tomato

Genetic resistance mediated by Cf cell-surface receptors is a cornerstone of tomato breeding against leaf mold disease caused by the fungal pathogen Fulvia fulva. After widespread deployment of the Cf-9 resistance locus, breeders increasingly relied on Cf-6, yet Cf-6-mediated resistance has already been overcome in multiple regions. The molecular basis of this breakdown, and the identity of the matching avirulence (Avr) effector, have remained unresolved. Here, we use comparative genomics and functional genetics to identify the F. fulva effector Avr6 as the previously described apoplastic protein Ecp5. Sequencing of Cf-6-breaking strains revealed either deletion of the Ecp5 locus or non-synonymous mutations in its coding sequence. Using transient expression, targeted gene knockout, and complementation assays, we show that Ecp5 is both necessary and sufficient for Cf-6-mediated recognition and defence activation. We then use Avr6-triggered cell death as a phenotypic marker in a bulked segregant analysis combined with Comparative Subsequence Sets analysis (CoSSa) to map Cf-6 to a [~]2 Mb interval on the short arm of chromosome 12 that overlaps the previously described Cf-Ecp5.12 locus. Sequencing of Avr6 in a broad strain collection reveals a predominantly conserved allele under apparent purifying selection, with recent independent loss-of-function variants in Europe and South America that confer virulence on Cf-6 plants. Together, these findings establish the Avr6-Cf-6 gene-for-gene pair, explain the erosion of Cf-6-mediated resistance, and illustrate how effector loss or mutation provides a rapid route for F. fulva adaptation, with important implications for designing more durable resistance strategies against tomato leaf mold.

microbiology↗

bioRxiv2025

Role of N-glycosylation as a determinant of ATG9A conformations and activity

In this study we investigate the effects of glycosylation at position N99 on the structural dynamics and lipid scrambling activity of ATG9A, a key autophagy protein, using microsecond all-atom molecular dynamics (MD) simulations. ATG9A is an integral membrane protein involved in autophagosome biogenesis, and glycosylation at N99 is known to play a critical, yet poorly understood role in its function. The MD simulations revealed that the hydrophilic central cavity of ATG9A supports lipid reorientation and partial transbilayer movements, consistent with its lipid scrambling activity observed experimentally. N-glycosylation at N99 was found to enhance cooperative interactions between protomers, facilitating lipid insertion and traversal within the central cavity. These findings align with the proposed mechanism of ATG9A role in lipid redistribution across the phagophore membrane during autophagy. However, mutagenesis experiments that abolish N-glycosylation in ATG9A (ATG9AN99A and ATG9AN99D mutants) did not show a significant change in autophagy flux, suggesting that further experimental approaches, such as lipid scramblase assays, are needed to pinpoint the function of glycosylation. In this study we also observed an asymmetric protomer conformations in ATG9A, contrasting with symmetric structures obtained from cryo-EM, suggesting that the structural heterogeneity of the protein could be further explored in cryo-EM datasets. Overall, the study highlights the importance of incorporating glycosylation in computational studies of membrane proteins and offers valuable insights into the molecular mechanisms of lipid transport in autophagy, with potential implications for other lipid scramblases and flippases.

biophysics↗

bioRxiv2024

Lipidomic Profiling Reveals Shared and Distinct Pathological Signatures in Sporadic Parkinson's Disease and GBA Mutation Carriers: Implications for Disease Mechanisms

Parkinsons Disease (PD) is a neurodegenerative disorder characterised by the deposition of protein-lipid inclusions, containing alpha-synuclein, neuronal cell loss and disruptions in lipid metabolism such as those associated with GBA mutations. GBA mutations are together an important genetic risk factor for PD and are associated with a decrease in glucocerebrosidase, a lysosomal glycoprotein encoded by GBA, increase in alpha-synuclein and changes in sphingolipids levels and composition. However, the extent of lipid metabolism disruptions associated to PD and their contributions to disease progression remain unclear. In this study, we used a combination of biochemical and lipidomic analyses of amygdala from healthy controls (HC) and people with sporadic (sPD) or GBA-associated PD (PD-GBA) to investigate the correlation between alpha-synuclein, glucocerebrosidase and lipids. We found extensive metabolic remodelling of brain lipids, including increased free cholesterol, diacylglycerides, sphingolipids and specific glycerophospholipids in amygdala from people with sPD and disease duration above 30 years (sPD>30y) and from people with PD carriers of a GBA risk mutation (PD-GBArisk) relative to HC. The levels of free cholesterol, diacylglycerides, sphingolipids and specific glycerophospholipids all correlated positively with pathological S and negatively with GCase activity. In contrast, the levels of phosphatidylethanolamine and cardiolipin only correlated positively with GCase activity. Moreover, we observed changes in the distribution of species for sphingolipids and glycerophospholipids in opposite directions for two categories of PD cases. We found a shift from short to long sphingomyelin and ceramide and from long to short phosphatidylserine and phosphatidylethanolamine in sPD>30y and PD-GBArisk cases and the opposite in sPD<10y and PD-GBAsevere cases. The relative proportion of lipid species affected in these samples all correlated with glucocerebrosidase activity and pathological alpha-synuclein levels. Together, these findings highlight the correlation between glucocerebrosidase, pathological alpha-synuclein and lipid levels in PD. Moreover, the identified opposite changes in lipid distribution for two categories of people with sPD and PD-GBA underscore the importance of patient stratification in clinical trials aiming at reverting PD-related lipid changes.

neuroscience↗

bioRxiv2024

First versatile reverse genetics system for feline coronavirus

Feline infectious peritonitis (FIP) is a fatal disease caused by feline coronavirus (FCoV). Although multiple gene mutations in FCoV likely account for FIP pathogenesis, molecular studies for FCoV have been limited due to the lack of a suitable reverse genetics system. In the present study, we established a rapid PCR-based system to generate recombinant FCoV using the circular polymerase extension reaction (CPER) method for both serotype 1 and 2 viruses. Recombinant FCoV was successfully rescued at sufficient titers to propagate the progeny viruses with high sequence accuracy. The growth kinetics of recombinant FCoV were comparable to those of the parental viruses. We successfully generated recombinants harboring spike gene from a different FCoV strain or a reporter HiBiT-tag using the CPER method. The chimeric virus demonstrated similar characteristics with the parental virus of S gene. The reporter tag stably expressed after five serial passages in the susceptible cells, and the reporter virus could be applied to evaluate the sensitivity of antiviral inhibitors using the luciferase assay system to detect HiBiT tag. Taken together, our versatile reverse genetics system for FCoV shown herein is a robust tool to characterize viral genes even without virus isolation and to investigate the molecular mechanisms of the proliferation and pathogenicity of FCoV. ImportanceFeline infectious peritonitis is a highly fatal disease in cats caused by feline coronavirus variants that can infect systemically. Because of a lack of versatile toolbox of manipulating the feline coronavirus genome, an efficient method is urgently needed for studying virus proteins responsible for the severe disease. Herein, we established a rapid reverse genetics system for the virus and demonstrated the capability of the recombinant viruses to be introduced desired modifications or reporter genes without any negative impacts on virus characteristics in cell culture. Recombinant viruses are also useful to evaluate antiviral efficacy. Overall, our system can be a promising tool to reveal the molecular mechanisms of viral life cycle of feline coronavirus and disease progression of feline infectious peritonitis.

microbiology↗