Biology subjects

Weng, Y.

Publications and source records attributed to Weng, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

KRT7CreER Ferrets Enable Lineage Tracing of Ductal Epithelia and Pancreatic Remodeling

Keratin 7 (KRT7) is expressed in simple and ductal epithelia and is associated with epithelial plasticity during development, injury, and disease. However, the in vivo fate and regenerative behavior of KRT7 cells remain poorly defined because lineage-tracing models are lacking in species that closely recapitulate human disease. To address this gap, we generated KRT7CreER ferrets and crossed them with ROSAmTmG Cre-reporter ferrets, with or without the CFTRG551D/G551D mutation. Following tamoxifen induction, KRT7-derived EGFP cells were identified in glandular and ductal epithelia across multiple organs. Pulse-chase lineage tracing revealed that KRT7BSND cells turn over rapidly during salivary gland development. In the pancreas, KRT7 lineage-labeled cells are present at all levels of the ductal tree under homeostatic conditions. In cystic fibrosis (CF) ferrets, KRT7-derived centroacinar cells and intercalated ductal lineages persisted and underwent marked remodeling, characterized by expansion of the SOX9 centroacinar cell pod into intercalated ducts. Although acinar cells were not lineage-labeled in the healthy pancreas, EGFP/CELA3B cells emerged in the CF pancreas and in acinar-derived organoids, consistent with induction of KRT7 during acinar-to-ductal metaplasia. These findings establish KRT7CreER ferrets as a versatile model for studying ductal epithelial lineage dynamics, pancreatic remodeling, and epithelial plasticity in both homeostatic and pathological conditions.

pathology↗

bioRxiv2026

mtDNA Activates AIM2-Mediated PANoptosis in Interstitial Macrophages to Promote Immune Checkpoint Inhibitor Pneumonitis

Immune checkpoint inhibitor pneumonitis (CIP) is a serious immune-related adverse event, yet its mechanisms remain unclear. Using a mouse model of anti-PD-1-induced CIP, we show that PD-1 blockade induces pulmonary inflammation and dysfunction, accompanied by accumulation of lung interstitial macrophages (IMs) and PANoptosis, preferentially in IMs rather than alveolar macrophages. Anti-PD-1 also causes mitochondrial stress and cytosolic mtDNA accumulation. AIM2 deficiency attenuates pulmonary inflammation, IM accumulation, and PANoptosis-associated signaling; NLRP3 or GSDMD deficiency similarly reduces inflammation and PANoptotic responses. In macrophages, TNF- plus IFN-{gamma} induces mitochondrial dysfunction and cytosolic mtDNA accumulation, and mtDNA amplifies cytokine-induced cell death and caspase-1/GSDMD activation, which is abolished by AIM2 deficiency. Thus, AIM2-mediated PANoptosis in lung IMs drives CIP, and mtDNA-associated innate immune signaling amplifies inflammatory macrophage death during CIP.

immunology↗

bioRxiv2026

Screening of Isolation and Culture Conditions of Lactic Acid Bacteria in Mongolian Horse Feces

ObjectiveThis study aimed to establish an efficient isolation, culture, and preservation system for lactic acid bacteria from Mongolian horse feces by systematically evaluating the effects of sampling methods, culture conditions, media types, and cryopreservation protocols. MethodsFecal samples were collected using rectal and natural defecation methods, and bacteria were isolated by the spread plate technique, with isolates subcultured and identified via 16S rRNA gene sequencing. The performance of five commercial media (A-E), aerobic versus anaerobic conditions, and different glycerol concentrations (10% and 30%), temperatures (-20 {degrees}C and -80 {degrees}C), and storage durations (7, 15, and 30 days) were compared. ResultsRectal sampling showed significantly higher lactic acid bacterial survival and greater species diversity (12 vs. 8). Anaerobic culture yielded substantially higher counts and diversity (707 strains, 12 species) compared to aerobic conditions (36 strains, 5 species). Medium C (M.R.S. AGAR) exhibited the best isolation performance, producing the highest number of strains (311) and species (11), with selective enrichment for both bacilli and cocci. Glycerol effectively improved strain survival during sample cryopreservation, with the optimal short-term storage ([≤]15 days) achieved at -20 {degrees}C with 30% glycerol. Functional screening of randomly selected strains from optimized conditions demonstrated promising growth, acid and bile salt tolerance, and antimicrobial activity. ConclusionRectal sampling combined with anaerobic incubation using Medium C is recommended for optimal isolation. For samples that cannot be processed immediately, short-term preservation at -20 {degrees}C with 30% glycerol prior to isolation is effective. This study provides practical technical references for the acquisition and preservation of equine intestinal lactic acid bacteria resources.

microbiology↗

bioRxiv2026

Kidney medulla macrophages maintain a free flow of urine by sensing force

Blockade by sedimentary particles, such as mineral crystals, is a continuous risk the kidney tubule faces. To prevent that, kidney resident macrophages form transepithelial protrusions and remove intratubular sedimentary particles, a behavior particularly prevailing in the medulla over the cortex. However, the molecular mechanisms underlying this characteristic behavior of medulla macrophages are incompletely understood. In this study, we identified that the medulla had higher mechanical stiffness than the cortex in steady state, which was further elevated when kidney stone formed. Increased tissue rigidity was sensed by medulla macrophages via mechanoreceptor Piezo1, which promoted macrophage protrusion formation and their ability to clean the tubules. Loss of Piezo1 expression in kidney macrophages predisposed mice to intratubular accumulation of mineral crystal in steady state and accelerated kidney stone formation during oxalate intake challenge. Signaling via Piezo1 mobilized molecules involved in cell adhesion and protrusion assembly, including Talin2 and focal adhesion kinase (FAK). Finally, we developed a first-of-its-kind cell-based therapy for the treatment of experimental nephrolithiasis by exploiting macrophage Piezo1 activity, and this strategy shows great promise for future translational research.

physiology↗

bioRxiv2026

Focal astrocyte Kir4.1 loss drives seizures, spreading depolarizations and postictal impairments

Astrocytic dysfunction is increasingly recognised as an important contributor to epileptogenesis and seizure dynamics. Kir4.1 potassium channels expressed in astrocytes play a critical role in activity-dependent extracellular potassium buffering, and their loss may impair network stability and promote pathological hyperexcitability. In epilepsy, seizures can be accompanied by spreading depolarizations (SDs), propagating waves of neuronal and glial depolarization. While seizure-associated SDs have been proposed to terminate seizures and limit seizure spread, they have also been implicated in postictal dysfunction and sudden unexpected death in epilepsy (SUDEP), and their significance in chronic epilepsy remains unclear. Here, we tested whether focal loss of astrocytic Kir4.1 in the adult hippocampus is sufficient to disrupt potassium buffering, generate spontaneous seizures, and promote seizure-associated SDs. Using astrocyte-targeted viral vector Cre recombinase in adult Kir4.1-floxed mice, we induced focal hippocampal reduction of Kir4.1 expression. This impaired activity-dependent potassium buffering, producing enhanced stimulation-evoked extracellular potassium accumulation and larger DC shifts in hippocampal slices. Chronic wireless EEG recordings demonstrated that focal astrocytic Kir4.1 loss was sufficient to induce spontaneous recurrent seizures and interictal epileptiform activity. To investigate seizure-associated SDs, we combined optogenetic stimulation with graphene-based micro-transistor recordings capable of stable full-bandwidth DC electrophysiology in awake head-fixed mice. Focal hippocampal loss of astrocytic Kir4.1 markedly increased susceptibility to evoked seizures accompanied by SDs. We used chronic wireless DC-coupled video-telemetry recordings to continuously monitor seizure and SD dynamics in freely moving mice. SDs occurred frequently during generalized seizures and were first detected in cortical channels. Seizures accompanied by SDs exhibited greater spectral power, longer duration, and prolonged postictal depression compared with seizures alone. Behaviourally, seizures accompanied by SDs were linked to postictal impairment characterised by behavioural arrest and abnormal motor behaviours. These findings highlight the utility of graphene micro-transistor arrays and chronic DC-coupled telemetry for resolving infraslow (<0.1 Hz) epileptic dynamics that are largely inaccessible using conventional electrophysiological approaches. Ground-truth DC-coupled recordings enabled identification of AC-band electrographic signatures that segregated seizures with SDs from seizures alone, raising the possibility that SD-associated seizures may be retrospectively inferred from conventional AC-coupled epilepsy datasets. We demonstrate that focal astrocytic Kir4.1 loss in the adult brain impairs potassium buffering and is sufficient to drive spontaneous seizures, supporting astrocytic potassium dysregulation as a determinant of seizure and spreading depolarization susceptibility in epilepsy. Furthermore, seizure-associated SDs are strongly linked to increased postictal impairments, supporting the concept that SDs are major determinants of pathological postictal states.

neuroscience↗

bioRxiv2026

An expansive animal gut microbiome dataset elucidates major compositional shifts across bilaterian evolution

Animal gut microbiomes provide key physiological functions and are critical for host health. They vary dramatically across the animal kingdom, and are shaped by factors including host diet, evolutionary history and environment. However, analyses of gut microbiomes spanning the entire metazoan clade are lacking, limiting our understanding of the fundamental principles governing gut microbiomes. Here we present the Gut Microbiome Tree of Life (GMToL), a curated 16S amplicon dataset of 17,366 samples from 1,553 host species across 26 host classes from 284 studies, enabling analysis of large-scale evolutionary trends. Using ancestral state reconstruction, we provide a critical baseline calculation of major compositional shifts in gut microbiomes throughout animal evolution. We show that the ancestral animal gut was likely dominated by Pseudomonadota. A major shift to Bacteroidota occurred during the evolution of tetrapods, followed by the emergence of Bacillota-dominated guts in mammals and birds. We identify conserved core gut microbes and demonstrate how GMToL can be leveraged to contextualize the evolutionary history of specific microbial taxa. Ultimately, this framework enables the predictive mapping of microbial symbionts across uncharacterized host lineages, and establishes a quantitative baseline for comparative microbiome research at scale.

microbiology↗

bioRxiv2026

A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data

Metaribosome profiling (metaRibo-Seq) enables genome-wide measurement of translation across complex microbial communities by sequencing ribosome-protected mRNA fragments, but the short length of these footprints creates substantial nonspecific mapping against large reference genome collections, leading to spurious taxonomic and functional assignments. Here we present MOPP (Multi-Omics Processing Pipeline), a modular reference-based workflow that denoises metaRibo-Seq data by leveraging matched metagenomic coverage breadth to identify genomes likely to be truly present in a sample before aligning metatranslatomic and optional metatranscriptomic reads. MOPP generates taxon-by-gene count tables across genomic, transcriptional and translational layers, enabling integrated downstream analyses of microbial function. We evaluated MOPP using a defined 79-member synthetic human gut community profiled by metagenomics and metaRibo-Seq. Coverage breadth filtering markedly improved detection accuracy relative to a standard baseline workflow, with performance remaining robust across a broad intermediate threshold range and peaking at 92-95% coverage breadth. At a 92% threshold, MOPP reduced the number of distinct detected operational genomic units by 99.4% while retaining 87.8% of aligned metaRibo-Seq reads on average, and increased the F1 score from 0.02 to 0.61. Residual false positives were predominantly attributable to genomes with extremely high nucleotide similarity to true community members, whereas false negatives were enriched among low-abundance taxa, indicating that remaining errors are driven primarily by biological similarity and detection limits rather than widespread nonspecific mapping. Together, these results establish MOPP as a high-throughput workflow for robust processing of metaRibo-Seq in the context of matched metagenomics and position it as a scalable framework for integrated taxonomic and functional analysis of microbial communities across genomic, transcriptional and translational layers.

bioinformatics↗

bioRxiv2026

Precision mapping and molecular contextualization of surgical outcome epicenters in temporal lobe epilepsy

AO_SCPLOWBSTRACTC_SCPLOWTemporal lobe epilepsy is the most common drug-resistant epilepsy, with surgical resection offering the primary path to seizure freedom. Despite standardized approaches, a substantial proportion of patients experience seizure recurrence, and the neurobiological substrates underlying these divergent outcomes remain unclear. We applied an individualized normative modeling framework to multimodal preoperative MRI data in a group that subsequently underwent surgical resection, to characterize patient-specific structural deviations and identify disease epicenters. Patients who became seizure-free exhibited spatially coherent abnormalities localized to the hippocampus and ipsilateral association regions, anchored in agranular limbic territories and enriched for genes linked to calcium-dependent signaling. Non-seizure-free patients, on the other hand, showed a more heterogeneous and distributed pattern of deviations, consistent with a "temporal-plus" network organization, and broader neuromodulatory dysregulation. Crucially, overlap between resected tissue and network-defined epicenters was closely associated with seizure freedom, independent of total resection volume. These findings provide a multiscale framework for precision surgical planning, shifting the focus from standardized tissue removal to targeted disconnection of patient-specific pathological hubs.

neuroscience↗

bioRxiv2026

Pan-repository analysis reveals a drug-activating function of microbial bile acid conjugation

Microbially modified bile acids shape host physiology by regulating nutrient absorption, glucose homeostasis, circadian rhythms and thermoregulation. Here we identify a previously unrecognized drug-activating function of microbial bile acid conjugation. By systematically mining human LC-MS/MS datasets across public repositories and linking uncharacterized bile acid spectra to health-associated metadata, we discovered conjugates of the >75-year-old anti-inflammatory drug 5-aminosalicylic acid (5-ASA) with primary and secondary bile acids, including cholic, deoxycholic and lithocholic acids. These bile acid-drug conjugates were detected specifically in individuals treated with 5-ASA or its prodrugs. Multiple gut bacteria, including members of the Bacteroidota and Bacillota, generated cholyl-5-ASA in vitro, and bile salt hydrolase-associated transaminase activity was required for conjugate formation. In a mouse model of colitis, cholyl-5-ASA was associated with reduced intestinal inflammatory pathology and showed markedly enhanced activation of PPAR-{gamma} in cell-based reporter assays compared with 5-ASA alone. Consistent with this activity, cholyl-5-ASA elicited selective immunophenotypic changes in CD4 T cells in vitro, including increased Foxp3+ regulatory T cells. Together with prior evidence that 5-ASA efficacy depends on the microbiome, these findings support a model in which microbial bile acid conjugation represents a key activation step for 5-ASA therapy. More broadly, this work demonstrates how pan-repository metabolomics can uncover previously unrecognized microbiome-dependent chemical functions with direct therapeutic relevance.

biochemistry↗

bioRxiv2026

Enabling Megascale Microbiome Analysis with DartUniFrac

We introduce a new algorithm, DartUniFrac, and a near-optimal implementation with GPU acceleration, up to three orders of magnitude faster than the state of the art and scaling to millions of samples (pairwise) and billions of taxa. DartUniFrac connects UniFrac with weighted Jaccard similarity and exploits sketching algorithms for fast computation. We benchmark DartUniFrac against exact UniFrac implementations, demonstrating that DartUniFrac is statistically indistinguishable from them on real-world microbiome and metagenomic datasets.

bioinformatics↗

bioRxiv2026

Faf2/Ubx2 potentiates p97/Cdc48 segregase activity via functional priming and reinforcement of the UT3 domain in Ufd1

The AAA+ segregase p97/Cdc48 extracts poly-ubiquitinated proteins from entrenched cellular environments to maintain proteostasis. However, its functional capacity is not uniform; extracting substrates from dense assemblies like stress granules or membrane necessitates a fully potentiated state. Here, using precisely synthesized ubiquitinated substrates, we show that the Faf2/Ubx2 cofactor hyperactivates p97/Cdc48, lowering its minimal ubiquitin chain requirement and broadening linkage specificity. Cryo-EM analysis of the activated complex demonstrates that Faf2/Ubx2 potentiates p97/Cdc48 segregase activity by structurally remodeling the substrate recognition module (K48-diUbProx) and priming its engagement with the AAA+ motor (p97/Cdc48-Npl4). These coordinated actions establish a pump-unit architecture that drives efficient substrate processing. Our findings illuminate a conserved mechanism that unlocks the maximal capacity of p97/Cdc48 and provide a blueprint for therapeutically targeting its hyper-activated state in disease.

biochemistry↗

bioRxiv2026

A searchable metadata network graph for microbiome metabolomics

Establishing the biological context of microbial metabolites remains a major challenge. We present microbiomeMASST, a metadata-driven network graph that maps metabolites across 467 available datasets with 144,424 mass spectrometry files from humans, animals, and microbial culture systems. MicrobiomeMASST integrates monocultures, synthetic communities, and host-associated samples across multiple body sites and plants. MS/MS spectra can be queried to trace occurrence across hosts, experimental conditions, and interventions, enabling cross-study integration. We demonstrate this framework by contextualizing microbial-conjugated bile acids and interrogating microbiome-mediated drug metabolism. Screening gut bacteria revealed deprolylation of the angiotensin-converting enzyme (ACE) inhibitor prodrug enalapril. Using microbiomeMASST, we traced this metabolite across human cohorts, microbial isolates, environmental samples, and in Gorilla gorilla. Structural modeling and enzymatic assays showed that microbial deprolylation abolishes ACE inhibition, thereby inactivating its therapeutic effect. Together, microbiomeMASST links MS/MS spectra to biological context, converting isolated observations into an interpretable microbiome map for cross-study analysis.

biochemistry↗

bioRxiv2025

Conformation-specific Antibody Deciphers K27-linked Ubiquitination in Chaperone-Mediated Proteostasis

Lysine 27 (K27)-linked polyubiquitination plays critical yet incompletely defined roles in proteostasis, innate immunity, and disease progression; however, investigations into this process have long been hindered by its extremely low abundance and the lack of conformation-specific enrichment tools. Herein, we describe the development of a long-sought conformation-specific antibody, K27-IgG, which can selectively recognize--among all ubiquitin chain types--the unique architecture of K27-linked polyubiquitin (K27-polyUb) characterized by a distinct buried K27-isopeptide bond, with high affinity (KD = 4.66 nM). This antibody was derived from synthetic antibodies initially generated via phage display, using chemically synthesized K27-linked diubiquitin (K27-diUb) as the antigen. High-resolution co-crystal structures uncovered the unique K27-diUb interface targeted by these sAbs. Subsequent reformatting of these sAbs into a full-length human immunoglobulin G (IgG) scaffold yielded K27-IgG, notably exhibiting markedly enhanced affinity without compromising selectivity. Using K27-IgG as a tool, we achieved sensitive detection and immunoprecipitation (IP) of endogenous K27-polyUb in cells, and delineated the intracellular interaction landscape of K27-polyUb through complementary proteomic approaches. Two key findings emerged: 1) The molecular chaperone DNAJB1 is a specific reader of K27-linked ubiquitin chains (but not other linkages) and that K27-polyUb chains themselves exhibit chaperone-like activity, suggesting a novel mechanism by which K27-polyUb regulates chaperone-mediated proteostasis; 2) The E2 enzyme UBE2Q1 assembles K27-diUb, identifying it as a potential writer for this ubiquitin chain topology. Collectively, this study establishes K27-IgG as a robust tool for deciphering the K27-linked ubiquitin code, thereby opening new avenues for investigating the biological functions of K27-linked polyubiquitination. HighlightsO_LIFirst K27-linkage conformation-specific antibody with nanomolar affinity overcomes a major barrier in the field. C_LIO_LIK27-IgG unlocks functional mapping of the K27 ubiquitin landscape under proteotoxic stress. C_LIO_LIMolecular chaperone DNAJB1 is a selective "reader" of K27-linked ubiquitin chains. C_LIO_LIK27 chains possess intrinsic chaperone activity, enabling protein refolding and suppressing aggregation. C_LIO_LIE2 enzyme UBE2Q1 is a "writer" that directly assembles K27-linked ubiquitin chains. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/695067v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@113b980org.highwire.dtl.DTLVardef@1f7c1a0org.highwire.dtl.DTLVardef@c91656org.highwire.dtl.DTLVardef@1d9a507_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Multivariate environmental exposures are reflected in whole-brain functional connectivity and cognition in youth

Each individuals complex, multidimensional environment, known as their "exposome", plays an essential role in shaping cognitive neurodevelopment. Understanding the mechanisms whereby childrens exposome influences their development is crucial to facilitate the design of interventions to foster positive developmental trajectories for all youth. Recent work has identified a general exposome factor associated with socio-economic inequality that is strongly related to cognition and individual differences in the spatial organization of functional brain networks in youth. Building on these findings, the current study explores whether alterations in functional connectivity may represent a potential mechanism linking variation in the exposome to cognitive performance. We apply a data-driven, cross-validated, whole-brain machine learning approach, connectome-based statistical inference, to identify patterns of functional connectivity associated with exposome scores among early adolescents enrolled in the Adolescent Brain Cognitive Development (ABCD) Study using data collected during three cognitive tasks and during rest. Additionally, we investigate whether the identified patterns of functional connectivity relate to individual differences in cognitive performance across three domains: General Cognition, Executive Functioning, and Learning/Memory. Models incorporating 10-fold cross-validation over 100 iterations identified consistent functional connections associated with the exposome across task and rest conditions (model performance: ns = 6,137 - 8,391, rs = 0.34 - 0.44, ps <.001). Results were robust across data collection sites and functional connections common across all significant models were associated with cognitive performance across domains (ps < 0.0009). Collectively, these findings reveal that multidimensional environmental exposures are reflected in patterns of functional connectivity and relate to cognitive functioning among youth. HighlightsO_LIPatterns of functional connectivity reflect multivariate environmental exposures. C_LIO_LIConsistent exposome-related connectivity patterns were observed across brain states. C_LIO_LIThe identified general exposome network was associated with cognitive performance across domains. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/688261v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@b5cc3aorg.highwire.dtl.DTLVardef@172f954org.highwire.dtl.DTLVardef@14f0d01org.highwire.dtl.DTLVardef@deccb5_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Neuronal SET1/COMPASS-mediated epigenetic regulation of de novo transcription drives accelerated forgetting with age

Forgetting is a critical component of memory, but its molecular regulation - particularly with age - is not well understood. Epigenetic modifications are a candidate for this regulation and may further drive age-related behavioral decline, as they are dramatically altered in the aging brain. We found that multiple components of the SET1/COMPASS complex, a conserved histone methyltransferase complex associated with active gene transcription, are upregulated with age in the C. elegans nervous system. Neuronal knockdown of the SET1/COMPASS components improves memory in young adult animals and slows memory decline in old animals. By pharmacological and genetic inhibition, optogenetics, and neuronal mRNA and chromatin profiling, we demonstrate that SET1/COMPASS-mediated active transcription promotes forgetting. SET1/COMPASS regulates the de novo activity-dependent transcription and release of a neuropeptidergic signal from the AWC olfactory sensory neuron, which erases the associative memory trace in downstream motor neurons, resulting in forgetting. We further found that increased SET1/COMPASS-dependent chromatin accessibility at these gene loci with age primes these loci for transcription, resulting in accelerated forgetting. Our results reveal the role of active gene transcription in the regulation of forgetting and altered SET1/COMPASS-mediated gene transcription as a mechanism of cognitive decline, implicating increased expression of COMPASS components as a driver of increased forgetting in the aging brain. This mechanism may offer a new target for slowing loss of cognitive function with age.

neuroscience↗

bioRxiv2025

Distinct and compensatory roles of Stag1 and Stag2 in post-mitotic genome refolding

The three-dimensional architecture of the eukaryotic genome is largely shaped by the cohesin complex, which contains either Stag1 or Stag2 subunits. Although both subunits contribute to chromatin organization, their specific functions in de novo loop formation during post-mitotic genome refolding remain elusive. Here, we leverage the mitosis-to-G1 transition to dissect their individual roles. We found that Stag1 depletion has a negligible impact on post-mitotic genome restructuring or transcription reactivation. In contrast, Stag2 orchestrates chromatin remodeling in a manner that is both cell cycle stage-specific and chromatin context-dependent. During early-G1, Stag2 preferentially associates with euchromatin, where it drives the rapid formation of small chromatin loops. This facilitates prompt promoter-enhancer (P-E) contact formation and enables efficient transcription activation. As the nuclear concentration of Stag2 increases by late-G1, it progressively suppresses large loops, likely due to its shorter chromatin residence time and its potential to competitively displace the more extrusion-capable Stag1-associated cohesin. Mechanistically, Stag2-mediated loop extrusion is constrained by CTCF-bound barriers, rather than by genomic travel distance. Although Stag2 associates rapidly with euchromatin in early-G1, its recruitment to heterochromatin is delayed until late-G1. Simultaneous depletion of both Stag proteins results in a synergistic loss of virtually all structural loops and a more severe disruption of transcription than that caused by individual deletions. Together, these results establish Stag2 as the principal regulator of post-mitotic genome reorganization among Stag paralogs, mediating spatiotemporal control of chromatin architecture, while Stag1 provides compensatory support to ensure functional robustness.

molecular biology↗

bioRxiv2025

Sustained alpha oscillations serve attentional prioritization in working memory, not maintenance

Recent theory on the neural basis of working memory (WM) has attributed an important role to "activity-silent" or -quiescent mechanisms, suggesting that sustained neural activity might not be essential in the retention of information. This idea has been challenged by reports of ongoing neural activity in the alpha band during WM maintenance, however. The precise role of these alpha oscillations is unclear: Do they reflect attentional prioritization of stored information, or do they serve as a general maintenance mechanism, for instance to periodically refresh synaptic traces? To address this, we designed a visual WM task involving two memory items, one of which was prioritized by being tested first for recall. The task included both short (1 s) and a long (3 s) delay intervals between encoding and retrieval. The long delay condition allowed us to test whether the alpha-based decoding effects persist beyond the early delay period, thereby putting accounts that attribute alpha activity to generic maintenance processes to the test. Time-resolved decoding analyses revealed that both tested-first and tested-second items were initially decodable following stimulus presentation. However, only the tested-first item exhibited sustained decodability throughout the delay, particularly in the long delay condition, where it transitioned into a stable coding scheme. This prolonged representation was selectively supported by induced alpha power, which reliably tracked the prioritized tested-first item, but not the deprioritized tested-second one. Impulse-based decoding further confirmed this asymmetry, showing a selective increase in readout for the tested-second item only when it became immediately task-relevant. Together, these findings suggest that sustained alpha-band activity primarily reflects attentional prioritization, rather than general memory maintenance. Unattended, deprioritized items appear to transition into an activity-quiescent state, consistent with models of synaptic storage in WM.

neuroscience↗

bioRxiv2025

Alternate Splicing Directs PMCA2 to Lysosomes and is Linked to Neurodegeneration

Plasma membrane calcium ATPases (PMCAs) are believed to function exclusively at the plasma membrane where they expel calcium from the cytosol. We have unexpectedly identified a splice variant-dependent localisation of the PMCA isoform PMCA2 to the lysosome, where it forms an evolutionarily conserved complex with NPC1, the lysosomal membrane protein defective in the rare lysosomal storage disease Niemann-Pick disease type C (NPC). This interaction is required for lysosomal Ca2+ homeostasis and implicates PMCA2 as a mediator of Ca2+ uptake into lysosomes. Disruption of the NPC1-PMCA2 complex contributes to the pathophysiology of both Niemann-Pick disease type C and Parkinsons disease, revealing an unrecognised intracellular function for PMCA2 and a shared mechanism linking lysosomal Ca2+ and lipid regulation in neurodegeneration.

cell biology↗