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Liu, L.

Publications and source records attributed to Liu, L..

At least 145 records · Page 8Linked to original sources

An Asynchronous Production Line of Meiotic Prophase I in the Mouse Fetal Ovary

The initiation of meiosis in the mammalian female germline has long been described as a synchronous event, occurring within a narrow developmental window. Here, we challenge this paradigm through a systematic, quantitative analysis of meiotic entry and progression in the mouse fetal ovary. Using dynamic expression profiling of key regulators Stra8, Sycp1, and Sycp3 alongside proliferation markers, we demonstrate that germ cells enter meiosis asynchronously and continuously between embryonic days E12.5 and E16.5. During this extended period, mitotic proliferation persists, indicating that germ cells are progressively recruited into the meiotic pathway rather than halting division simultaneously. Homologous chromosome synapsis, marked by Sycp1/Sycp3 co-localization, initiates at E14.5 and is completed prenatally by E18.5. Integrating these data into a continuous-time Markov chain model, we derive a "meiotic clock" that predicts fixed temporal intervals from meiotic entry to synapsis completion ([~]72 hours) and to meiotic arrest ([~]91 hours), regardless of entry time. This model provides a predictive framework for germ cell development and establishes that female meiotic initiation is a prolonged, asynchronous production line rather than a synchronized transition, reshaping our understanding of oogenesis and its regulatory logic. TEASERThe initiation of female meiosis in mice is redefined as an asynchronous, continuous production line from E12.5 to E16.5, supported by a predictive "meiotic clock" model with fixed temporal intervals for synapsis and arrest.

developmental biology↗

Myeloid PINK1 represses mtDNA release and immune signaling that impacts neuronal pathology in patient-derived idiopathic PD models

Parkinsons disease (PD) is a neurodegenerative disorder marked by the development of cardinal motor deficits preceded by a protracted prodromal period of non-motor symptoms often involving the gastrointestinal (GI) tract. There is an emerging consensus that both the peripheral immune system and local neuroinflammation play key roles in the etiology of PD. We previously demonstrated a critical function for the Parkinsons related proteins PINK1 and Parkin as repressors of the innate to adaptive immune response in cultured cells and mouse models of infection. However, it remained unclear whether these processes were conserved in patient-derived models, and precisely how immune signaling may ultimately drive the death of dopaminergic neurons. Here we show that GI infection of PINK1 knockout (KO) mice triggered acute neurodegeneration which was evident early in the enteric nervous system. Treating wild type enteric or dopaminergic neurons with conditioned medium from immune-stimulated PINK1 KO macrophages was sufficient to promote neuronal disruption in both mouse and human neurons in vitro. Within immune-activated macrophages, we reveal that loss of PINK1 led to an enhanced release of mitochondrial DNA (mtDNA) within mitochondrial derived vesicles, leading to the activation of cGAS/STING pathways. These changes were seen in both mouse/human in vitro models and in PD patient-derived primary macrophages. Notably, pharmacological modulation using a PINK1 activator with high therapeutic potential attenuated pro-inflammatory profiles elicited by the mtDNA-dependent STING/NF-{kappa}B pathway in idiopathic patient-derived macrophages. Ultimately, our study lays the foundation for understanding PINK1-related peripheral macrophage mechanisms in idiopathic PD and provides a target for further development to treat the disease at early stages. Graphical abstractPINK1-related immune mechanisms of Parkinsons disease and associations with early neurodegenerative events. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/694713v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@6f6488org.highwire.dtl.DTLVardef@13139aaorg.highwire.dtl.DTLVardef@c0d4d1org.highwire.dtl.DTLVardef@1d41e25_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

TSTScope Unifies Single-Cell Multi-Omics to Identify Functional T Cell States Predictive of Immunotherapy Response

Immune checkpoint blockade (ICB) can produce durable responses in cancer, but reliable predictors of benefit are still lacking. CD8 tumor-specific T cells are essential for ICB efficacy, yet it remains unclear which functional states of these cells determine therapeutic success. To address this, we developed TSTScope, an interpretable deep learning framework that integrates single-cell transcriptomic and T-cell receptor sequencing data to generate unified representations of CD8 T-cell identity. By applying TSTScope to non-small cell lung cancer (NSCLC) datasets, we characterized the gene programs defining tumor specificity and computationally inferred a population of potential TSTs. Crucially, we demonstrate that clinical response is not a product of TST abundance, but is instead governed by their functional state. We derived the MPR score, a metric capturing this functional potential, which proved to be a robust predictor of treatment outcomes. In an independent validation cohort, the MPR score significantly outperformed established biomarkers. Collectively, TSTScope identifies a distinct functional state of tumor-specific T cells as a primary determinant of ICB efficacy, providing both a mechanistic framework and a potent tool for precision immunotherapy.

bioinformatics↗

Transcriptional Heterogeneity Reveals a Synaptic Gene Program in Developing and Adult Human Oligodendrocyte Precursor Cells

Human oligodendrocyte precursor cells (OPCs) arise early in gestation and expand broadly during cortical development, yet the extent of their heterogeneity remains poorly defined. Here, we isolated >2,300 highly pure OPCs from post-conceptional week (PCW) 17 human cortex using an optimized PDGFR-based immunopanning and performed single-cell RNA sequencing. Unsupervised clustering revealed four transcriptionally distinct embryonic OPC subsets, including a previously unrecognized population that expressed genes linked to synaptic development, synaptic signaling, and neuromodulation. This subset - designated embryonic synaptic OPCs (eSyn-OPCs) - comprised approximately 28.5% of all embryonic OPCs in the cortex and was characterized by robust expression of synapse-associated secreted factors (THBS2, WNT5A, WNT7A, PLAT, ACHE) and multiple neurotransmitter receptor subunits. Histological analyses across PCW 12-22 demonstrated that eSyn-OPCs first appear around PCW 15 and are enriched in proliferative germinal zones. Spatial transcriptomics confirmed their localization near neural stem and progenitor cells, suggesting proximal neuron-OPC communication during early cortical assembly. Purified eSyn-OPCs differentiated into mature oligodendrocytes in vitro, confirming their oligodendrocyte lineage identity. Reanalysis of adult human single-nucleus RNA-seq datasets uncovered a transcriptionally analogous OPC subset (adult synaptic OPCs, aSyn-OPCs), though with reduced representation of structural synaptic genes and neurotransmitter receptor diversity compared to eSyn-OPCs. Together, these results identify a synaptically specialized OPC population in both developing and adult human cortex and reveal that eSyn-OPCs possess unexpectedly rich synaptic signaling machinery. These findings suggest that human OPCs may participate directly in neuron-glia communication during early cortical development and raise the possibility of developmental stage-specific roles for eSyn-OPCs in shaping neural circuit formation.

neuroscience↗

Discovery of Abundant Nano-scale Lymphatic-like Vessels in Brains

As one of the most metabolically active organs, the brain requires an exceptionally efficient system for waste clearance to sustain its high metabolic demands. However, whether such a system exists--and, if so, what structural features enable its efficiency--remains incompletely understood. More than a decade ago, the "glymphatic system" was proposed to describe neurofluid transport through cerebrospinal fluid (CSF) and perivascular spaces (PVS), in conjunction with dural and meningeal lymphatic pathways. Nevertheless, it remains unresolved whether neurofluid transport is organized as a structured, vessel-like flow network. Moreover, in stark contrast to the dense network of blood capillaries in the brain, only a sparse population of lymphatic vessels has been identified, raising doubts as to whether the currently recognized lymphatic architecture alone can support efficient metabolic waste clearance. By combining expansion microscopy with CRANAD-3, a pan-{beta}-amyloid fluorescent probe, we discovered abundant nanoscale lymphatic-like vessels (NLVs) within the brain parenchyma of both mice and humans. The majority of these structures have diameters below 1,000 nm and exhibit moderate positivity for multiple lymphatic markers, including LYVE-1, Prox-1, PDPN, and VEGFR3. NLVs frequently coil around blood vessels, and putative connections between vascular structures were observed. Notably, some NLVs traverse multiple cortical layers and display distinct orientation patterns that vary across cortical laminae. This discovery reveals a previously "hidden" vascular network in the brain parenchyma and raises the possibility that an abundant, highly organized system of nanoscale tubular structures may provide an efficient conduit for metabolic waste clearance. Such a system could represent a critical, previously unrecognized component supporting the brains extraordinary metabolic demands.

neuroscience↗

Multimodal AI for Single cfDNA Profiling and Cancer Screening

Cell-free DNA (cfDNA) serves as a non-invasive biomarker for cancer detection, but conventional methods face challenges due to the ultra-low abundance of tumor-derived cfDNA (ctDNA) among normal cfDNA. Though nucleosome-bound cfDNA harbors rich epigenomic features that could enable ctDNA identification by single-molecule multi-omics cross-validation, this remains unexplored due to methodological limits. Here, we developed a cfDNA sequencing approach integrating methylation, fragmentomics, and histone modifications at the single-molecule level; together with gene semantics and epigenomic annotations, these modalities were vectorized and fused to represent each cfDNA molecule. We trained a Transformer-based model (cfAI) to profile and evaluate ctDNA likelihood at molecule, gene, and sample levels. cfAI achieved [~]10-fold enrichment of cancer-derived signals over noise and reached 72.6% sensitivity at 93.1% specificity for multi-cancer detection. Our study establishes an innovative framework that overcomes the inherent signal-to-noise limitations of conventional assays and reveals biological features at molecular resolution for cancer detection.

bioinformatics↗

Adipocyte-related genes analysis contributes to the prognosis of atrial fibrillation

BackgroundPatients with mild left atrial appendage fibrosis have a significantly lower rate of atrial fibrillation (AF) recurrence after 5 years compared to those with moderate or severe fibrosis, which presented a significantly increased positive area of cellular senescence. MethodsGSE135445, a RNA-sequencing dataset between epicardial adipose tissue (EAT) from patients with persistent non-valvular AF and sinus rhythm (SR), was downloaded and analyzed and hub genes were obtained. To obtain the abundance of immune cells, the CIBERSORT algorithm with 100 permutations was applied. The senescent hub genes were obtained and validated using human blood samples. ResultsA total of 164 up-regulated and 317 down-regulated DEGs was obtained between EAT from subjects with AF and SR. Using immune infiltration analysis in whole PAT related DEGs, the abundance of M0 macrophages was significantly different between PAT and SAT and 22 M0 macrophages-related DEGs were also obtained, such as MMP7, APOE, CCND1, MMP12 and APOC1. Venn diagram was utilized to obtain the same transcripts between senescence datasets and DEGs and PPI network was used to 94 overlapping genes. The top15-degree senescence adipicytes hub genes were explored. To investigate senescence-related hub genes effects on AF progression, we collected the blood samples of patients with paroxysmal atrial fibrillation and persistent atrial fibrillation. There were no significant differences at baseline characteristics and laboratory examinations at 1d after admission except heart failure history and function examinations, for instance, ALT, LDL, LVEF and LA diameters. Using univariate analysis and multivariate analysis, heart failure history, ALT and LA diameters can be prognostic factors for AF progression. BMP7, COL4A3, COL4A4, CHRD, IRX1, SPON1, ALPL, TCF19 and SIX2 were validated to be highly expressed in persistent atrial fibrillation compared to paroxysmal atrial fibrillation. ConclusionBased on our current study, BMP7, COL4A3, COL4A4, CHRD, IRX1, SPON1, ALPL, TCF19 and SIX2 were validated to be highly expressed in persistent atrial fibrillation compared to paroxysmal atrial fibrillation, which may be potential therapeutic targets to treat AF progression and improve patients prognosis.

genetics↗

Polus: a Transformer-based Soft-decision Codec Enhancement Platform for DNA Storage

DNA storage offers exceptional information density and archival longevity, but is constrained by the complex, heterogeneous errors inherent to synthesis, storage, and sequencing. Conventional error-correction schemes often rely on excessive logical redundancy to mitigate these biochemical imperfections, thereby compromising storage efficiency. Here, we introduce Polus, a deep-learning-enabled platform that bridges the gap between biochemical constraints and digital reliability through soft-decision decoding. At its core is SeqFormer, a Transformer-based channel model that synergizes sequence context with quality signals to characterize platform-specific error profiles, generating calibrated per-base confidence scores. This mechanism transforms uncertain biochemical noise into informative "soft" erasures. In in silico benchmarks, Polus significantly enhances mainstream codecs: it reduces the sequencing coverage required for DNA Fountain by 38.9% --increasing effective physical density by [~]80%--and eliminates persistent indel-induced errors in the Yin-Yang codec. Furthermore, it enables a targeted resequencing strategy that achieves full recovery with 99.9% less overhead than brute-force deepening. To formalize these gains and address the lack of systematic benchmarking in the field, Polus establishes a standardized nine-metric evaluation framework that rigorously quantifies the trade-offs between reliability, density, and cost. This work provides a reproducible, quantitative foundation for next-generation, context-aware DNA storage systems.

bioinformatics↗

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↗

STUltra: scalable and accurate integration for subcellular-level spatial omics data

High-resolution spatial transcriptomics (ST) is generating massive datasets involving multiple tissue sections, continuous developmental stages, or various disease conditions. Yet, their scale, biological heterogeneity, and substantial batch effects hinder data integration for further analysis, particularly the temporal interpretation of disease-associated spatial domains within tissue organization landscapes. Here, we present STUltra, a scalable hypergraph framework that integrates multi-sample ST data for precise domain detection and genome-wide association study (GWAS)-based disease trait mapping. From ST datasets, STUltra first constructs interval-sampled integrative hypergraphs, in which hyperedges capture tissue neighborhoods within the slices as well as shared biological contexts across the slices. It then combines a robust graph autoencoder with contrastive learning to learn batch-corrected, spatially informed embeddings for identifying spatial domains across the tissue sections. These embeddings are then coupled with GWAS statistics to map trait-associated signals onto the integrated tissue sub-structure landscapes spanning different sections, developmental stages, and disease conditions. STUltra substantially outperforms competing methods, especially being much faster, on diverse integration benchmarks, enabling efficient processing of datasets containing millions of spots. As a case study on a mouse embryo dataset, STUltra recovered continuous developmental programs and mapped congenital heart disease signals beyond cardiac regions to broader programs including vascular and mesenchymal domains. On a mouse Alzheimer's disease dataset, STUltra prioritized localized AD-associated genetic signals to microglia and a disease-expanded C1QA/HEXB-high astrocyte state. Together, STUltra provides a scalable framework to bridge the gap between spatiotemporal tissue structures and complex disease traits, facilitating discoveries from previously unrecognized molecular and cellular architectures across diverse contexts.

bioinformatics↗

Selective Activation of NaV1.3 Restores Lymphatic Contractility in Age and Injury

BackgroundIntrinsic lymphatic contractility is essential for tissue fluid balance, immunity and organ function, yet no FDA-approved pharmacologic treatments specifically restore lymphatic contractility. Lymph is returned to the circulation by ion channel-driven cyclic contractions of collecting lymphatic vessels. Although voltage-gated sodium (NaV) channels drive cardiomyocyte excitability, their role in lymphatic muscle cell (LMC) physiology is not well defined. We identified NaV1.3, a NaV channel historically viewed as developmentally restricted and limited in adult tissues, as unexpectedly and selectively expressed in adult lymphatic muscle but absent from heart, vascular smooth muscle, and mature brain. We tested whether selective NaV1.3 activation restores impaired lymphatic pumping in aging and radiation injury. MethodsNaV1.3 expression in LMCs was confirmed through single-cell RNA sequencing analysis and immunostaining of mouse and human lymphatic vessels. Lymphatic contractility was quantified by in vivo fluorescence lymphangiography and interstitial fluid clearance was measured with a new bioluminescence assay. NaV1.3 function was assessed in young, aged, and radiation-injured mice. NaV1.3 knockout (Scn3a-/-) mice established the requirement of NaV1.3 for basal lymphatic excitability and responsiveness to the NaV1.3-specific activator, Tf2. ResultsIn mouse and human lymphatic vessels, NaV1.3 is expressed in adult LMCs. Although dispensable for basal lymphatic contractions, NaV1.3 acted as a pharmacologically recruitable reserve that amplified contractile output. Acute NaV1.3 activation with Tf2 increased lymphangion ejection fraction and accelerated interstitial fluid clearance. Tf2 fully restored lymphatic pumping in aged mice and partially rescued radiation-induced contractile deficits. All Tf2 responses were abolished in Scn3a-/- mice, confirming NaV1.3 dependence. ConclusionsNaV1.3 is a selectively druggable ion channel in adult lymphatic muscle that can be recruited to restore lymphatic pump function across aging and injury. Targeted NaV1.3 activation provides a molecular entry point for treating diseases characterized by lymphatic pump failure, a domain with no existing pharmacologic therapies.

physiology↗

Pancreatic δ-cells are resistant to auto- and paracrine inhibition in human type-2 diabetes

Somatostatin secretion from pancreatic {delta}-cells inhibits nearby -and {beta}-cells, and tunes the bodys glycemic set-point. The role of {delta}-cells in diabetes remains unclear, in part due to the difficulty separating intrinsic regulation from intra-islet paracrine effects. Here we compared the function of isolated {delta}-cells of cadaveric non-diabetic and type-2 diabetic donors, by single cell TIRF-microscopy and electrophysiology. Elevated glucose stimulated exocytosis of somatostatin, which was further amplified by glucagon, exendin-4, or forskolin, independent of diabetic status. GABA enhanced exocytosis and electrical activity, while insulin had no effect. Adrenaline and somatostatin strongly inhibited {delta}-cell activity, leading to autocrine feedback inhibition of somatostatin exocytosis. In type-2 diabetes, {delta}-cell inhibition by somatostatin and adrenaline was lost, together with a marked reduction in somatostatin receptor (SSTR2) surface expression. We further show that resistance to somatostatin leads to hyperactive {delta}-cells in type-2 diabetes, and propose that this mechanism contributes to defective blood glucose control.

cell biology↗

A global atlas of deep-sea cold seep viruses uncovers extensive genomic novelty, pervasive viral dark matter, and biotechnological potential

Cold seeps are globally distributed deep-sea ecosystems harboring diverse chemosynthetic microbial communities, yet their viral components remain poorly understood. Here, we establish the Global Cold Seep Virome, a comprehensive catalog of 191,937 species-level viral operational taxonomic units (vOTUs) and 2.44 million viral protein clusters reconstructed from 314 metagenomes spanning 18 cold seep sites worldwide. Most vOTUs are distinct from those in existing environmental viromes, suggesting that cold seeps harbor a largely unexplored viral reservoir. Host prediction suggests diverse viral associations with key prokaryotes, including anaerobic methanotrophic archaea. Protein annotation reveals that these viruses encode widespread uncharacterized proteins and viral hallmark proteins with divergent physicochemical properties, potentially contributing to their ecological adaptability. We also identify putative auxiliary metabolic genes, anti-defense genes, and lysins, and experimentally validate representative anti-defense proteins and lysins with strong activities. This resource expands current knowledge of deep-sea viral diversity and provides a foundation for studying virus-host interactions, testing biogeochemical hypotheses, and exploring biotechnological potential in cold seep ecosystems.

microbiology↗

ERAD Activity Distinguishes the Functional Heterogeneity of Hematopoietic Stem Cells

Hematopoietic stem cells (HSCs) rely on precisely controlled proteostasis to sustain lifelong self-renewal, yet whether intrinsic proteostatic characteristics can prospectively define functional diversity within the HSC pool remains unknown. In this study, we developed a dual-fluorescence reporter system to visualize endoplasmic reticulum-associated degradation (ERAD) activity in vivo and discovered that ERAD activity can prospectively predicts the long-term reconstitution potential of HSCs. Remarkably, ERAD states were maintained through self-renewal, revealing an inheritable "proteostatic memory" within the HSC pool. Transcriptomic and functional analyses identified SOCS2 as a key regulator of this process: SOCS2 inhibits JAK2 signaling to sustain ERAD activity, whereas hyperactive JAK2 interacts with the ERAD E3 ligase Hrd1 and suppresses VCP-mediated misfolded substrate. These findings define a SOCS2-JAK2-ERAD axis that connects cytokine signaling to intrinsic proteostasis remodeling, establishing ERAD activity as a predictive and heritable marker of HSC function and providing a conceptual framework for understanding hematopoietic stem cell heterogeneity.

cell biology↗

Steric Gating Dictates Selective Activation of BIRC6 by UBA6 Over UBA1

The giant E2-E3 chimera BIRC6 is specifically activated by the ubiquitin-activating enzyme UBA6, but not by UBA1. This specificity allows BIRC6 to ubiquitinate downstream substrates (e.g., caspases) and thereby regulate apoptosis. However, the molecular mechanism that underlies UBA6mediated specific activation of BIRC6 remains elusive. Here, we used a UbDha (Ub residue 76 dehydroalanine) probe to achieve one-step, activity-based trapping of the transient transthioesterification intermediate, and resolved the cryo-EM structures of two key complexes: 1) the doubly loaded UBA6-BIRC6UBC-UbT-UbA complex (3.4 [A] resolution) and 2) the singly loaded UBA6-BIRC6UBC-UbT complex (3.3 [A] resolution). Structural analysis reveals that the specific BIRC6-UBA6 pairing is dictated by steric compatibility between an insertion loop (residues 4649- 4653) in BIRC6s UBC domain and UBA6s gate helix. Unlike UBA1, UBA6 avoids steric clash with this insertion loop via two key conformational changes: a ~30{degrees} clockwise rotation and a 19 [A] displacement of its gate helix. These conformational changes collectively create a compatible cavity to accommodate the insertion loop. Biochemical validation confirms two key findings: 1) truncating BIRC6s insertion loop rescues UBA1-mediated ubiquitin charging of BIRC6UBC; 2) swapping UBA6s gate helix with that of UBA1 abolishes UBA6s transthioesterification activity towards BIRC6UBC. Our study provides key structural insights into the molecular basis of E1-E2 pairing specificity and advances our mechanistic understanding of apoptotic signalling.

biochemistry↗

Beyond Inheritance: De novo Fast Motion Computation in Primate Visual Cortex

Objects move through space and time, generating sequential visuotopic activations in all sighted animals leading to motion perception of velocity defined by direction and speed. Humans can effortlessly see motion with speeds ranging from 0.25 to 500{degrees}/s. However, direction-selective neurons in the primary visual cortex (V1)--from which all subsequent processing is presumed to derive-- only encode directionality at low speeds. To resolve this paradox, we recorded neuronal responses to moving dots, gratings, and movies across the LGN, V1, MT and MST of the macaque motion pathway. Regardless of cell type and motion stimuli, V1 neurons lost direction selectivity at [~]29{degrees}/s while MT and MST neurons maintained it up to [~]82{degrees}/s and [~]183{degrees}/s, respectively. A cascaded spatiotemporal integration model reveals that at each cortex direction-selective neurons can generate velocity selectivity de novo, by integrating sequential visuotopic activations from preceding areas, irrespective of speed and directionality. By computing velocity anew, the primate brain effectively uses the cortical hierarchy itself to shift gears to efficiently encode slow and fast motion. Thus, five visual areas from the retina into the brains processing hierarchy, external spatiotemporal information is being computed afresh, offering insights for motion processing in other species, modalities and machine vision.

neuroscience↗

Machine learning for integrative multi-omics clustering and feature gene identification

Multi-omics integrative analysis provides a powerful means for elucidating complex molecular mechanisms and biological processes, yet remains challenging in effectively representing the multi-dimensional relationships inherent to multi-omics data. Here we present MIA, a tensor-based representation learning framework that preserves the multi-dimensional structure of multi-omics data for accurate sample clustering and feature discovery. Unlike existing algorithms that primarily rely on two-dimensional representations, MIA models multi-omics data as a three-dimensional tensor and integrates tensor decomposition, fuzzy c-means, and an enhanced random forest model within a unified framework for clustering and feature discovery. Benchmarking on simulated and empirical datasets demonstrates that MIA consistently outperforms representative state-of-the-art algorithms in both clustering and feature identification. Application to multiple TCGA cancer types further shows its ability to stratify samples and identify molecular features associated with clinically relevant outcomes. Specifically, in glioblastoma, MIA reveals three previously uncharacterized subtypes with distinct prognostic profiles and uncovers feature genes strongly associated with subtype identity. These genes are further linked to therapeutic response and retain discriminative power across major glioblastoma cellular populations at single-cell resolution. Collectively, our results establish MIA as a generalizable computational framework for multi-omics integrative analysis, enabling systematic molecular stratification and interpretable feature discovery across diverse biological systems.

bioinformatics↗

The functional divergence of two ethylene receptor subfamilies that exhibit Ca2+-permeable channel activity

Ethylene is a gaseous plant hormone crucial for regulating plant growth, development, and stress adaptation, yet the molecular basis underlying ethylene receptor function remains elusive. Here, we show that subfamily I receptors constitute core ethylene-sensing module and function epistatically to subfamily II receptors. Notably, we discover that only subfamily I receptors possess Ca2+-permeable channel activity, which are indispensable for ethylene-induced cytosolic calcium influx. Overall, this work supports a mechanistic framework in which subfamily I receptors integrate ethylene sensing with Ca2+ influx, providing new insight into how plants translate hormonal cues into downstream signaling events.

plant biology↗