Biology subjects

Yuan, H.

Publications and source records attributed to Yuan, H..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Mycoelectronics: Bioprinted Living Fungal Bioelectronics for Artificial Sensation

The intelligence of the human biological system is enabled by the highly distributed sensing receptors on soft skin that can distinguish various stimulations or environmental cues, thus establishing the fundamental logic of sensing and physiological regulation or response. To replicate biological perception, two approaches have emerged: artificial nervous systems that utilize soft electronics as biomimetic receptors to convert external stimuli into frequency-encoded signals, and biohybrid solutions that integrate living cells, plants, or even live animals with electronic components to decode environmental cues for life-like sensations. However, most current biohybrid approaches for artificial sensation are based on eukaryotic cells, which suffer from slow growth, stringent culture conditions, environmental susceptibility, and short lifespans, thus limiting their integration into practical wearables or robotic sensory skins. Here, we introduce fungi-based printable "Mycoelectronics", which are created by additive bioprinting of living fungal mycelium networks onto stretchable electronics, as a practical living thermo-responsive sensory platform. This Mycoelectronics approach leverages fungis capacity for rapid biological responsiveness, cultivability with exponential growth, stability and self-healing in ambient conditions, bioprintability for scalable manufacturing, and mechanical flexibility for seamless integration with soft electronics. Critically, we discovered that the thermal responsiveness of the fungal network arises from intrinsic cellular processes--specifically, heat-induced vacuole remodeling and fusion, which modulate ionic transport and thus the electrical conductivity of the mycelial cells and networks, enabling a rapid temperature response. By bridging the gap between cell biology and soft electronics, the Mycoelectronics device with a living mycelium network functions as a thermal sensation system with rapid response and intrinsic self-healing properties, autonomously restoring sensing capabilities after damage or autonomously establishing sensor pathways in hard-to-reach locations. Furthermore, by integrating fungal thermal sensing with electronic circuits, we established a hybrid bioelectronic reflex arc that can actuate muscles and initiate diverse actions, suggesting promising applications in future neurorobotics and neuroprosthetics.

bioengineering↗

bioRxiv2025

JMJD1B-mediated FEN1 demethylation allows timely switching of Okazaki fragment maturation core enzymes to avoid mutagenic flap ligation by PARP1-LIG3

Efficient and faithful Okazaki fragment maturation (OFM) depends on the PCNA-coordinated actions of core enzymes Pol{delta}, FEN1, and LIG1. We demonstrate that Pol{delta}, FEN1, and LIG1 sequentially but not simultaneously bind to PCNA in mammalian cells. The association of FEN1 with PCNA, which lies at the center of this orderly program, is mediated by FEN1 R192 methylation, which is also crucial for preventing premature loading of LIG1. Conversely, FEN1 demethylation by the recently identified arginine demethylase JMJD1B promotes FEN1 dissociation from PCNA and LIG1 recruitment. Disruption of the sequential PCNA binding program in R192Q or Jmjd1b-/- cells results in unprocessed 5 flaps that prevent OFM and induction of PARP1-dependent recruitment of LIG3, which has flap ligation activity to join incompletely processed OFs. This alternative OFM process supports cell survival but causes duplications and other DNA mutations. Our findings define fundamental and alternative DNA replication processes underlying mutagenesis and cell survival. HighlightsO_LIThe core enzymes involved in Okazaki fragment maturation (OFM), DNA polymerase {delta} (Pol{delta}), flap endonuclease 1 (FEN1), and ligase 1 (LIG1), sequentially bind to the scaffold protein PCNA for their concerted actions C_LIO_LIFEN1 R192 methylation enables FEN1 binding to PCNA; JMJD1B-mediated FEN1 arginine demethylation provokes FEN1 exit from PCNA and LIG1 recruitment C_LIO_LIFEN1 R192Q mutation and JMJD1B deficiency oppositely alter dynamic PCNA interactions with FEN1 and LIG1 and result in distinct OFM DNA intermediate structures C_LIO_LIActivation of PARP1 at replication forks due to disruption of the sequential PCNA binding program induces LIG3-mediated alternative mutagenic 5 flap ligation for survival. C_LI

cell biology↗

bioRxiv2025

Discrete interneuron subsets participate in GluN1/GluN3A excitatory glycine receptor (eGlyR)-mediated regulation of hippocampal network activity throughout development and evolution.

Decades of studies implicating GluN3A N-methyl-D-aspartate receptor (NMDAR) subunits in physiological and pathological function have largely been interpreted through direct regulation of conventional glutamatergic NMDARs. However, emerging evidence indicates that GluN3A frequently assembles with GluN1 forming unconventional glutamate-insensitive NMDARs that operate as native excitatory glycine receptors (eGlyRs). Here we demonstrate that hippocampal somatostatin and neurogliaform interneurons (Sst-INs and NGFCs) express functional eGlyRs from early postnatal through adult ages. In the developing hippocampus eGlyR-mediated excitation of NGFCs with ambient glycine dramatically increases GABAergic tone, with consequences for the generation of giant depolarizing potentials (GDPs). In the mature hippocampus, eGlyR- mediated excitation of Sst-INs regulates sharp wave ripples (SWRs). Finally, we reveal evolutionary conservation of hippocampal Sst-IN eGlyRs and eGlyR- mediated SWR regulation in non-human primates confirming functional eGlyR availability for therapeutic potential in higher species. Our findings underscore that eGlyR mediated regulation of cell and circuit excitability through both cell autonomous and cell non-autonomous mechanisms must be considered to understand GluN3A roles in brain development, plasticity, and disease.

neuroscience↗

bioRxiv2025

Synthesis and In Vitro Characterization of OGA-2506 as a High Affinity Radioligand for O-GlcNAcase

O-GlcNAcase (OGA) is a glycoside hydrolase that regulates protein O-GlcNAcylation, a dynamic post-translational modification implicated in numerous cellular processes. Dysregulation of OGA alters cellular O-GlcNAc homeostasis and has been linked to neurodegenerative and other chronic diseases. The development of radioligands targeting OGA, particularly those derived from well-characterized tool compounds, could substantially advance drug discovery in this area. Herein, we report the radiosynthesis of a novel tritium (3H)-labeled radioligand 7 (code name [3H]OGA-2506) derived from a chiral piperidine scaffold, and its preliminary in vitro binding evaluation. Starting from iodine precursor 8, palladium-catalyzed tritiation afforded [3H]7 with excellent molar activity (1822 GBq/mmol) and high radiochemical purity (>99%). Saturation binding studies revealed that [3H]7 binds OGA with high affinity to rat striatum homogenates (Kd = 3.56 nM; Bmax = 42.62 nM). Competition assays yielded an IC50 of 5.55 nM, and preliminary autoradiography demonstrated heterogeneous regional distribution in the brain with specific binding. These findings highlight [3H]7 as a valuable tool for OGA binding studies and provide a foundation for the future development of novel positron emission tomography (PET) ligands to probe O-GlcNAc signaling in the brain.

pharmacology and toxicology↗

bioRxiv2025

Sarbecovirus Rc-o319 S-Protein Structures Reveal Highly Specialized Adaptation to Rhinolophus cornutus ACE2

Bat sarbecoviruses often exhibit species-dependent ACE2 specificity. Understanding the determinants of receptor specificity enables better assessment of the cross-species transmission potential of sarbecoviruses. Here, we characterize the S-protein of Rc-o319, a sarbecovirus identified in Japanese Rhinolophus cornutus bats. Featuring an unusual 9-amino-acid deletion within its receptor binding motif (RBM), Rc-o319 S-protein utilizes its cognate R. cornutus ACE2 (bACE2R.cor) but not human ACE2 (hACE2), demonstrating highly restricted receptor specificity. Cryo-EM structures reveal two locked prefusion conformations of the Rc-o319 S-trimer and define a novel type-1b receptor-binding domain (RBD), featuring a distinct beta-loop (BL) within the RBM due to the RBM-deletion. The Rc-o319-RBD:bACE2R.cor complex structure reveals unique interactions mediated by the specialized BL and RBM-loop of Rc-o319-RBD and by a bACE2R.corglycan. Structure-guided mutagenesis demonstrates that changes in BL and RBM-loop within the Rc-o319 S-RBD must occur simultaneously to allow medium-to-high-affinity hACE2 binding. Comparative assays further show that the bACE2R.cor receptor supports only a subset of sarbecoviruses, highlighting its restricted sarbecovirus compatibility. Our findings establish the Rc-o319 S-protein as a structurally and functionally specialized adaptation to R. cornutus ACE2 and identify the structural constraints limiting its cross-species transmission potential. Author SummarySARS-related viruses are widely found in horseshoe bats. Some can bind the human ACE2 receptor with variable affinities, whereas others bind only bat ACE2 receptors. Understanding the basis for this difference is critical for assessing spillover risk. We studied the spike protein of a bat sarbecovirus, Rc-o319, isolated from Japanese Rhinolophus cornutus horseshoe bats. Although Rc-o319 is genetically related to SARS-CoV-2, it is unable to bind the human ACE2 receptor. Structural analyses and functional experiments revealed that the Rc-o319 spike protein possesses a distinct receptor-binding motif (RBM). This RBM features a specialized "beta-loop" that replaces the "large-loop" found in human-infecting sarbecoviruses. The beta-loop enables high-affinity binding to its cognate Rhinolophus cornutus bat ACE2 receptor while simultaneously preventing optimal interaction with human ACE2. We further found that acquisition of high affinity for the human ACE2 receptor would require coordinated changes across multiple regions of the RBM, including changing the beta-loop into a large-loop structure. Together, our findings demonstrate that the Rc-o319 spike protein is highly adapted to its cognate bat ACE2 receptor and faces substantial structural constraints that limit its ability to switch to binding human ACE2.

microbiology↗

bioRxiv2025

High-Fat Diet-Induced Obesity Impairs Endothelium-Dependent Relaxation via MLCK Activation: Reversal by ML-7 in Rabbits

ObjectiveObesity is an independent risk factor for CVD(cardiovascular diseases) and elevated cardiovascular mortality, though the precise mechanisms remain incompletely elucidated. Impaired endothelium-dependent relaxation is an early manifestation of cardiovascular diseases. This study investigated the impact of HFD(high-fat diet)-induced obesity on endothelium-dependent relaxation function and explored the potential role of MLCK(myosin light chain kinase) signaling. MethodsForty-five New Zealand White rabbits were randomized into three groups: a control group (normal diet), HFD(high-fat diet) group, and an ML-7 group (HFD plus the MLCK inhibitor ML-7). After 8 weeks of feeding, vascular endothelial function was assessed in vivo by measuring FMD(flow-mediated dilation). Serum lipids and blood glucose levels were determined. Endothelium-dependent vasodilation was evaluated ex vivo using aortic ring assays. The protein expression levels of MLCK and eNOS(endothelial nitric oxide synthase), as well as the phosphorylation level of MLC(myosin light chain), in rabbit arteries were analyzed by Western blot. ResultsHFD-fed rabbits developed obesity, dyslipidemia (elevated TC[total cholesterol], LDL-C[low-density lipoprotein cholesterol], and ox-LDL[oxidized low-density lipoprotein]), perirenal adipose tissue deposition, and significant endothelial dysfunction, evidenced by impaired endothelium-dependent relaxation function and morphological endothelial damage. Western blot analysis revealed upregulated MLCK and eNOS expression, along with increased phosphorylation of MLC in the arterial walls of obese rabbits, despite no significant change in NO(nitric oxide) levels compared to controls. Treatment with ML-7 ameliorated endothelium-dependent relaxation function impairment. Furthermore, the inherent limitations of FMD as a non-invasive technique in terms of accuracy and sensitivity for evaluating endothelium-dependent dilation. ConclusionsObesity-induced endothelial dysfunction arise from visceral fat accumulation, dyslipidemia, oxidative stress, and MLCK overexpression. Notably, MLCK inhibition via ML-7 restores vascular function, highlighting its therapeutic potential in obesity-related vascular injury.

physiology↗

bioRxiv2025

Helicobacter pylori genome aggregation database reveals complex evolutionary forces shaping its genomic landscape and clinical impact in East Asia

We assembled HPgnomAD, a comprehensive global genome aggregation database of Helicobacter pylori (H. pylori) featuring 7,544 high-quality genomes from 278 populations, along with the first species-wide haplotype reference panel for genotype imputation. The panel provides high accuracy across diverse H. pylori populations, including those from low-coverage data, and is openly accessible with integrated analysis tools (https://www.hpgnomad.top/). Variant discovery revealed 1.82 million SNPs and 0.65 million InDels, with African strains exhibiting the most tremendous diversity and East Asian strains showing unexpectedly high novel variation. Fine-scale analysis of the hpEAsia lineage revealed six new sublineages shaped by altitude-, latitude-related divergence and region-specific admixture. Phylogenomic dating revealed two divergence waves in East Asia, paralleling Upper Paleolithic settlement and Neolithic human expansions, with highland-lowland separation at [~]18.8 kya, followed by the formation of complex geography-related population substructures. Genome-wide scans revealed adaptive loci related to metal acquisition, nitrogen metabolism, surface adhesion, and membrane transport, including altitude-associated highly differentiated variants linked to antibiotic resistance and gastric disease. By integrating genomic, evolutionary, environmental, and clinical data, HPgnomAD offers a framework for understanding H. pylori evolution, host-pathogen adaptation, and precision medicine worldwide.

evolutionary biology↗

bioRxiv2025

Lessons from a gene knockout mouse model: no phenotypes induced by deletion of the TPR4 domain of Ttc22

The TTC22 gene encodes a protein containing seven tetratricopeptide repeats (TPRs), which mediate protein-protein interactions as chaperones. We previously reported that the level of TTC22 transcript variant 1 (TTC22v1) was downregulated in human colon adenocarcinoma (COAD) and that TTC22 upregulated m6A-mediated WTAP and SNAI1 expression via the TTC22-RPL4 interaction and subsequently promoted COAD metastasis. Thus, a commercially available C57BL/6N mouse model in which the Ttc22 exon 2&3 encoding the TPR4 (equal to the human TTC22 TPR3) domain was knocked out via CRISPR-Cas9 was used to evaluate the contribution of Ttc22 to the development of mice and COAD. To determine the status of Ttc22 expression in Ttc22 knockout mice, we prepared a rabbit polyclonal antibody against the mouse Ttc22 protein, which could bind both wild type Ttc22 and TPR4-deleted Ttc22 proteins overexpressed in HEK293T cells, as determined by Western blot analysis. Ttc22 proteins were detected in colon tissue samples from wild-type mice and Ttc22 hemi-knockout (Ttc22 -/+) mice but not in those from fully Ttc22 knockout (Ttc22-/-) mice. Unfortunately, the long-term observation results demonstrated that Ttc22 knockout (KO, including Ttc22-/+ or Ttc22-/-) did not affect the body weight, development, fertility, or spontaneous tumor incidence of male or female mice. No differences in the incidence of AOM/DSS-induced COAD were observed between these mouse groups, although Ttc22 deletion partially resulted in the upregulation of genes related to the host adaptive response to inflammation in the colon mucosa. In conclusion, no phenotypes were induced by Ttc22 inactivation in C57BL/6N mice. HighlightsO_LIKnockout of Ttc22 exons 2 and 3 completely disrupted gene expression. C_LIO_LIKnockout of Ttc22 does not affect the development of C57BL mice. C_LIO_LIKnockout of Ttc22 does not affect the induction of mouse colon cancer by AOM/DSS. C_LI

molecular biology↗

bioRxiv2025

Identification of biomarkers for ulcerative morphology in carotid atherosclerosis plaques through single-cell RNA sequencing data

BackgroundCarotid atherosclerotic stenosis (CAS) is a major risk factor for stroke, particularly when associated with ulcerative plaque morphology. However, the molecular mechanisms underlying ulceration remain inadequately defined. In this study, we aimed to construct single-cell atlases of ulcerative and non-ulcerative CAS plaques to identify biomarkers associated with ulcerative lesions. MethodsPlaque tissues from four ulcerative and three non-ulcerative CAS samples were collected and subjected to single-cell RNA sequencing (scRNA-seq). Cell types were identified through scRNA-seq analysis, and differential cell types were determined by comparing their proportions between the 2 groups. Candidate genes were identified by intersecting differentially expressed genes (DEGs) within these differential cell populations. Subsequently, the Molecular Complex Detection (MCODE) plugin in Cytoscape was employed to confirm the biomarkers. Functional annotation and regulatory network analysis were then performed to investigate underlying biological mechanisms. ResultsscRNA-seq analysis identified 7 cell types, of which 6 showed differential proportions, leading to the identification of 61 candidate genes and 7 key biomarkers (KLF2, JUNB, FOS, HSPA1A, DUSP1, JUND, and ZFP36). Enrichment analysis indicated that these biomarkers may influence ulcerative CAS plaques via RNA polymerase II-mediated transcription and stress-response pathways. Regulatory network analysis revealed complex interactions, with RBMX, STAT3, YTHDF3, DDX3X, and ELAVL1 identified as potential upstream regulators. ConclusionsKLF2, JUNB, FOS, HSPA1A, DUSP1, JUND, and ZFP36 were identified as biomarkers, offering novel insights into the molecular mechanisms underlying ulcerative morphology in CAS.

pathology↗

bioRxiv2025

Borzoi-informed fine mapping improves causal variant prioritization in complex trait GWAS

1Genome-wide association studies (GWAS) have identified thousands of trait-associated loci. Prioritizing causal variants within these loci is critical for characterizing trait biology. Statistical fine mapping identifies causal variants at trait-associated loci, but linkage disequilibrium (LD) and limited GWAS sample sizes prevent the resolution of many associations. Functionally informed approaches augment fine mapping by estimating variant prior causal probabilities based on overlap with trait-relevant functional annotations. However, functional enrichment provides only an indirect proxy for variant functional impact. Sequence-to-function models directly estimate variant effects on molecular phenotypes from underlying sequence context. Borzoi is a long-context model that predicts sequence determinants of transcription, splicing, and polyadenylation across diverse tissues and cell types. Here we present Sniff, a Borzoi-informed fine-mapping approach that integrates broad genomic functional annotations with Borzoi-predicted variant effects via PolyFun to estimate variant prior causal probabilities. Applied to 15 UK Biobank traits, Sniff identifies 9.45% additional fine-mapped variants compared to PolyFun-Baseline at posterior inclusion probability (PIP) > 0.8. Sniff-prioritized variants exhibit allele-specific activity in reporter assays and are predicted to have tissue-specific activity in trait-relevant tissues. For most traits, genes nominated by Sniff receive higher scores from the orthogonal gene prioritization method PoPS compared to genes nominated using functional annotations alone. Because differentially prioritized variants are driven by Borzoi predictions, we leverage attribution techniques to characterize sequence features underlying fine mapping and generate mechanistic hypotheses for GWAS associations.

genetics↗

bioRxiv2025

A triple fluorescence approach to measure O-GlcNAc dyshomeostasis in stem cells

O-GlcNAcylation is an essential post-translational modification, the complete loss of which results in lethality. Despite modifying thousands of nucleocytoplasmic proteins, O-GlcNAc is controlled by just two enzymes: O-GlcNAc transferase (OGT), which adds the modification, and O-GlcNAcase (OGA), which removes it. Disruptions in O-GlcNAc homeostasis, such as an imbalanced OGT/OGA ratio or aberrant O-GlcNAc levels, are implicated in a wide range of human diseases, including Alzheimers disease, cancer, intellectual disability, and diabetes. As such, O-GlcNAc and its regulatory enzymes represent valuable therapeutic targets. However, current tools do not permit informative, large-scale drug or genetic screening, hindering the development of O-GlcNAc-targeted therapies. Here, we present a triple fluorescence stem cell sorting approach in which both endogenous OGT and OGA are tagged with spectrally distinct fluorescent proteins and O-GlcNAc levels can be quantified. We demonstrate that this system faithfully reports disruptions in O-GlcNAc homeostasis. Furthermore, we show that the O-GlcNAc feedback regulation is not solely dependent on O-GlcNAc levels, indicating a role for non-catalytic functions of OGT and OGA. Overall, we provide a high-throughput screening platform that enables reliable and quantitative measurement of O-GlcNAc homeostasis, paving the way for identifying compounds and pathways that target protein O-GlcNAcylation.

molecular biology↗

bioRxiv2025

Recurring Transient Brain-Wide Co-Activation Patterns from EEG Spatially Resembling Time-Averaged Resting-State Networks

It has long been established that human brains remain functionally active at rest, as demonstrated with the discovery of resting-state networks (RSNs) underlying spontaneous neural activity. Recent studies suggest that classical RSNs estimated from functional magnetic resonance imaging (fMRI) data using time-domain functional connectivity measures might be driven by recurring point-process events. Due to the slow hemodynamic response, fMRI is not able to reveal such point-processes at the timescale of neuronal events while electroencephalography (EEG) holds the promise due to its millisecond temporal resolution and successful reconstruction of fMRI-like RSNs from EEG. The present study reported a set of recurring transient (<100 milliseconds) cortical co-activation patterns (CAPs) derived from resting-state EEG using a clustering algorithm with spatial-domain measures (i.e., k-means). Our results indicate that this set of CAPs exhibit strong spatial correspondence with known RSNs, not only those derived from the same EEG data using time-domain measures (i.e., independence), but also those from fMRI literature, covering visual, auditory, motor, limbic, high-order, and default mode networks. CAPs exhibit the properties of hemispheric symmetry, spatially separatable sub-systems, and intersubject variability gradient across functional systems, which have all been observed in classical RSNs. In terms of differences between CAPs and RSNs beyond their timescales, CAPs demonstrate greater intersubject reproducibility of spatial patterns compared to their time-averaged RSNs counterparts. These findings suggest that classical RSNs might be driven by recurring transient neuronal activations captured in CAPs. More importantly, CAPs can reveal much fast dynamics of such brain-wide networked neuronal activations (e.g., different CAPs exhibit significantly different occurrences and lifetimes) and benefit from their great intersubject reproducibility, thus underscoring their potential to advance our understanding on neuronal mechanisms of spontaneous large-scale brain activation phenomena.

bioengineering↗

bioRxiv2025

Predicting cell type-specific coverage profiles from DNA sequence

Predicting expression profiles from RNA-seq experiments provides a powerful approach for universal sequence-based variant effect prediction, enabling researchers to score variants that affect total gene expression and relative isoform abundances. These models can be repurposed for new prediction tasks through transfer learning. However, current base models train primarily on bulk RNA-seq profiles derived from tissues and cell lines, overlooking the wealth of single-cell 3-seq data that captures cell type-specific gene regulation. Here, we extend the capabilities of our recently developed Borzoi model by training on single-cell 3-seq expression profiles from the Tabula Sapiens, Tabula Muris, and the Adult Brain Atlas, aggregated by cell type. This new model, Borzoi Prime, enables accurate variant interpretation across diverse cells, spanning erythrocytes to microglia. Training on 3-seq profiles improves the models ability to predict cell- and tissue-specific alternative polyadenylation, even in the original bulk RNA-seq data. Through UTR-wide mutagenesis experiments of alternatively polyadenylated genes, we highlight determinants of cell type-specific 3 UTR regulation learned by the model. This cell type-resolved approach opens new possibilities for understanding genetic variant effects via multiple layers of regulation in specific cellular contexts.

genomics↗

bioRxiv2025

An atlas of TF driven gene programs across human cells

Combinations of transcription factors (TFs) regulate gene expression and determine cell fate. Much effort has been devoted to understanding TF activity in different tissues and how tissue-specificity is achieved. However, ultimately gene regulation occurs at the single cell level and the recent explosion in the availability of single cell gene expression data now makes it possible to understand TF activity at this granular level of resolution. Here, we leverage a large collection of Human Cell Atlas (HCA) single cell data to explore TF activity by examining cell-type and tissue-specific sets of target genes, or regulons. We compile a regulon atlas, CellRegulon, and map the activity of TFs in an extensive set of healthy adult and foetal tissues spanning hundreds of cell types. Using CellRegulon, we describe dynamic patterns of co-regulation, associate TF-modules with different cellular functions and characterise the distribution of active TFs and TF families across cell types. We show that CellRegulon can link disease gene expression signatures to cell types and TFs relevant to the disease. Finally, using a newly generated multiome dataset of the adult lung, we show how CellRegulon can be extended into an enhancer-gene regulatory network (eGRN) to improve cell-type associations with genetic risk loci for diseases, such as childhood onset asthma, COPD and IPF, and to identify high risk gene modules. Our database for easy download and interactive exploration allows researchers to understand key gene modules activated at cell type transitions and will therefore be valuable for tasks such as cell type engineering (https://www.cellregulondb.org).

genetics↗

bioRxiv2025

Parameter-Efficient Fine-Tuning of a Supervised Regulatory Sequence Model

1DNA sequence deep learning models accurately predict epigenetic and transcriptional profiles, enabling analysis of gene regulation and genetic variant effects. While large-scale training models like Enformer and Borzoi are trained on abundant data, they cannot cover all cell states and assays, necessitating new model training to analyze gene regulation in novel contexts. However, training models from scratch for new datasets is computationally expensive. In this study, we systematically evaluate a transfer learning framework based on parameter-efficient fine-tuning (PEFT) approaches for supervised regulatory sequence models. We focus on the recently published state-of-the-art model Borzoi and fine-tune to new RNA-seq datasets, enabling accurate and efficient analysis of gene regulation across different biological systems. Our results demonstrate that PEFT substantially improves memory and runtime efficiency while achieving high accuracy. The transferred models effectively predict held-out gene expression changes, identify regulatory drivers of differentially expressed genes, and predict cell-type-specific variant effects. Our findings underscore the potential of PEFT to enhance the utility of large-scale sequence models like Borzoi for broader application to study genetic variants and regulatory drivers in any functional genomics dataset. Code for efficient Borzoi transfer is available in the Baskerville codebase https://github.com/calico/baskerville.

bioinformatics↗

bioRxiv2025

Coupling Anaerobic Oxic and Integrated Fixed Activated Sludge Processes for Removal and Transformation of Refractory Organic Matter in Livestock and Poultry Digestate

Effective treatment of livestock and poultry digestate remains challenging due to its high content of refractory organic matter. In this study, a coupled anaerobic-oxic (A/O) and integrated fixed-film activated sludge (IFAS) system was investigated to evaluate its capacity for organic removal and molecular transformation. The IFAS system outperformed the A/O system, achieving an organic removal efficiency of 43%, compared to 17% in the A/O process. Molecular analyses revealed distinct transformation pathways: the A/O process tended to increase the molecular weight and structural complexity of dissolved organic matter, whereas the IFAS process promoted oxidative fragmentation, resulting in the formation of smaller, oxygen-rich compounds. These changes were reflected in key molecular indices (DBE, NOSC, AImod) and the accumulation of carboxyl-rich intermediates. Microbial community analysis associated Bacteroidota with the degradation of oxygenated compounds via hydrolytic processes, while Actinobacteria and Deinococcota were linked to the transformation of lignin- derived aromatics. The integration of advanced molecular characterization with microbial profiling highlights the IFAS systems enhanced capability for both structural simplification and biodegradation of complex organics, providing a promising strategy for the treatment of high-strength organic wastewater.

microbiology↗

bioRxiv2025

DNA2 and MSH2 activity collectively mediate chemically stabilized G4 for efficient telomere replication

G-quadruplexes (G4s) are widely existing stable DNA secondary structures in mammalian cells. A long-standing hypothesis is that timely resolution of G4s is needed for efficient and faithful DNA replication. In vitro, G4s may be unwound by helicases or alternatively resolved via DNA2 nuclease mediated G4 cleavage. However, little is known about the biological significance and regulatory mechanism of the DNA2-mediated G4 removal pathway. Here, we report that DNA2 deficiency or its chemical inhibition leads to a significant accumulation of G4s and stalled replication forks at telomeres, which is demonstrated by a high-resolution technology: Single molecular analysis of replicating DNA (SMARD). We further identify that the DNA repair complex MutS (MSH2-MSH6) binds G4s and stimulates G4 resolution via DNA2-mediated G4 excision. MSH2 deficiency, like DNA2 deficiency or inhibition, causes G4 accumulation and defective telomere replication. Meanwhile, G4-stabilizing environmental compounds block G4 unwinding by helicases but not G4 cleavage by DNA2. Consequently, G4 stabilizers impair telomere replication and cause telomere instabilities, especially in cells deficient in DNA2 or MSH2.

molecular biology↗

bioRxiv2025

Temporal evolution of hemodynamics in murine arteriovenous fistula: a micro-CT based computational fluid dynamics study

In this study, we investigated the hemodynamic characteristics of arteriovenous fistulae (AVF) in murine models using micro-CT based computational fluid dynamics (CFD). By combining high-resolution micro-CT imaging with ultrasound flow measurements, our methodology offers a cost-effective and efficient alternative to traditional MRI-based approaches. CFD simulations performed at 7 and 21 days post-surgery revealed significant temporal changes in both geometry and hemodynamics. Geometric analysis showed that: the proximal artery diameter increased from 0.29 mm to 0.38 mm, while the initial 2 mm fistula segment showed a 21.6% decrease (0.74 mm to 0.58 mm). Blood flow through the AVF nearly doubled from 1.33 mL/min to 2.57 mL/min. Time-averaged wall shear stress (TAWSS) peak values increased from 142 Pa (day 7) within the proximal artery to 200 Pa (day 21), in the stenotic region. The oscillatory shear index (OSI) showed marked elevation at the anastomosis (increasing from 0.22 to 0.48), indicating disturbed flow development. An inverse relationship between TAWSS and OSI was identified consistent with previous studies. Our methodology demonstrates the capability to analyze relationships between early hemodynamics and subsequent geometric changes. This approach could enable identification of regions susceptible to stenosis development and monitoring of AVF maturation, which could ultimately lead to quantitative metrics to evaluate surgical outcomes and early therapeutic interventions.

bioengineering↗