Biology subjects

Huang, H.

Publications and source records attributed to Huang, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

STEP-PTMs: Sequential TMT-based Enrichment and Profiling of Post-Translational Modifications

Comprehensive characterization of protein abundance and multiple post-translational modifications (PTMs) from the same biological samples is essential for understanding cellular regulation and PTM crosstalk but remains analytically challenging. Here, we present STEP-PTM (Sequential Tag-based Enrichment of Post-Translational Modifications), a modular TMT-multiplexed workflow that enables integrated quantitative analysis of the proteome, metabolome and multiple PTM classes from a single peptide preparation. Proteins are digested, isobarically labeled using tandem mass tags (TMT), and combined into a single multiplexed peptide pool prior to sequential PTM enrichment, thereby minimizing technical variability, reducing sample requirements and facilitating direct quantitative integration across datasets. STEP-PTM supports flexible sequential enrichment of phosphopeptides, peptides containing free and reversibly modified cysteines, sialylated N-linked glycopeptides, lysine-acetylated peptides and S-palmitoylated peptides, while preserving non-modified peptides for global proteome analysis. PTM-specific database searches further improve identification confidence and quantitative accuracy, and the modular workflow can readily be adapted by incorporating or omitting enrichment modules according to the biological question. Application of STEP-PTM to TMT16-plex cerebral brain organoids enabled the quantification of 10,413 proteins, 2,969 metabolites, 19,655 phosphopeptides, 28,876 peptides containing reversibly modified cysteines, 9,723 peptides containing free cysteines, 1,716 intact sialylated N-linked glycopeptides and 771 lysine-acetylated peptides from the same biological samples. We further demonstrate the applicability of the workflow to multiple mouse tissues, highlighting its broad utility for integrated systems-level characterization of protein expression and PTM regulation across diverse biological models.

biochemistry↗

bioRxiv2026

Inhibition of the Notch signaling pathway promotes AQP2 plasma membrane accumulation in renal epithelial cells by depolymerizing actin and reducing endocytosis

The Notch signaling pathway plays a central role in development and cell fate determination. Its function depends on tightly regulated intracellular trafficking of the Notch receptor and the Notch intracellular domain (NICD) after cleavage by {gamma}-secretase. Notch signaling is essential for principal cell differentiation within the renal collecting duct and for proximal-distal patterning during kidney development. Notch activity has also been shown to influence the trafficking of several membrane proteins, including nephrin in kidney cells and monocarboxylate transporter 1 in brain endothelial cells. Aquaporin-2 (AQP2) is the key vasopressin-regulated water channel in the collecting duct, and proper AQP2 trafficking and recycling are required for physiologically appropriate urine concentration. To determine whether and, if so, how Notch signaling modulates AQP2 trafficking, we performed studies using LLCPK1 renal epithelial cells stably expressing AQP2 (LLCPK1-AQP2). Exposing cells to 35 M DAPT (which inhibits y-secretase, preventing cleavage and activation of Notch receptor signaling) for 30 min significantly increased AQP2 membrane accumulation in LLCPK1-AQP2 cells as revealed by immunofluorescence staining. Using a rhodamine-transferrin internalization assay, we found that DAPT reduced clathrin-mediated endocytosis by 60%. This blockade increases AQP2 membrane accumulation by preventing the reinternalization of AQP2 that is delivered to the plasma membrane by exocytosis during its constitutive recycling pathway. Using an F-actin polymerization assay, we then found that Notch inhibition decreases F-actin polymerization by de-activating the small GTPase RhoA, using GSTRBD, a substrate that binds to active RhoA, as seen by western blotting using phospho-specific antibodies. Because actin polymerization is required for AQP2 endocytosis, RhoA inhibition by DAPT would result in the decreased internalization of AQP2 that we observed by immunofluorescence. While the mechanism by which DAPT inhibits RhoA activity remains to be determined, our study shows that AQP2 trafficking is regulated by the Notch signaling pathway in vitro and suggests that modulation of Notch signaling may represent a novel strategy to address water balance disorders that involve defects in the AQP2 trafficking process.

cell biology↗

bioRxiv2026

Extracellular vesicles drive cross-genus mycovirus transmission and suppress two fungal diseases

Mycoviruses are typically transmitted vertically through fungal reproduction or horizontally via hyphal anastomosis, but identical viruses in phylogenetically divergent fungi hint at unknown inter-species transmission mechanisms. Here, we identify fungal extracellular vesicles (EVs) as mediators of cross-genus mycovirus transmission. Using the hypovirulent Botrytis cinerea strain IBc-374 (harboring 16 mycoviruses) as a donor, we show that up to 13 mycoviruses are horizontally transmitted to Sclerotinia sclerotiorum during dual culture or plant co-inoculation, even though these two fungi belong to different genera and are generally considered incapable of hyphal anastomosis. Electron microscopy reveals abundant vesicle structures in IBc-374 hyphae, and nanoparticle tracking analysis showed that the strain secretes >11-fold more EVs than a virus-free strain. RT-PCR detects genomic RNAs of 7 mycoviruses in purified EVs, and the full-length viral genome in EVs was further validated with BcHV5 as example by fluorescence in situ hybridization and RT-PCR. Incubation of protoplast-derived germlings of S. sclerotiorum or B. cinerea with IBc-374 EVs leads to infection by 4-6 donor mycoviruses, demonstrating EV-mediated cross-genus transmission. Injection of mycovirus-carrying EVs into tobacco leaves followed by fungal inoculation also transmits two hypoviruses to both species. Application of IBc-374 hyphal fragment suspension significantly reduces lesion sizes caused by both pathogens on plants, and rescued two pathogens carrying multiple mycoviruses exhibit hypovirulence and impaired growth. Our findings reveal EVs as a cell-free vector that bypasses vegetative incompatibility, providing a mechanistic basis for cross-species viral spread and opening avenues for EV-based virus cocktails to control multiple fungal diseases. IN BRIEFWu et al. discover that fungal extracellular vesicles (EVs) can package and transmit multiple mycoviruses across genera from Botrytis cinerea to Sclerotinia sclerotiorum. EV-mediated delivery overcomes vegetative incompatibility barriers and reduces disease caused by both fungal pathogens, offering a cell-free strategy for mycovirus-based biological control.

microbiology↗

bioRxiv2026

IOBRpy enables agentic multi-omics decoding of anti-tumor immunity

Decoding the tumor immunity is pivotal for cancer immunotherapy, yet transcriptomic pipelines remain bottlenecked by fragmented tools and biased interpretations. Here we present IOBRpy, a Python toolkit driven by an innovative AI dual-agent layer for automated, highly standardized immuno-oncology workflows. Moving beyond conventional expression profiling, IOBRpy enables agentic multi-omics decoding. From raw FASTQ or TPM matrices, it seamlessly integrates upstream quality control, transcript quantification, and downstream TME parsing, encompassing signature scoring, ligand-receptor crosstalk, and cellular deconvolution. Crucially, IOBRpy expands data dimensions by incorporating complementary immunogenomic layers, empowering concurrent high-resolution SpecHLA typing and TRUST4-based TCR/BCR repertoire reconstruction from sequencing data. Deployed across two large-scale cohorts (IMvigor210 and OAKPOPLAR), IOBRpy successfully captured multi-dimensional prognostic insights. While broad HLA-I heterozygosity showed negligible impact, it precisely unmasked treatment-stratified, allele-specific survival associations (e.g., HLA-A*01 and HLA-DPA1*02) tightly coupled with distinct immunosuppressive ligand-receptor networks (such as HMGB1-THBD and EFNB2-EPHB6) and dynamic TCR clonal diversity shifts. Empowering this lifecycle is a paired agent framework: a workflow agent automatically audits project states to execute validated, path-aware commands, while a result agent evaluates tool provenance, handles method-aware adaptive visualizations, and organizes findings into evidence-constrained biological hypotheses. Collectively, IOBRpy provides a reproducible, scalable, and intelligence-augmented Python gateway to transform raw sequencing data into multi-omic, interpretation-ready discoveries for cohort-scale precision immunotherapy (https://iobr.github.io/IOBRpy/).

bioinformatics↗

bioRxiv2026

Reconstructing sequence-grammar trajectories enables interpretable and tunable cis- regulatory element design

Designing synthetic cis-regulatory elements (CREs) with cell-type-specific activity remains challenging, and optimization is usually treated as a black box, obscuring how regulatory grammar emerges and why design trajectories fail. Here, we present GO-CRE (Guided Optimization of Cis-Regulatory Elements), which combines efficient sequence generation, predictor-guided reinforcement learning, and trajectory-level interpretation. GO-CRE reconstructs iterative sequence changes in a shared sequence-grammar landscape and identifies coordinated update programs corresponding to search, commitment, and optimization. Productive trajectories in HepG2 and K562 progressively acquired cell-type-associated grammar, whereas SK-N-SH trajectories remained confined to local basins. In HepG2, trajectory analysis revealed a low-complexity polyG trap; introducing a polyG penalty redirected optimization toward HNF/FOXA-associated features. Final designs retained sequence diversity while converging on cell-type-associated motif patterns. Lentiviral MPRA validated cell-type-specific activity in K562 and HepG2 and showed higher average activity of HepG2 designs than endogenous CREs. Together, these findings establish sequence-grammar trajectory reconstruction as a basis for interpretable and tunable synthetic CRE design.

genomics↗

bioRxiv2026

NK-like and networked CD8+ T cell immunity mediates exceptional HIV control

Durable treatment-free remission remains a defining goal for people living with HIV (PLWH). Studies of spontaneous elite controllers have revealed that functional CD8 T cells targeting structurally networked viral epitopes can mediate durable viral suppression1,2. However, rare reservoir-defined exceptional controllers within the spectrum of elite control3-5, characterized by the absence of intact provirus or proviruses confined to transcriptionally repressed genomic regions6, provide a unique opportunity to define mechanisms of cure-like immunity. Here, we integrate functional epitope mapping, single-cell transcriptomics, and infected cell elimination assays to identify networked HIV epitope targeting and a natural killer (NK)-like killer-cell immunoglobulin-like receptor (KIR) CD8 T cell subset as key features of exceptional control. This NK-like subset was selectively enriched within HIV-specific, but not CMV-specific, CD8 T cells from controllers, and was transcriptionally similar to highly cytotoxic subsets within the broader KIR+ CD8+ T cell compartment. Flow cytometry revealed increased frequencies of KIR CD8 T cells in exceptional controllers relative to antiretroviral therapy (ART)-suppressed individuals, and unexpectedly, enrichment of dual KIR+ NKG2A+ CD8 T cells. Functional depletion of KIR CD8 T cells significantly impaired the elimination of autologous HIV-infected CD4 T cells, despite preserved recognition by proliferative networked HIV-specific CD8 T cells. These findings thereby identify an NK-like KIR CD8 T cell state as a previously unrecognized component of exceptional HIV immunity that complements networked epitope targeting, providing a novel framework for immunotherapeutic HIV cure strategies.

immunology↗

bioRxiv2026

P-DOpE probes reveal local amplification of phasic noradrenergic release in the hippocampus

Fiber photometry (FP) has become a tool of choice for in vivo monitoring of genetically encoded biosensors. The ability to record and optogenetically manipulate circuits through the same fiber stub is powerful, but limited, as biosensors typically do not sample membrane voltage, leaving the experimenter blind to the direct effects of opsin photoactivation. Here we developed the Photometry Device with Optogenetics and Electrophysiology (P-DOpE) probe, fabricated via a new convergence taper-break (CTB) method that integrates industry-standard silica optical waveguides with low-impedance metal electrodes that can be arranged in experimenter-defined configurations. We demonstrate that chronically implanted P-DOpE probes provide months-long recordings of local field potential, single unit recording, and fiber photometry, with parallel optogenetic circuit perturbation. Conducting fiber photometry with same-site optogenetic stimulation, we identified a robust fluorescence signal that scaled with network activity and survived biosensor antagonism. As this confound could not be eliminated with standard isosbestic controls, we propose a simple correction strategy. As a first application, we used the probe to test a proposed mechanism for focal modulation of noradrenergic signaling in and by cortical circuits receiving afferents from the locus coeruleus. We found that increasing spiking activity in CA1 amplifies noradrenergic signaling evoked by contextual arousal by [~]50%, but does not induce norepinephrine release in the absence of a phasic trigger - thus supporting the central prediction of the glutamate amplifies noradrenergic effects (GANE) hypothesis. The P-DOpE probe thus enables optogenetic manipulation and multimodal readout in a configurable low-cost, scalable, and robust format.

neuroscience↗

bioRxiv2026

A Selective Multivalent NET-Associated Chromatin Neutralizer Resolves Infection-Associated Inflammation in Severe Sepsis

Targeting the overwhelming inflammation driven by neutrophil extracellular traps (NETs) during infection provides an opportunity to manage severe sepsis. This potential needs to be realized by exploring selective NET-neutralization materials, which remains a challenge. Herein, we report a multivalent macromolecular strategy that targets NET-associated DNA-histone chromatin complexes while preserving antibacterial activity of aminoglycoside. We identify 8-arm PEG-conjugated netilmicin (8-arm Netil) as a lead NETs-neutralizer from a library of multivalent aminoglycoside-displayed materials. When compared with 2- and 4-arm counterparts, 8-arm Netil exhibits potent antibacterial activity and high-affinity binding to DNA-histone chromatin complexes through stable multivalent noncovalent interactions, thereby suppressing NET-induced TLR4/TLR9 activation and macrophage inflammatory responses. In severe septic mice, intravenously administered 8-arm Netil preferentially accumulates in inflamed tissues, leading to improved survival protection, owing to the reduction of bacterial dissemination, NET accumulation, systemic cytokine production, and multiple-organ injury. These findings establish NET-associated DNA-histone chromatin complexes as actionable extracellular targets and demonstrate multivalent chromatin targeting as a rational material design strategy for selective NET neutralization and inflammation control in severe sepsis.

bioengineering↗

bioRxiv2026

Population structure of the rice blast fungus Pyricularia oryzae in the context of elevated host heterogeneity

In a context where pathogen emergence threatens global food security, crop resistance to pathogens is crucial for preventing and controlling epidemics. Agrosystems with high intraspecific cultivated diversity are expected to better mitigate infectious diseases compared with homogeneous ones. However, the long-term impact of cultivated genotypic heterogeneity on pathogen populations is still under debate. The 1,300-year-old traditional agrosystem of the Yuanyang Terraces (YYT) in China exhibits an outstanding level of rice diversity. The rice blast fungus Pyricularia oryzae has been recorded in the area, making this area ideal for studying the impact of long term heterogeneous cultivation on plant-pathogen coevolution. In this study, we analysed 94 P. oryzae genomes from the YYT and compared them to 198 genomes representative of the worldwide diversity. We report elevated levels of genomic diversity of P. oryzae in the YYT. Whereas the worldwide diversity of this species is organized in four lineages, we detected seven lineages within the YYT, four of which are restricted to this area. The sampling dates of the YYT isolates (2009 to 2017) provided sufficient temporal signal to date nodes of the phylogenetic tree of isolates. Endemic lineages appeared to have arisen several centuries ago but later than the origin of the YYT themselves. We also detected recent introductions of worldwide lineages. Linkage disequilibrium analyses and in vitro cross experiments suggest that P. oryzae reproduces asexually in the YYT. These results suggest that long-term intraspecific crop diversity in the YYT has promoted the emergence and maintenance of a highly diverse, locally adapted pathogen population.

evolutionary biology↗

bioRxiv2026

RNAquarium: an archive-scale atlas of zebrafish gene expression coupled with pan-taxonomic profiling reveals diverse viral drivers of transcriptomic states

Zebrafish RNA-seq studies span diverse developmental, physiological, and disease contexts, yet most analyses remain confined to individual experiments and disregard the non-zebrafish component of the data. We present RNAquarium, a scalable framework for joint transcriptomic and metatranscriptomic analysis of RNA-seq data and apply it to all publicly available zebrafish RNA-seq datasets in the Sequence Read Archive. This resource captures transcriptomic structure across development and tissues, reveals diverse microbial and viral associations, and identifies previously undescribed zebrafish viruses including a close relative of human influenza B virus linked to distinct host transcriptional states. We further demonstrate that archive-scale transcriptomes can support foundation-model training and prediction of infection-associated transcriptomic signatures. RNAquarium provides an open framework and interactive portal for exploring the breadth of zebrafish gene expression patterns and associated taxa profiled across a large re-search community and establishes a generalizable strategy for integrating transcriptomic and metatranscriptomic analyses across the diversity of life represented in public sequencing archives.

genomics↗

bioRxiv2026

Distinguishing Photoacoustic and Photothermal Neuron Stimulation Through Quantitative Mapping Spatiotemporal Field Evolution

Neuromodulation is a rapidly advancing strategy for modulating brain function and treating neurological disorders, yet the mechanisms of optical neural stimulation remain incompletely understood. A central challenge is that photoacoustic (PA) and photothermal (PT) effects are typically generated simultaneously and evolve on overlapping spatial and temporal scales, making their contributions to neuronal activation difficult to distinguish. Here, we overcome this limitation by integrating two carbon-based emitters with a spatial-offset pump-probe imaging platform to distinguish PA and PT neuromodulation through direct mapping of spatiotemporal field evolution. The two emitters produce nearly identical thermal fields while exhibiting a 26-fold difference in acoustic output, enabling decoupled comparison of thermal and acoustic contributions. To directly characterize the physical fields, we establish a spatial-offset pump-probe imaging system capable of visualizing both temperature and pressure evolution, confirming matched thermal profiles between the two emitters. Neuronal stimulation experiments further show that neurons are markedly more responsive to PA stimulation than to PT stimulation. Beyond resolving a longstanding mechanistic question, this work demonstrates the enhanced efficiency of PA stimulation and provides general guidance for designing high-performance optical neural interfaces.

neuroscience↗

bioRxiv2026

Predicting Autopsy-Confirmed Neuropathology across Clinical, Neuroimaging, and CSF Biomarkers using Machine Learning

Accurate in vivo prediction of neuropathology is critical for advancing diagnosis and treatment of Alzheimers disease and related dementias (ADRDs). As many individuals with ADRDs have mixed pathologies ({beta}-amyloid, pathologic tau, cerebrovascular disease, vascular brain injury, pathologic TDP-43, hippocampal sclerosis, Lewy bodies), there is interest in determining how accurately we can infer these pathologic changes from clinical data, biofluid assays (e.g., CSF), and neuroimaging. Here we evaluated automated machine learning models trained on data curated by the AD Sequencing Project Phenotype Harmonization Consortium (N=7,894 individuals), to predict 26 autopsy-confirmed neuropathological outcomes. Predictors included in vivo clinical and cognitive composite scores, brain measures from 3D structural MRI and diffusion tensor imaging, image-derived measures of white matter hyperintensities (WMH), and CSF biomarkers. Predictive models were trained using ensemble learning with stratified cross-validation. We assessed performance using Spearmans rank correlation and Matthews correlation coefficient, to accommodate co-occurring pathologic changes. The added value of neuroimaging and CSF versus clinical features alone was quantified. Braak stage was among the most consistently predicted outcomes. CSF biomarkers best predicted {beta}-amyloid and tau pathology, but diffusion MRI metrics best captured vascular brain injury and white matter injury, and outperformed clinical and cognitive measures and anatomical MRI in predicting Lewy body disease. Anatomical measures from structural MRI outperformed standard clinical assessments in assessing neurodegeneration and hippocampal sclerosis, and WMH complemented cognitive measures in predicting TDP-43 pathology. These results establish a baseline for comparing modalities for inferring neuropathology.

neuroscience↗

bioRxiv2026

Monoclonal anti-dsRNA antibody-based metagenomics (MADAM) reveal Pyricularia oryzae mycovirome

This study introduces MADAM (Monoclonal Anti-dsRNA Antibody-Based Metagenomics), a novel approach that integrates multiple technical modules previously used independently in other protocols. MADAM combines monoclonal antibody-mediated double-stranded RNA (dsRNA) enrichment, sequence-independent RT-PCR, and Oxford Nanopore Technologies (ONT) sequencing. Applied to Pyricularia oryzae, the causal agent of rice blast disease, MADAM enabled the comprehensive characterization of mycovirus genomes from four fungal isolates collected in Yunnan, China. The approach achieved high viral read recovery rates (46.9-72.7%) and identified 18 P. oryzae-associated RNA viruses spanning seven families: Botourmiaviridae, Deltaormycoviridae, Mymonaviridae, Partitiviridae, Polymycoviridae, Splipalmiviridae, and Ambiguiviridae. Seventeen nearly complete to complete viral genomes (1,226-6,085 nucleotides) were recovered, with sequence coverage ranging from 88% to 100%. Co-infections were detected in three of the four isolates, with notable discoveries including the first deltaormycovirus reported in P. oryzae, a putative novel member of Botourmiaviridae, and an additional genomic segment of a polymycovirus. MADAM successfully detected positive-sense, negative-sense ssRNA, and dsRNA viruses, demonstrating its broad applicability. By uncovering novel viruses and resolving complex co-infections, this method proves invaluable for fungal virology, with potential applications in diagnostics, surveillance, and biological control. Ultimately, MADAM advances our understanding of fungal viral diversity and paves the way for further exploration of mycovirus ecology and evolution.

microbiology↗

bioRxiv2026

Gene-Modulated Network Diffusion for Improved Modeling of Amyloid-β Spread in Alzheimer's Disease

Understanding the pathogenesis of amyloid-{beta} pathology in Alzheimers Disease (AD) proves to be a challenge. In this work, we expand upon the application of network diffusion models (NDM) to study pathophysiological spread of amyloid-{beta} throughout white matter structural brain networks. We found that the NDM successfully recaptures subpopulation-level spatial patterns (Pearsons R=0.45-0.48, PFDR < 0.01) of amyloid-{beta} deposition in the Alzheimers Disease Neuroimaging Cohort at a regional level, but with drawbacks in mechanism interpretability. We then moved to an extended NDM framework (eNDM), including a protein synthesis term to better reflect the role of amyloid-{beta} metabolism, as well as including regional vulnerability using spatial transcriptomics from the Allen Human Brain Atlas to modulate the region-level rate parameters of the synthesis term. The novel gene eNDMs exhibited significant performance increases in Pearsons correlation (Steigers Z, PFDR < 0.10) over baseline NDM performance in mild cognitive impairment and AD groups using APOE, SORL1, and FGL2 for gene modulation. The results were robust and replicable when testing on an external cohort of the Alzheimers Disease Sequencing Project. The study thus demonstrates the importance of regional genetic vulnerability, in conjunction with network diffusion mechanisms, in improving the modelling and prediction of amyloid-{beta} pathophysiological spread.

bioinformatics↗

bioRxiv2026

A layered standards framework for integrating single-cell and spatial omics data into brain cell atlases

The BRAIN Initiative Cell Atlas Network (BICAN) is generating large-scale multimodal datasets to profile cell types in the human, non-human primate, and mouse brain. The diversity of single-cell and spatial transcriptomic and epigenomic assays, combined with varied experimental contexts, multiple data-generating laboratories and distributed infrastructure, poses substantial challenges for data integration and reuse in BICAN. To address this, we implemented a standards framework that enables layered integration of these data into knowledge-ready products for interoperable brain cell atlases. This framework organizes data based on three progressively structured layers. First, we introduced an assay-agnostic modeling layer that unifies the representation of single-cell and spatial omics data using a common set of biological entities and processes assessed by diverse experimental techniques. Second, we implemented harmonized metadata standards that capture key experimental features linked to biospecimen provenance across heterogeneous tissue sources, species, and preparations, supporting integration and validation while minimizing burden on data contributors. Third, we present an extensible representation for data-driven cell type taxonomies that integrates molecular data with annotations, ontology mappings, and evidence. Together, these contributions represent an end-to-end framework that transforms heterogeneous datasets into structured, interoperable resources that support broad community reuse via mapping algorithms, annotation systems, and visualization platforms. This approach links biospecimen provenance with cell-level outputs and embeds these in a standardized taxonomy format, enabling downstream applications such as cross-dataset integration, reference mapping, and knowledge-driven analysis. More broadly, our work demonstrates a generalizable strategy for enabling an efficient data-to-knowledge pipeline in a large-scale consortium setting.

genomics↗

bioRxiv2026

YIPPEE/YPEL5 regulates circadian period by modulating PER ubiquitination and stability

Circadian clocks rely on evolutionarily conserved transcriptional-translational feedback loops to align physiology and behavior with the 24-hour day-night cycle. Post-translational modifications, especially ubiquitination, critically control core clock protein stability and circadian pace. In both fruit flies and mammals, the abundance of key pacemaker protein PERIOD (PER/PER2) must be tightly regulated to sustain circadian rhythms. However, the canonical phosphorylation-dependent pathway cannot fully account for turnover of PER in Drosophila. Here we identify Yippee as a critical regulator of PER level through a genetic screen of downregulating ubiquitination pathways. Knockdown of Yippee in circadian pacemaker neurons significantly lengthens the circadian period by [~]2 hours and elevates PER levels. Indeed, YIPPEE physically interacts with PER in fly head. Mechanistically, its mammalian homolog YPEL5 binds PER2, promotes K63-linked polyubiquitination and proteasomal degradation of PER2 independently of FASP-region phosphorylation. Lastly, downregulating YPEL5/Ypel5 prolongs circadian periods in human U2OS cells and mice. Our findings reveal an evolutionarily conserved mechanism in which Yippee/YPEL5 regulates circadian rhythms by mediating ubiquitin-dependent degradation of PER/PER2.

molecular biology↗

bioRxiv2026

Plasmid-plasmid interactions reshape extracellular vesicle cargo and gene transfer potential

Plasmids are key drivers of horizontal gene transfer, yet their dissemination is not limited to conjugation. Extracellular vesicles (EVs) can transport plasmid DNA, but the factors governing plasmid incorporation into EVs remain poorly understood. Here, we tested whether principles of conjugative plasmid transfer, including plasmid mobility type and plasmid-plasmid interactions, extend to EV-mediated export. Using a conjugative plasmid (pKJK5) and a mobilizable plasmid (RSF1010) in two Gram-negative hosts, we quantified plasmid incorporation into EVs under single- and dual-plasmid conditions. When present individually, the conjugative plasmid was preferentially incorporated into EVs, exceeding RSF1010 by 10-23-fold despite its lower intracellular abundance. Under co-residence, this pattern reversed: RSF1010 became enriched by 13-39-fold, while pKJK5 was reduced by 2-7-fold. Consequently, EV-associated plasmid cargo shifted to RSF1010 dominance, deviating strongly from the expected 10-fold higher pKJK5 cargo if a stochastic model based on intracellular abundance and single-plasmid conditions were applicable. We propose that mobilizable plasmids under coexistence exploit conjugative plasmid transfer machinery to access membrane-associated sites, increasing their likelihood of incorporation into EVs. Our findings demonstrate that plasmid-plasmid interactions reshape EV cargo and identify a previously unrecognized mechanism that may influence extracellular gene transfer potential in microbial communities.

microbiology↗

bioRxiv2026

Highly replicable multisite patterns of adolescent white matter maturation

The Adolescent Brain Cognitive Development (ABCD) Study is the largest U.S.-based neuroimaging initiative of adolescent brain maturation. Diffusion MRI (dMRI) provides unique insights into white matter organization, yet applying advanced processing pipelines and managing technical variability across scanning environments remains challenging at scale. To address these issues, we present ABCD-BIDS Community Collection (ABCC) release 3.1.0, including a curated resource of more than 24,000 fully processed ABCD dMRI datasets. ABCC provides fully processed images, nuanced image quality metrics, advanced microstructural measures, and person-specific bundle tractography. Evaluating these rich data revealed that measures of diffusion restriction and non-Gaussianity--in particular the intracellular volume fraction from NODDI and return-to-origin probability from MAP-MRI--were highly sensitive to neurodevelopment and robust to variation in image quality. Additionally, harmonization of microstructural features markedly improved the cross-vendor generalizability of developmental effects. Together, ABCC accelerates reproducible, rigorous research on adolescent white matter development.

neuroscience↗