Biology subjects

Sun, J.

Publications and source records attributed to Sun, J..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Guess till correct: Gungnir codec enabling high error-tolerance and low-redundancy DNA storage through substantial computing power

DNA has emerged as a compelling archival storage medium, offering unprecedented information density and millennia-scale durability. Despite its promise, DNA-based data storage faces critical challenges due to error-prone processes during DNA synthesis, storage, and sequencing. In this study, we introduce Gungnir, a codec system using the proof-of-work idea to address substitution, insertion, and deletion errors in a sequence. With a hash signature for each data fragment, Gungnir corrects the errors by testing the educated guesses until the hash signature is matched. For practicality, especially when sequenced with nanopore long-read, Gungnir also considers biochemical constraints including GC-content, homopolymers, and error-prone motifs during encoding. In silico benchmarking demonstrates its outperforming error resilience capacity against the state-of-art methods and achieving complete binary data recovery from a single sequence copy containing 20% erroneous bases. Gungnir requires neither keeping many redundant sequence copies to address storage degradation, nor high-coverage sequencing to address sequencing error, reducing the overall cost of using DNA for storage.

bioinformatics↗

bioRxiv2025

Respiratory viral infections prime accelerated lung cancer growth

The COVID-19 pandemic has highlighted long-term health concerns of viral pneumonia, yet its potential impact on cancer development and growth remains poorly understood. Here, we demonstrate that prior infection with SARS-CoV-2 or influenza virus promoted lung tumor progression by reprogramming the local immune landscape. Retrospective clinical analysis revealed that patients hospitalized with COVID-19 exhibited increased lung cancer incidence. Using multiple murine lung cancer models, we show that prior severe respiratory viral infections accelerated tumor growth and reduced survival. Mechanistically, prior viral pneumonia epigenetically remodeled the lung to establish a pro-tumor microenvironment, including the local accumulation of SiglecFhi tumor-associated neutrophils, a transcriptionally reprogrammed, immunosuppressive population whose signature predicted poor prognosis in human lung adenocarcinoma. In parallel, epithelial compartments exhibited altered differentiation trajectories, with persistence of injury-associated alveolar intermediates positioned along tumorigenic lineages. We observe sustained chromatin remodeling at key cytokine loci in immune and structure cells, linking inflammatory memory to persistent immune suppression. Therapeutically, combined inhibition of neutrophil recruitment via CXCR2 and PD-L1 signaling restored CD8 T cell infiltration and suppressed tumor growth. Together, our findings establish a direct causal relationship between viral pneumonia, including COVID-19, and lung tumorigenesis, highlighting the urgent need to monitor survivors for elevated cancer risk and to develop targeted interventions and therapies aimed at preventing potential cancer bursts in COVID-19 convalescents. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/672566v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1c6705borg.highwire.dtl.DTLVardef@fa728eorg.highwire.dtl.DTLVardef@76fc6corg.highwire.dtl.DTLVardef@1b65336_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Inhibition of CaV1.4 channels by CaV3 channel antagonists ML218 and Z944

Among the three classes of voltage-gated Ca2+ channels (Cav1, Cav2, Cav3), Cav3 T-type channels are drug targets for disorders including epilepsy and pain. Antagonists such as Z944 and ML218 are highly selective for Cav3 compared to the Cav1.2 L-type channel but whether they have additional activity on other Cav1 subtypes is unknown. Here, we investigated the effects of Z944 and ML218 on the Cav1.4 channel which regulates neurotransmitter release from retinal photoreceptors. In HEK293T cells transfected with Cav1.4 and the auxiliary {beta}2x13 and 2{delta}-4 subunits, Z944 and ML218 inhibited Ca2+ currents with IC50 values of [~]30 {micro}M and 2 {micro}M, respectively. Structure-based modeling combined with functional studies revealed the importance of a cluster of methionine residues, particularly M1004, within the DHP binding site for the effects of ML218. Compared to mutation of a conserved threonine (T1007) that is required for DHP sensitivity of Cav1 channels, mutation of M1004 had a 10-fold greater impact in diminishing the potency of ML218. Cav1.2 was significantly less sensitive to ML218 inhibition (IC50[~] 37 {micro}M) than Cav1.4, which could not be attributed to a valine in place of M1004 in Cav1.2. We conclude that ML218 and Z944 are dual Cav1/Cav3 modulators of CaV1.4 and should be used with caution when dissecting the contributions of CaV3 channels in tissues where Cav1.4 is expressed.

biophysics↗

bioRxiv2025

Structural insights on the ligand selectivity of the mouse trace amine-associated receptor TAAR7e

Trace amine-associated receptors (TAARs), a subclass of G protein-coupled receptors involved in detecting volatile amines, are co-expressed with odorant receptors in the main olfactory epithelium. Although many behaviorally relevant amines have been identified for olfactory TAARs, the molecular mechanisms underlying their selectivity for amines with varying carbon chain lengths and degrees of amine substitution remain unclear. In this study, we used mTAAR7e as a model to investigate these mechanisms. Homology modeling revealed a conserved ligand-binding pocket, supported by sequence-structure covariance analysis across TAARs. Structure-activity relationship profiling revealed key chemical determinants integral to mTAAR7e-mediated odorant recognition and provided, for the first time, a structural explanation for its selective preference toward longer carbon chains and tertiary amines. Computationally predicted interactions between mTAAR7e and the representative ligand N,N-dimethylcyclohexylamine (DMCHA) were validated through site-directed mutagenesis. Furthermore, conformational dynamics of mTAAR7e during receptor activation were characterized, providing insights into activation-related structural rearrangements. Together, these findings offer novel insights into the molecular logic of TAAR ligand selectivity and may advance our understanding of how TAARs mediate both olfactory and systemic aminergic signaling.

molecular biology↗

bioRxiv2025

PXDesign: Fast, Modular, and Accurate De Novo Design of Protein Binders

PXDesign achieves nanomolar binder hit rates of 17-82% across six of seven diverse protein targets, surpassing prior methods such as AlphaProteo. This experimental success rate is enabled by advances in both binder generation and filtering. We develop both a diffusion-based generative model (PXDesign-d) and a hallucination-based approach (PXDesign-h), each showing strong in silico performance that outperforms existing models. Beyond generation, we systematically analyze confidence-based filtering and ranking strategies from multiple structure predictors, comparing their accuracy, efficiency, and complementarity on datasets spanning de novo binders and mutagenesis. Finally, we validate the full design process experimentally, achieving high hit rates and multiple nanomolar binders. To support future research and broaden community adoption, we release the full PXDesign pipeline (https://github.com/bytedance/PXDesign), provide public access to PXDesign through a dedicated web server (https://protenix-server.com), and make all designed binder sequences available at the project page (https://protenix.github.io/pxdesign). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/670450v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@2a414aorg.highwire.dtl.DTLVardef@248f85org.highwire.dtl.DTLVardef@4a6afdorg.highwire.dtl.DTLVardef@1b622dd_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

In Vivo Evolution of Monoclonal Antibody CR3022 to Achieve Cross-Neutralization of SARS-CoV-2 and Implications for Vaccine Strategies Against SARS-Related Viruses

The epitope that monoclonal CR3022 binds to represents a promising target for broad protection against a wide range of human and zoonotic coronaviruses. We developed a powerful model to evaluate antibody affinity maturation in vivo using immunoglobulin (Ig)-humanized mice that express the predicted germline heavy chain of antibody CR3022. SARS-CoV/SARS-CoV-2 sequential immunization led to the convergent evolution of the germline CR3022 through somatic hypermutation (SHM) that resembled the affinity-matured CR3022 from a human, but now also adapted to key variants and divergent sarbecoviruses. While simple prime-boost strategies drove CR3022-epitope targeting, an intensive vaccination protocol elicited dominant responses to other epitopes. X-ray crystal structures revealed that SARS-CoV-2-neutralizing CR3022-like antibodies exhibit enhanced affinity by increasing polar and electrostatic interactions. Overall, these findings show CR3022-like clones can be readily adapted through SHM to increase breadth and potency to sarbecoviruses by relatively minor shifts in affinity with appropriate vaccination strategies.

immunology↗

bioRxiv2025

Population genomics of the endangered scaly-foot snail defines conservation units amid deep-sea mining threats in Indian Ocean vents

Hydrothermal vents in the Indian Ocean face imminent deep-sea mining, yet lack baseline high-resolution connectivity data for their endemic fauna. We present the first population genomic study of the endangered scaly-foot snail (Chrysomallon squamiferum), an iconic species distributed across three vent biogeographic provinces. Analysing 125 individuals from eight vent fields using 14 million single-nucleotide polymorphisms, we identify five genetic groups that warrant recognition as evolutionarily significant units. Demographic modelling reveals critical contributions from extinct or unsampled phantom populations to the contemporary genetic structure. Together with physical ocean modelling, we show that the deep currents drive asymmetric south-to-north gene flows, while transform faults act as dispersal barriers. We propose Longqi-Duanqiao fields on the Southwest Indian Ridge and Wocan field on the Carlsberg Ridge as two isolated populations prioritised for protection. Given its exceptional adaptations, wide distribution, and public recognition, the scaly-foot snail is well-positioned to serve as both a flagship and umbrella species to ensure the survival of a broader suite of vent biodiversity. As the International Seabed Authority finalises its Mining Code in 2025, our findings provide essential genomic evidence to mitigate the impacts of mining on genetic diversity and inform transboundary conservation strategies for this vulnerable ecosystem.

ecology↗

bioRxiv2025

Activation-Free Upgrading of Carboxylic Acids to Aldehydes and Alcohols

Advances in organic and gas waste valorization have enabled high-yield production of carboxylic acids, positioning them as promising feedstocks for the bioeconomy. However, carboxylic acids must be activated before downstream use, typically requiring ATP, CoA, or reduced ferredoxin to overcome unfavorable thermodynamics. These activators are costly to generate and divert carboxylic acids into CO2-releasing pathways, reducing carbon efficiency. Here, we demonstrate that aldehyde dehydrogenases (ALDHs) can directly reduce carboxylic acids to aldehydes without prior activation, a process previously thought to be biologically inaccessible. Screening 133 ALDHs revealed that this activity is remarkably widespread within the protein family, enabling production of aliphatic aldehydes and alcohols, diols, and aromatic alcohols, at titers >1 g/L, in some cases, after optimization of thermodynamic driving forces. Additionally, we applied this system to upgrade waste-derived carboxylic acid effluent streams from wastewater sludge, food waste, and waste gas (CO2). This activation-free process, termed "reverse aldehyde oxidation" (rAOX), establishes a broadly applicable, energy-efficient platform for carboxylic acid valorization at 100% carbon yield. Analogous to the reverse tricarboxylic acid cycle (rTCA) and reverse {beta}-oxidation (rBOX), rAOX exemplifies that metabolic reactions classically defined as unidirectional may have unexpected plasticity to operate in reverse and open new avenues in biomanufacturing.

synthetic biology↗

bioRxiv2025

A Parietal Memory Strength Signal Linked to Evidence Accumulation in Recognition Decisions

Recognising objects from memory requires an integration of sensory and mnemonic information. This process has been theorised to occur via a stochastic evidence accumulation process implemented within the parietal cortex. Recent electroencephalographic (EEG) evidence indicates that the widely studied parietal Late Positive Component (LPC) shows characteristics of such a mnemonic accumulation signal. Here, we formally investigated this hypothesis using generative computational modelling that links a trial-level memory strength variable in the Diffusion Decision Model (DDM) with LPC amplitudes prior to the time of the decision. We recorded EEG from 24 participants making recognition judgements based on either studied or novel words. Each participant completed up to three testing sessions. We replicated recent findings that the LPC ramps up and peaks around the time of the decision and corresponding motor response. LPC amplitudes also covaried with accuracy and response time, as expected of a neural correlate of memory strength. By fitting DDMs to LPC amplitudes and behavioural data using specialised neural network tools, we demonstrate that LPC amplitudes are selectively associated with the rate of evidence accumulation, signifying memory strength. This association was stronger for previously studied words compared to novel words, and strongest at the time window immediately prior to the recognition decision. Our findings therefore recast the LPC as a neural signature of mnemonic strength linked to the rate of evidence accumulation during recognition memory decisions.

neuroscience↗

bioRxiv2025

O-GlcNAcylation-Ubiquitin Crosstalk of METTL1 Drives m7G Epitranscriptomic Collapse and Lipid Metabolic Reprogramming in Diabetic Cardiomyopathy

BackgroundMetabolic remodelling and memory in cardiomyocytes is a pivotal mechanism underlying cardiomyopathy pathogenesis. Clinical observations demonstrate persistent progression of hyperglycaemia-induced multiorgan damage following blood glucose stabilization, which is predominantly mediated through epigenetic regulation. While prior studies have identified epigenetic contributions to hyperglycaemic myocardial injury, the involvement of RNA methylation-particularly N7-methylguanosine (m7G) modification-in this regulatory network remains undefined. MethodsClinical specimens were collected from diabetic patients, and cardiomyocyte-specific METTL1 and ob/ob knockout murine models were established in parallel. Multiomic profiling (proteomics, glycoproteomics, ubiquitinomics, m7G-MeRIP sequencing, and metabolomics) was systematically conducted. The molecular mechanisms governing METTL1 regulation via O-GlcNAcylation and ubiquitination were elucidated through integrated in vitro and in vivo assays. A DUB siRNA library and computational strategies combining molecular docking with molecular dynamics simulations were employed for screening drugs targeting METTL1 O-GlcNAcylation, followed by in vivo therapeutic validation. ResultsComparative analysis of diabetic murine and human samples revealed strong METTL1 downregulation in cardiomyopathy contexts. Tamoxifen-inducible METTL1 knockout mice presented exacerbated diabetic cardiomyopathy phenotypes, confirming its cardioprotective function. Multiomic integration demonstrated that METTL1-mediated m7G modification critically regulates cardiomyocyte fatty acid metabolism. Mechanistically, hyperglycaemia was found to induce O-GlcNAcylation at the METTL1-T268 residue, suppressing m7G methyltransferase activity by 38% (p < 0.01). Subsequent investigations revealed that USP5 deubiquitinase activity is impaired under hyperglycaemic conditions, leading to accelerated METTL1 degradation. Notably, administration of the first-in-class small drug HIT106265621 significantly attenuated cardiomyopathy-associated pathological alterations in ob/ob mice in vivo. ConclusionHyperglycaemia promotes METTL1 O-GlcNAcylation, which impedes USP5-mediated deubiquitination, consequently reducing cardiomyocyte METTL1 protein levels and m7G modification. METTL1 deficiency drives diabetic cardiomyopathy progression through fatty acid metabolic dysregulation, inflammatory activation, and myocardial hypertrophy. Pharmacological inhibition of the OGT-METTL1 interaction using HIT106265621 has therapeutic potential for metabolic cardiomyopathy intervention.

pathology↗

bioRxiv2025

Myocyte Damage and Mass Loss Drives Increasing Water Content, Compliance, and Survival in Septic Cardiomyopathy

Introduction/PurposeDuring the septic cardiomyopathy, the mechanism and relationship to outcome of changes in left ventricular (LV) end diastolic volume (EDV) and ejection fraction (EF) remains obscure. We compared serial changes in LVEF and LVEDV to successive alterations in LV wall ultrastructure, water content, and total mass to investigate whether these measures can explain their basis. MethodsWe performed cardiac magnetic resonance imaging at 0,6,18,30,42,54, and 92h post-bacterial challenge in a large-animal model (n=57) that mimics human septic cardiomyopathy. LV tissue was obtained for electron microscopy (EM) upon death and 66h in sacrificed survivors. ResultsBetween 0-6h post-challenge, LV compliance and EDV reached its greatest decline. Non-survivors (n=18) exhibited significantly greater reductions in LVEDV, along with more myocyte edema, mitochondrial swelling and myofilament fragmentation on EM. This increased tissue damage may explain why non-survivors developed worse LV compliance and a greater decline in LVEDV, which persisted until death. From 6-30h, LVEDV significantly improved to baseline in non-survivors, while survivors experienced [~]20% increases (n=39). Concurrently, there was significant LV mass loss and increases in percent water content that were significantly associated with increases in LVEDV. This is consistent with a passive mechanism for rapidly improving LV compliance and EDV. Full recovery of EF required additional days. We hypothesize the prolonged significant mass loss over 5d reflects an active process for remodeling fragmented myofilaments, eliminating myocyte edema, and mitochondrial swelling, ultimately restoring contractile function. ConclusionThe septic cardiomyopathy constitutes a diffuse ultrastructural injury to myocytes with three phases. Initially, there is a decrease in LVEDV, and EF due to myocyte damage within 6h of bacterial challenge; next, the patient sees a passive LVEDV recovery from 6-30h, where LV mass loss increases relative wall percent water content, which facilitates wall compliance and LVEDV; and lastly, the patient sees mass loss beyond 30h consistent with an active repair mechanism of myocytes, returning systolic function to normal. Therefore, EDV changes are a pathophysiological biomarker for sepsis outcomes. A lower LVEDV indicates persistent unrepairable ultrastructure damage with worsening wall compliance and poorer outcomes. LVEDV dilation is a sign of near-full recovery of ultrastructure injury, augmenting wall compliance and improving outcomes. Clinical ImplicationsWe explain herein why septic cardiomyopathy findings dont have clinical implications like heart failure. Septic patients who exhibit signs of heart failure, low LVEF with high EDVs, are doing well - reflecting mild myocyte injury, effective damaged tissues clearance, increased relative LV wall water content, and compliance. This augments the LVEDV, lowering the LVEF. Septic patients who deteriorate rapidly, contrary to heart failure patients, show high/normal LVEF and low/normal LVEDV. Here, the myocyte damage is severe, leading to insufficient wall repair, and this decreased wall compliance persists, preventing the LV from dilating and making LVEDV low which ultimately raises the LVEF.

physiology↗

bioRxiv2025

A moderated statistical test for detecting shifts in homeolog expression ratios in allopolyploids

Allopolyploids arise through hybridization between related species, carrying multiple sets of chromosomes from distinct progenitor, referred to as subgenomes. Within allopolyploids, duplicated genes across subgenomes, called homeologs, are thought to enhance environmental robustness by shifting their expression ratios depending on environmental and developmental changes. However, existing methods for detecting such ratio shifts, including HomeoRoq and Fishers exact test, are limited to allopolyploids with two subgenome sets inherited from two progenitors, and thus cannot handle more complex cases (e.g., allohexaploid wheat). Here, we present the HOmeolog Bias Identification Test (HOBIT), a statistical method for detecting shifts in homeolog expression ratios across different conditions using RNA-Seq count data. HOBIT performs a likelihood ratio test for each homeolog, comparing a full model allowing homeolog expression ratios to vary across conditions with a reduced model assuming constant ratios. Simulation benchmarks for allotetraploids and allohexaploids demonstrated that HOBIT outperforms existing methods in both area under the receiver operating characteristic curve and F1 score. Application to real RNA-Seq datasets from allotetraploid Cardamine flexuosa, allotriploid Cardamine insueta, and Triticum aestivum (wheat) produced biologically consistent results reflecting experimental settings. HOBIT provides a promising framework for uncovering homeolog regulation and adaptive responses in allopolyploids, without restrictions of ploidy complexities.

bioinformatics↗

bioRxiv2025

PD-L1 ligation on NK cells induces a metabolic shift from glycolysis to fatty acid oxidation, enhancing tumor infiltration and control

PD-L1 blockade benefits even PD-L1-negative tumors, suggesting that non-tumor cells contribute to PD-L1 expression. Natural killer (NK) cells, vital mediators of innate immunity, vigorously express PD-L1 upon activation. We demonstrate that the ligation of PD-L1 on circulating and tumor-infiltrating NK cells with the therapeutic anti-PD-L1 antibody atezolizumab, soluble PD-1, or PD-1+ cells enhances NK cell-mediated tumor clearance via changes in metabolism, adhesion, and migration. PD-L1 engagement increases NK cell tumor infiltration via the CXCR3 pathway and cytoskeletal remodeling, supported by a metabolic shift from glycolysis to fatty acid oxidation (FAO). Loss of a key FAO enzyme, CPT1A, in NK cells abrogates the PD-L1-mediated anti-tumor effect, supporting a critical role for FAO in enhanced NK cell killing. The PD-L1-triggered shift away from glycolysis permits NK cells to remain highly effective at tumor killing in glucose-restricted TME. Taken together, PD-L1 ligation enhances NK cell cytotoxicity and tumor infiltration and contributes to NK resilience in challenging TME conditions, resulting in a more effective anti-tumor immunity. One sentence summaryPD-L1 engagement on NK cells enhances their tumor infiltration and cytotoxic activity by inducing a metabolic switch from glycolysis to fatty acid oxidation, enabling sustained function in the glucose-deprived tumor microenvironment.

immunology↗

bioRxiv2025

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering

Spatial omics technologies have revolutionized the study of tissue architecture and cellular heterogeneity by integrating molecular profiles with spatial localization. In spatially resolved transcriptomics, delineating higher-order anatomical structures is critical for understanding how cellular organization affects tissue and organ function. Since 2020, more than 50 spatially aware clustering (SAC) methods have been developed for this purpose. However, the reliability of current benchmarks is undermined by their narrow focus on Visium and brain tissue datasets, as well as incorrect interpretation of manual annotation as ground truth. Here, we present SACCELERATOR, a community-driven, extensible framework that standardizes data formatting, method integration, and metric evaluation, and is designed to rapidly incorporate new methods and datasets. SACCELERATOR currently includes 22 SAC methods applied to 15 datasets spanning 9 technologies and diverse tissue types. Our analysis revealed substantial limitations in the generalizability and reproducibility of SAC methods across tissues and platforms. We also demonstrate that anatomical labels commonly used as ground truths are often biased, potentially error-prone, and, in some cases, unsuitable for benchmarking efforts. Rather than scoring and comparing methods, we propose a consensus-guided workflow that aggregates clustering results to generate consensus representations. Descriptive spatial metrics highlight areas of high entropy where method disagreement is highest, enabling targeted feedback for tissue experts. Applied to brain and cancer datasets, this approach uncovered biologically meaningful patterns overlooked by individual methods and manual annotations. Our results underscore the need for iterative, expert-in-the-loop analysis and reveal that traditional evaluation metrics do not always capture the subjective qualities of results. By improving tissue annotation and addressing key benchmarking limitations, SACCELERATOR provides a robust foundation for advancing spatial omics research.

genomics↗

bioRxiv2025

Development of a method for large-scale single-molecule analysis of tau proteoforms

Proteins exist as diverse proteoforms resulting from a combination of genetic variation, alternative splicing, and post-translational modifications. Current methods struggle to capture this complexity at the single-molecule level. Here we introduce Iterative Mapping of Proteoforms (IMaP), a method that enables the massively-parallel interrogation of millions to billions of single-protein molecules through iterative probing with fluorescently labeled antibodies. Using 12 site-specific antibodies, the method is capable of measuring 212 (4,096) potential proteoform groups. We used IMaP to measure proteoform group profiles of the tau protein, a key player in neurodegenerative diseases, using two pan anti-tau antibodies (Tau-13, Tau-216), three isoform-specific antibodies (Anti-0N, Anti-2N, Anti-4R), and seven phosphosite-specific antibodies (Anti-pT181, Anti-pS202+pT205, Anti-pT205, Anti-pS214, Anti-pT217, Anti-pT231, and Anti-pS396). The method demonstrates high sensitivity (detecting proteoforms at 0.1% abundance), high reproducibility (median CV <5.5%), and broad dynamic range (>3 orders of magnitude), outperforming conventional techniques in resolving closely related proteoform groups. We demonstrated that the method can be used on relevant biological samples by examining various neuronal models (iNeuron cells, organoids, MiBrains, and mouse brains) and human samples. This examination revealed 130 distinct tau proteoform groups with as many as six phosphorylation events. The non-random distribution of these phosphorylation events suggests ordered and site-specific modification processes rather than random, stochastic accumulation. Certain combinations of phosphorylation events were more abundant than others; for example, pT217 preferentially co-occurred with pT181. In validating the applicability of the assay to human disease samples, we noted a specific pattern of multiple phosphorylation events in an advanced Alzheimers disease patient that suggests a sequential pathway of pathological tau modification. Iterative Mapping of Proteoforms provides insights into proteoform complexity at the single-molecule level, with significant implications for understanding protein regulation in neurodegenerative diseases and beyond.

biochemistry↗

bioRxiv2025

HIF-1α+ CD4 T cells coordinate a tissue resident immune cell network in the lung

A deeper understanding of how tissue localized immune cells arise and function is critical for developing mucosal vaccines. Currently, there are no murine models that specifically target tissue T cells while leaving their lymphoid counterparts untouched. Here we leverage the observation that during influenza infection, HIF-1 regulatory activity is higher in the lung compared to lymph node CD4 T cells. Inducible deletion of Hif1a in CD4 T cells, at the onset of its activity in the lung, reduces the tissue resident T cell compartment with minimal impact on peripheral immunity. HIF-1-active CD4 T cells occupy the border of tertiary lymphoid structures, where they coordinate an IL-21-dependent network of spatially co-localized immune cells including macrophages, NK cells and IgA+ B cells. A similar HIF-1-dependent network is engaged in a lung adenocarcinoma model, highlighting a broader role for HIF-1+ CD4 T cells in integrating protective immunity during infection and cancer.

immunology↗

bioRxiv2025

Spatial and temporal scale-dependent feedbacks govern dynamics of biocrusts in drylands

Biota could be ecosystem engineers in generating an intrinsic heterogeneous landscape through scale-dependent feedbacks. Thereby, they can form resource enriched patchiness or islands of fertility, comprising of self-organizing spatial patterns. Research so far has largely focused on the self-organized spatial patterns of plant communities in drylands. It, however, remains unclear whether and how biocrusts having distinct morphology and life history from plant communities could self-organize themselves and form unique spatial patterns. Here we conducted field observations of biocrusts across successional stages and employed a probabilistic Cellular Automaton (CA) model to investigate the distinct self-organized spatial patterns exhibited by mosaic patches of mosses and lichens with different patch size distributions (PSDs). Our study demonstrates that short-range positive feedbacks initially promote the development of patches, featured with a heavy-tailed PSD, while long-range negative feedbacks subsequently curtail further expansion of big patches, thereby establishing a characteristic patch scale with regular PSDs. Strikingly, only lichens reverted back to the heavy-tailed PSD in the late succession stage, presumably implying self-organized critical fragmentation of lichen patches. Field measurements of biocrust performance at the center and edge of patches of varying sizes along succession stages further support the classic scale-dependent feedback mechanism for Turing pattern formation. Collectively, our results clearly demonstrate the capability of the biocrust communities to self-organize themselves to form distinct spatial patterns governed by the spatial and temporal scale-dependent feedbacks, potentially impacting dryland ecosystem functions and resilience. Significance StatementAn intriguing phenomenon is the capability of biota to form striking self-organized spatial patterns. Biocrusts serve as the soils skin and have different morphology and life history as compared to plant communities. We investigated these distinct self-organized spatial patterns exhibited by mosaic patches of mosses and lichens across succession stages through field surveys and a probabilistic Cellular Automaton (CA) model. Our results provide empirical evidence that biocrusts act as ecosystem engineers, forming self-organized spatial patterns. Simulations and field measurements of biocrust performance elucidate the mechanism of spatial and temporal scale-dependent feedbacks in governing biocrust spatial pattern formation. This self-organizing ability of biocrusts holds significant implications for ecosystem functions and the resilience of dryland ecosystems.

ecology↗

bioRxiv2025

Composition of Carotid Plaques Differs Between Chinese and United States Patients: A Histology Study

BackgroundThe clinical manifestations of cerebrovascular disease are known to differ between the Chinese and United States (U.S.) populations as do the plaque features on imaging. ObjectivesThe aim of this study was to investigate and compare the histological features of excised carotid plaques from Chinese and U.S. patients. MethodsCarotid endarterectomy specimens collected from two prospective studies were included. The entire plaque was serially sectioned (10 {micro}m thickness) at 0.5-1 mm intervals. Hematoxylin and eosin staining and Mallorys trichrome staining were performed. The morphology and components of the plaques were measured and compared between the two groups. ResultsA total of 1,152 histological sections from 75 Chinese patients and 1,843 sections from 111 U.S. patients were analyzed. The Chinese group had significantly smaller minimum lumen diameters (median: 1.1 vs. 1.3 mm, p=0.046) and a larger percent wall volume (median: 74% vs. 70%, p=0.018) than the U.S. group. After adjusting for confounding factors, carotid plaques in the Chinese population were more likely to have more lipid pools ({beta}=10.0%, 95%CI: 4.9 to 15.9%), more recent intraplaque hemorrhage (IPH; {beta}=8.4%, 95%CI: 4.5 to 12.7%), and less late IPH ({beta}=-8.2%, 95%CI: -11.3 to -5.4), and fewer fibrous cap disruptions (45% vs. 67%, p=0.061). Chinese plaques were more homogeneous and had a higher percentage of plaques with features of xanthomas than did U.S. plaques (20% vs 2.7%, p<0.001). ConclusionsThe histology of Chinese plaques differs significantly from that of U.S. plaques, suggesting substantial differences in the pathophysiology of atherosclerotic cerebrovascular disease between Chinese and North American populations, which could enhance the gap in racial pathology comparison, indicating a need for a different management approach. Central illustration O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/658993v1_ufig1.gif" ALT="Figure 1"> View larger version (83K): org.highwire.dtl.DTLVardef@14f16corg.highwire.dtl.DTLVardef@f60d66org.highwire.dtl.DTLVardef@1e9a822org.highwire.dtl.DTLVardef@11d7a31_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗