Biology subjects

Yu, Z.

Publications and source records attributed to Yu, Z..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Roles of K-channel activity in feather bud morphogenesis

Bioelectricity plays a key role in shaping tissues during early development. In developing chick skin, we previously demonstrated that a transient standing electrical current loop forms within individual feather buds as they start to elongate. Current flows into the feather bud tip via calcium channels, facilitating collective distal dermal cell movement, thus determining bud orientations. Here, we further evaluate the hypothesis that potassium channels carry the current that flows out of the bud base. We found potassium channel blockers convert periodic feather primordia into horizontal stripes and alter bud aspect ratios by disrupting the bud elongation process. Bioelectric characterization showed the entire current loop is altered, not only the outward current at the base, but also the inward current at the feather bud tip. In situ hybridization shows beta-catenin and Sonic Hedgehog, both feather bud markers, are reduced, resulting in altered periodic patterning and bud shaping. These findings show that a complex multiscale interdependency of ion channel function across a multicellular cell collective is essential for periodic feather patterning and shaping of 3-dimensional feather architecture during skin morphogenesis. Summary StatementCalcium channels at the feather bud tip and potassium channels at the base maintain a standing current loop, creating an essential multicell collective for proper feather bud patterning and morphology.

developmental biology↗

bioRxiv2025

Mechanism of Sanliangsan Lipid-Lowering in treating hyperlipidemia: insights from network pharmacology and molecular docking

Background and ObjectiveThis study aimed to identify the active ingredients, key targets, and signaling pathways of Sanliangsan Lipid-Lowering (SLL) in the treatment of hyperlipidemia (HLP) using network pharmacology, and to further clarify the material basis and mechanism responsible for its lipid-lowering efficacy. MethodsAll active ingredients of SLL were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), followed by the identification of target proteins corresponding to each active ingredient. Target genes associated with these target proteins were obtained from the Uniprot database, with duplicate genes excluded to generate the predicted targets of the active ingredients.Cytoscape was utilized to construct the "Herb-Active Ingredient-Predicted Target" network for SLL. Targets related to hyperlipidemia (HLP) were retrieved from the GeneCards, OMIM, and DrugBank databases using "hyperlipidemia" as the keyword. The intersection of the predicted targets of SLL active ingredients and HLP-related targets was defined as the potential therapeutic targets of SLL for HLP. Utilizing Cytoscape 3.9.1 software, the top 20 targets with the highest Degree values were selected to construct the "Herb-Active Ingredient-Target-Disease" network, (esignated as the "Herb-Active Ingredient-Target Network of SLL against HLP." The STRING database was employed to build a protein-protein interaction (PPI) network of the potential therapeutic targets, which was subsequently analyzed using the Network Analysis, CytoNCA, and CytoHubba plugins in Cytoscape to identify the top 10 key targets. The Metascape platform was used for Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the key targets, and the Bioinformatics online tool was applied to visualize the analytical results. Furthermore, AutoDock Tools 1.5 software was utilized to perform molecular docking between the active ingredients and key targets, thereby validating the results of the network pharmacology analysis. ResultsA total of 115 active ingredients and 255 corresponding predicted targets of SLL were screened from the TCMSP database. Additionally, 2106 HLP-related targets were retrieved from the aforementioned databases, and 140 common targets (potential therapeutic targets) were identified through intersection analysis. From these common targets, the top 20 with the highest Degree values were selected for the construction of the "Active Ingredient-Potential Target-Disease" network. Network analysis revealed that kaempferol, quercetin, and formononetin were the top three active ingredients in terms of content, while tumor necrosis factor (TNF), interleukin-6 (IL6), protein kinase B1 (AKT1), interleukin-1{beta} (IL1B), prostaglandin-endoperoxide synthase 2 (PTGS2), peroxisome proliferator-activated receptor {gamma} (PPARG), caspase 3 (CASP3), and hypoxia-inducible factor 1 (HIF1A) were the targets associated with the largest number of active ingredients. The PPI network consisted of 140 nodes and 3,207 edges. By using the CytoHubba plugin for analysis, six key targets were identified: AKT1, TNF-, IL-1 {beta}, IL6, PPARG and PTGS2. The GO functional enrichment analysis revealed 30 entries, which encompassed 10 biological processes (such as positive regulation of transcription by RNA polymerase II), 10 cellular components (such as extracellular space), and 10 molecular functions (such as transcription coactivator binding). Additionally, 10 KEGG signaling pathways were identified, including Lipid and atherosclerosis, the AGE-RAGE signaling pathway in diabetic complications, and Fluid shear stress and atherosclerosis. The findings indicated that SLL exerts a therapeutic effect on HLP by regulating multiple signaling pathways. Molecular docking results demonstrated that the binding energies of the three core ingredients--kaempferol, quercetin, and formononetin--with all key targets were less than -5.0 kJ/mol, with the lowest binding energy (-10.1 kJ/mol) observed between formononetin and PTGS2, indicating a strong binding affinity between these two molecules. ConclusionThis study identified the potential active ingredients, key targets, and core signaling pathways of SLL in treating HLP, confirming that SLL exerts its lipid-lowering effect through a synergistic "multi-component, multi-target, multi-pathway" mechanism. It provides a theoretical basis for further experimental validation and clinical application of SLL in managing HLP.

molecular biology↗

bioRxiv2025

Real-Time Viability Assessment of Ex Vivo Mouse Kidneys for Transplant Applications Using Dynamic Optical Coherence Tomography

Kidney transplantation remains the preferred treatment for patients with end-stage kidney disease. However, the ongoing shortage of donor organs continues to limit the availability of transplant treatments. Existing evaluation methods, such as the kidney donor profile index (KDPI) and pre-transplant donor biopsy (PTDB), have various limitations, including low discriminative power, invasiveness, and sampling errors, which reduce their effectiveness in organ quality assessment and contribute to the risk of unnecessary organ discard. In this study, we explored the dynamic optical coherence tomography (DOCT) as a real-time, non-invasive approach to monitor the viability of ex vivo mouse kidneys during static cold storage over 48 hours. The dynamic metrics logarithmic intensity variance (LIV), early OCT correlation decay speed (OCDSe), and late OCT correlation decay speed (OCDSl) were extracted from OCT signal fluctuations to quantify temporal and spatial tissue activity and deterioration. Our results demonstrate that DOCT provides complementary functional information to morphological assessment offered by conventional OCT imaging, showing potential to improve pre-transplant organ evaluation and clinic decision-making.

bioengineering↗

bioRxiv2025

Identification and characterization of a novel exo-glycosidase activity of NGLY1 on ENGase-digested N-GlcNAc proteins in vitro

N-Glycanase 1 (NGLY1) is known for its activity to completely remove conjugated N-glycans from glycoproteins. Early studies illustrated that NGLY1 defects were associated with a rare disease named NGLY1-related congenital disorder of deglycosylation (NGLY1-CDDG). Although extensive research has been conducted over the past decade on the biological impact of NGLY1s endo-(N-)glycanase activity in cells and on disease, whether NGLY1 also exhibits an exo-(N-)glycanase activity remains open. In this study, an exo-(N-)glycanase activity of NGLY1 on the N-GlcNAc proteins was firstly reported and characterized in vitro. To distinguish for the conventional endo-(N-)glycanase activity and the newly reported exo-(N-)glycanase activity of NGLY1, the active sites of exo-NGLY1 were predicted and compared with those of endo-NGLY1. In addition, the correlation between NGLY1s exo-(N-)glycanase activity in vitro and NGLY1-CDDGs clinical characterization was investigated and discussed. The observation of NGLY1s novel exo-(N-)glycanase activity expanded the functional repertoire of NGLY1 beyond canonical endo-(N-)glycanase-mediated deglycosylation, and may provide a new framework to explain the clinical heterogeneity of NGLY1-CDDG.

biochemistry↗

bioRxiv2025

Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease

Interstitial lung disease (ILD) is present in over 60% of patients with systemic sclerosis (SSc) and is the leading cause of SSc-related deaths. Profibrotic monocyte-derived alveolar macrophages (MoAM) play a causal role in the pathogenesis of pulmonary fibrosis in animal models where their persistence in the niche requires signaling through Colony Stimulating Factor 1 Receptor (CSF1R). We hypothesized that the presence and proportion of MoAM in bronchoalveolar lavage (BAL) fluid from patients with SSc-ILD may be a biomarker of ILD severity. To test this hypothesis, we analyzed BAL fluid from 9 prospectively enrolled patients with SSc-ILD and 13 healthy controls using flow cytometry and single-cell RNA sequencing. Patients with SSc-ILD had more MoAM and interstitial macrophages in BAL fluid than healthy controls, and their abundance was associated with lung fibrosis severity. We identified changes in the MoAM transcriptome as a function of treatment with mycophenolate, an effective therapy for SSc-ILD. In SSc-ILD lung explants, spatial transcriptomics identified an expanded population of interstitial macrophages spilling into the alveolar space. Our findings suggest that the proportion of profibrotic MoAM and interstitial macrophages in BAL fluid may serve as a biomarker of SSc-ILD and credential them as possible targets for therapy.

immunology↗

bioRxiv2025

Functional contributions of quantal and non-quantal hair cell synaptic transmission in the vestibular periphery

Information about head motion and gravity is conveyed to the brain by vestibular nerve afferents which are subdivided by their spontaneous firing properties into regular and irregular subtypes thought to be differentially responsible for vestibulo-ocular vs vestibulo-spinal reflexes. In the vestibular periphery, afferents make glutamatergic synapses with type II hair cells (HCs) in all vertebrates. During the evolutionary transition to land, however, amniotes (reptiles, birds, and mammals) additionally developed type I vestibular HCs in which unique calyceal afferent terminals cover the basolateral walls of one or more HCs, enabling a nonquantal (NQ) form of synaptic transmission. Most afferents receive inputs from both types of HCs, but the roles of type I vs type II HCs in generating vestibular afferent firing patterns and behaviors remains unclear. Using optogenetics in mice (both sexes), we confirm that stimulation of type II HCs drives conventional quantal glutamatergic transmission, whereas type I HC stimulation evokes nonquantal responses. In mice with disrupted glutamatergic quantal transmission, NQ transmission effectively drove afferent responses to a wide range of head movement frequencies, as assessed by both vestibular sensory evoked potentials and the vestibulo-ocular reflex. Although the distribution of afferent discharge regularity was unaffected, loss of glutamatergic transmission impaired detection of gravity as evidenced by abnormal contact righting reflex behavior. These results indicate that nonquantal glutamatergic transmission from type I HCs is sufficient to generate normal afferent firing patterns and dynamic vestibular behaviors and that glutamatergic release from type II HCs is required for the detection of gravity. Significance StatementThe vestibular system enables balance and spatial orientation by detecting head movements and gravity. During vertebrate evolution, amniotes developed a unique form of synaptic communication--non-quantal (NQ) transmission--between type I hair cells and calyceal afferent nerve fibers in vestibular sensors. This study reveals that NQ transmission can robustly drive vestibular responses across a wide stimulus range, even in the absence of conventional glutamate-based (quantal) signaling. Using electrophysiology, optogenetics and behavioral assays, we show that NQ and quantal transmission serve distinct but complementary roles: NQ supports rapid, broad-range signaling, while quantal transmission is critical for precise gravity detection. These findings highlight how evolutionary innovations in synaptic transmission enhance vestibular function, contributing to our understanding of balance disorders and sensory processing.

neuroscience↗

bioRxiv2025

Programmed meiotic errors facilitate dichotomous sperm production in the silkworm, Bombyx mori

The goal of meiosis is typically to produce haploid gametes (eggs or sperm). Failure to do so is catastrophic for fertility and offspring health. However, Lepidopteran (moths and butterflies) males produce two morphs of sperm: nucleated (eupyrene) sperm which fertilize the egg, and anucleated (apyrene) sperm, both of which are essential for fertilization. The meiotic differences in the two types of spermatogenesis have not been well characterized, and our knowledge of the molecular differences between eupyrene and apyrene spermatogenesis are extremely limited in all systems. The only factor identified as being required for apyrene spermatogenesis is Sex-lethal (Sxl). Here, we show through cytological analysis of early meiotic events that there are several key differences in the genesis of apyrene sperm and eupyrene sperm. Specifically, apyrene spermatocytes fail to condense and pair their chromosomes during meiotic prophase I. In addition, telomeres do not attach to the nuclear envelope. Due to these differences, full-length synaptonemal complex does not form. RNA sequencing of both eupyrene- and apyrene-producing testes revealed distinct changes in transcriptional programs, including down-regulation of a myriad of meiotic genes and cell cycle checkpoint factors during apyrene meiosis. By comparing wild-type and Sxl-knockout apyrene testes, we found that Sxl is not required for the changes in the expression of the meiotic genes but instead plays a role in checkpoint inactivation to allow this error-prone meiosis to proceed. Together, our findings reveal significant insights into two converging molecular pathways that promote the formation of dimorphic sperm in Lepidoptera.

genetics↗

bioRxiv2025

Administration of barcoded AAV capsid library to the putamen of non-human primates identifies variants with efficient retrograde transport

Adeno-associated viral vectors have become a leading choice for gene therapy in the central nervous system due to their safety profile, efficient neuronal transduction, and capacity for sustained transgene expression. We previously reported that AAV2-derived capsids developed using the BRAVE (Barcoded Rational AAV Vector Evolution) approach have enhanced retrograde transport properties in the rodent brain, compared to parental AAV2. Retrograde transport enables broader coverage of connected brain regions after a single focal intraparenchymal brain injection and is therefore a powerful tool for delivery of vectors to distant sites with potentially higher specificity, transduction efficacy and safety. Because transport properties can vary among species, we further characterized a barcoded library of 25 BRAVE-derived AAV2 capsid variants, along with the parental AAV2 serotype and benchmark AAV capsids, in brains of adult cynomolgus monkeys after intraputaminal dosing. Based on RNA and DNA amplicon sequencing, single-nucleus RNA sequencing, and histological assessment, we report here capsid variants with enhanced retrograde transport and expression compared to the parental AAV2 capsid. These properties make them potentially useful for disease indications in which broader brain coverage is desirable beyond the injection site.

neuroscience↗

bioRxiv2025

From Development to Regeneration: Insights into Flight Muscle Adaptations from Bat Muscle Cell Lines

Skeletal muscle regeneration depends on muscle stem cells, which give rise to myoblasts that drive muscle growth, repair, and maintenance. In bats--the only mammals capable of powered flight--these processes must also sustain contractile performance under extreme mechanical and metabolic stress. However, the cellular and molecular mechanisms underlying bat muscle physiology remain largely unknown. To enable mechanistic investigation of these traits (Graphical Abstract), we established the first myoblast cell lines from the pectoralis muscle of Pteronotus mesoamericanus, a highly maneuverable aerial insectivore. Using both spontaneous immortalization and exogenous hTERT/CDK4 overexpression, we generated two stable cell lines that retain proliferative capacity and differentiate into contractile myotubes. These cells exhibit frequent spontaneous contractions, suggesting robust functional integrity at the neuromuscular junction. In parallel, we performed transcriptomic and metabolic profiling of native pectoralis tissue to define molecular programs supporting muscle specialization. Gene expression analyses revealed enriched pathways for muscle metabolism, development, and regeneration, highlighting the supporting roles in tissue maintenance and repair. Consistent with this profile, the flight muscle is triglyceride-rich, which serves as an important fuel source for energetically demanding processes, including muscle contraction and cellular recovery. Integration of transcriptomic and metabolic data identified three key metabolic modules--glucose utilization, lipid handling, and nutrient signaling--that likely coordinate ATP production and support metabolic flexibility. Together, these complementary tools and datasets provide the first in vitro platform for investigating bat muscle research, enabling direct exploration of muscle regeneration, metabolic resilience, and evolutionary physiology. Graphical AbstractEstablishment of bat muscle cell cultures from the Mesoamerican mustached bat (P. mesoamericnus) provides an in vitro platform to investigate muscle regeneration and flight muscle biology. The pectoralis major muscle was isolated to generate primary myoblast cultures, which were expanded and immortalized using hTERT/CDK4. The resulting myoblast lines retain proliferative and differentiation capacity. RNA sequencing of native pectoralis muscle tissue revealed molecular signatures of myogenic regulation, stress resilience, and tissue remodeling, supporting the relevance of these in vitro models for studying muscle maintenance and regenerative mechanisms. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/662643v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@490f49org.highwire.dtl.DTLVardef@8ab615org.highwire.dtl.DTLVardef@b840e1org.highwire.dtl.DTLVardef@ab92eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Potent Efficacy of Computer-Aided Designed Peptide Degrader Drug on PCSK9-Mediated Hypercholesterolemia

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a key regulator of low-density lipoprotein receptor (LDLR) degradation, which leads to increased levels of low-density lipoprotein cholesterol (LDL-C) and a heightened risk of hypercholesterolemia. Existing therapeutic strategies--such as monoclonal antibodies and gene-editing approaches--are limited by high production costs, potential safety concerns, and limited effectiveness in targeting intracellular PCSK9. Targeted protein degradation (TPD) represents a promising alternative capable of overcoming these limitations. In this study, we utilized computer-aided drug design (CADD) to develop a peptide-based degrader, Cadd4, aimed at selectively reducing PCSK9 levels. Through molecular docking and structural refinement, a peptide sequence with strong binding affinity to PCSK9 was identified. Functional evaluation was conducted both in vitro using human LX-2 cells and in vivo in high-fat diet (HFD)-induced hypercholesterolemic mouse models. Cellular uptake, PCSK9 degradation, and LDLR restoration were assessed via confocal microscopy, western blotting, and biochemical analysis. Safety was evaluated by monitoring liver enzyme levels and general physiological parameters. Cadd4 exhibited efficient intracellular delivery and selective PCSK9 degradation in LX-2 cell. In HFD-fed mice, hepatic PCSK9 expression was reduced by 38%, accompanied by a marked increase in LDLR levels. These changes translated into a 25% reduction in total plasma cholesterol and a 29% decrease in LDL-C concentrations. Biodistribution studies indicated liver-specific accumulation of Cadd4, consistent with its intended site of action. Experiments using human liver tissue further confirmed its ability to decrease PCSK9 and enhance LDLR levels. No signs of liver toxicity or adverse systemic effects were observed throughout the study. This work introduces Cadd4 as a CADD-designed peptide-based degrader capable of lowering plasma cholesterol by promoting LDLR recovery via PCSK9 degradation. Its intracellular mechanism of action addresses key gaps in current PCSK9-targeted therapies and supports the broader utility of TPD platforms in managing hypercholesterolemia. These findings offer a foundation for developing cost-effective, scalable therapies within the context of precision cardiovascular medicine.

pharmacology and toxicology↗

bioRxiv2025

Neurogranin Unlocks the L-type Ca2+ Channel and Directs Calmodulin Delivery

Neurogranin (Ng) is enriched in the postsynaptic density, with mounting evidence of its importance to neural pathophysiology. Ng has long been recognized as a dedicated calmodulin (CaM)- binding/buffering protein. This study demonstrates that Ng, through its CaM-binding IQ domain, directly binds the distal C-terminus (DCT) of the L-type Ca2+ (CaV1) channel, as a de novo mechanism regulating excitation-transcription coupling. The Ng/DCT interaction attenuates autonomous C- terminus-mediated inhibition and promotes specific CaM delivery to CaV1, cooperatively enhancing channel gating (activation and inactivation), Ca2+ influx and downstream neuronal signaling. Phosphorylation of Ng leads to the dissociation of the CaM C-lobe, while transiently forming the linkage with the CaM N-lobe. In contrast to neurodegenerative disease-related Ng mutants, WT Ng, within the above transient complex, enables the "targeted CaM transfer" to the proximal C-terminus of CaV1. Collective evidence from electrophysiology, binding assays, structural modeling and Ca2+ imaging supports a paradigm of dynamic intra- and inter-molecular interactions/facilitations underlying Ng and CaV1, both of which are representative CaM-binding proteins. This work proposes a mechanistic scheme potentially applicable to a broad scope of CaM-related physiology.

biophysics↗

bioRxiv2025

Genome editing of phylogenetically distinct bacteria using portable retron-mediated recombineering

Advanced genome editing technologies have enabled rapid and flexible rewriting of the Escherichia coli genome, benefiting fundamental biology and biomanufacturing. Unfortunately, some of the most useful technologies to advance genome editing in E. coli have not yet been ported into other bacterial species. For instance, the addition of bacterial retrons to the genome editing toolbox has increased the efficiency of recombineering in E. coli by enabling sustained, abundant production of ssDNA recombineering donors by reverse transcription that install flexible, precise edits in the prokaryotic chromosome. To extend the utility of this technology beyond E. coli, we surveyed the portability and versatility of retron-mediated recombineering across three different bacterial phyla (Proteobacteria, Bacillota and Actinomycetota) and a total of 15 different species. We found that retron recombineering is functional in all species tested, reaching editing efficiencies above 20% in six of them, above 40% in three of them, and above 90% in two of them. We also tested the extension of the recombitron architecture optimizations and strain backgrounds in a subset of hosts to additionally increase editing rates. The broad recombitron survey carried out in this study forms the basis for widespread use of retron-derived technologies through the whole Bacteria domain.

bioengineering↗

bioRxiv2025

Using evolution as a tool: Replacing corolla in Drosophila melanogaster with its Drosophila mauritiana ortholog creates a novel hypomorphic allele

In Drosophila melanogaster females, as in most organisms, the segregation of meiotic chromosomes depends on the proper distribution of crossovers along paired maternal and paternal chromosomes. In most cases, crossovers require the synaptonemal complex (SC), a conserved multi-protein structure that forms between homologous chromosomes in meiotic prophase I. Recent studies leveraging hypomorphic alleles suggest that the SC plays a more direct role in the distribution of crossover events. However, identifying additional hypomorphic mutations that avoid catastrophic phenotypes by partially disrupting the SC has been challenging. Here, to create a new hypomorphic allele of the D. melanogaster SC gene corolla, we used CRISPR/Cas9 to replace it with the coding sequence of its Drosophila mauritiana ortholog, yielding corollamau. Since the amino acid sequence of SC proteins is rapidly diverging while maintaining the general tripartite structure of the SC, we hypothesized that this replacement would enable the assembly of the SC but show defects in crossover distribution. Indeed, at 25 {degrees}C corollamau homozygous females exhibited full-length SC with defects in SC maintenance and crossover formation, resulting in moderate levels of chromosome missegregation. At 18 {degrees}C, SC maintenance was rescued, and recombination rates were improved, although they remained significantly lower than observed in wild type. Importantly, these phenotypes are less severe than observed in corolla null mutant flies, suggesting corollamau is a hypomorphic allele. Unexpectedly, in homozygotes we also observed unique polycomplexes composed of the SC proteins Corolla and Corona but lacking the transverse filament protein C(3)G. Overall, we report a novel hypomorphic allele of corolla that will enable future studies on the role of the SC in crossover distribution. Further, the unique polycomplexes found in mutant flies may provide new insights into SC protein-protein interactions and SC architecture. Author SummaryIn many species, the success of sexual reproduction relies on a protein structure called the synaptonemal complex (SC). The SC forms between the maternal and paternal copies of chromosomes and functions to ensure crossing over. Most prior studies have used SC mutants that have grave defects, preventing the study of nuances in SC function. Here, we replace one of the SC genes in Drosophila melanogaster with the ortholog of a close relative, creating a new allele that displays a partial loss-of-function phenotype. At the standard rearing temperature, flies homozygous for this allele exhibit SC maintenance defects, a reduced number of crossover events, and aberrant chromosome segregation. In flies reared at a lower temperature, SC maintenance is rescued but the defects in recombination and chromosome segregation persist. We also found a unique SC protein aggregate in these flies. Altogether, this new mutant reflects a novel approach to study the structure and function of the SC.

genetics↗

bioRxiv2025

Features fusion or not: harnessing multiple pathological foundation models using Meta-Encoder for downstream tasks fine-tuning

The emergence of diverse pathological foundation models has empowered computational pathology tasks, including tumor classification, biomarker prediction, and RNA expression prediction. However, variations in model architecture and data sources lead to inconsistent downstream performance and complicate centralized training. Specifically, the lack of data sharing makes retraining foundation models with pooled data infeasible. Alternatively, the release of model parameters enables combining multiple models during fine-tuning. Inspired by the meta-analysis method, we propose the Meta-Encoder framework, which integrates features from multiple foundation models to generate a comprehensive representation, improving downstream fine-tuning task performance. Comparative experiments demonstrate that Meta-Encoder is more effective than individual foundation models, with its strengths more pronounced in handling complex tasks. While single models may perform sufficiently well for simple tasks, Meta-Encoder can match or even surpass the best-performing single model, alleviating concerns over model selection. Moderately challenging tasks benefit from Meta-Encoders concatenation or self-attention strategies, with the latter demonstrating superior performance in more challenging scenarios. For highly complex tasks, such as high-dimensional gene expression prediction, self-attention proves to be the most effective Meta-Encoder strategy, balancing feature integration and computational efficiency. For three patch-level spatial gene expression prediction tasks (HEST-Benchmark, CRC-inhouse, and Her2ST), the self-attention strategy improved the Pearson correlation by 38.58%, 26.06%, and 20.39%, respectively, compared to the average performance of three patch-level single models. Similarly, for the TCGA-BRCA, TCGA-NSCLC, and TCGA-CRC WSI-level bulk gene expression prediction tasks, the Pearson correlation increased by 14.36%, 9.27%, and 42.55%, respectively, compared to the average performance of two WSI-level single models. By leveraging multiple pathological foundation models using Meta-Encoder, it can further improve molecular characterization in pathology images to advance precision oncology.

bioinformatics↗

bioRxiv2025

The recombination landscape of Drosophila melanogaster can be repatterned by a single gene

Meiotic recombination plays an important role in ensuring proper chromosome segregation during meiosis I through the creation of chiasmata that connect homologous chromosomes. Recombination plays an additional role in evolution by creating new allelic combinations. Organisms display species-specific crossover patterns, but how these patterns are established is poorly understood. Drosophila mauritana displays a differing recombination pattern compared to Drosophila melanogaster, with D. mauritiana experiencing a reduced centromere effect, the suppression of recombination emanating from the centromeres. To evaluate the contribution of the synaptonemal complex (SC) C(3)G protein to these recombination rate differences, the D. melanogaster allele was replaced with D. mauritiana c(3)G coding sequence. We found that the D. mauritiana C(3)G could interact with the D. melanogaster SC machinery to build full length tripartite SC and chromosomes segregated accurately, indicating sufficient crossovers were generated. However, the placement of crossovers was altered, displaying an increase in frequency of the centromere-proximal euchromatin indicating a decrease in the centromere effect similar to that observed in D. mauritiana. Recovery of chromatids with more than one crossover was also increased, likely due to the larger chromosome span now available for crossovers. As replacement of a single gene mediated a strong shift of one species crossover pattern towards another species, it indicates a small number of discrete factors may have major influence on species-specific crossover patterning. Additionally, it demonstrates the SC, a structure known to be required for crossover formation in many species, is likely one of these discrete factors. Lay AbstractMeiotic crossovers are important for ensuring proper chromosome segregation and generating genetic diversity. Different species display unique crossover patterns but the mechanisms that establish these patterns are poorly understood. The synaptonemal complex (SC) is built between meiotic chromosomes and promotes crossover formation. Replacement of the SC gene c(3)G in the fruit fly Drosophila melanogaster with Drosophila mauritiana c(3)G resulted in full-length SC assembly and proper chromosome segregation, but the D. melanogaster crossover pattern was shifted to appear more similar to D. mauritiana. This demonstrates that crossover patterning can be largely influenced by minor changes in the makeup of the SC.

genetics↗

bioRxiv2025

Tracking Conditioned Fear in Pair-Housed Mice Using Deep Learning and Real-Time Cue Delivery

Post-traumatic stress disorder (PTSD) is a complex and prevalent neuropsychiatric condition that arises in response to exposure to a traumatic event. A common diagnostic criterion for PTSD includes heightened physiological reactivity to trauma-related sensory cues, in safe or familiar environments. Understanding complex PTSD criteria requires new pre-clinical paradigms and technologies that integrate sensory physiology (e.g., auditory, visual, olfactory) with behavior. Here we present a novel Pavlovian-based paradigm using an open-source software plus deep learning-based pose estimation to investigate the effects of a recurrent conditioned stimulus (CS) on fear behaviors in pair-housed mice within the home cage. Simultaneous home cage video recording and analysis of CS-evoked freezing behaviors were performed using a deep learning model, with consideration for light-dark circadian cycles. Fear- conditioned dyad mice exhibited high CS-evoked freezing, with evidence of extinction learning (characterized by low freezing) during the mid-phase of the 2-week paradigm. Females exhibited reduced CS-evoked home cage freezing compared to males with circadian differences between the light (low freezing) and dark (high freezing) periods. Following the 2-week paradigm, fear-conditioned mice, compared to controls, exhibited heightened context-dependent freezing, while males but not females showed heightened startle reactivity. Taken together, these results demonstrate a novel software application for examining conditioned defensive and fear behaviors over time in mouse dyads within an ethologically relevant environment. Future applications could be used for more integrative analysis and understanding of neural circuits and heightened sensory threat reactivity, potentially improving the understanding and treatment of PTSD.

animal behavior and cognition↗

bioRxiv2025

Rapid enrichment of progenitor exhausted neoantigen-specific CD8 T cells from peripheral blood

Neoantigen-reactive peripheral blood lymphocytes (NeoPBL) are tumor-specific T cells found at ultra-low frequencies in the blood. Unlike tumor-infiltrating lymphocytes (TIL), NeoPBL exist in a favorable less dysfunctional phenotypic state in vivo, but their rarity has precluded their effective use as cell therapy. Leveraging a priori knowledge of bona fide neoantigens, we combined high-intensity neoantigen stimulation with bead extraction of neoantigen peptide-pulsed target cells to enable the enrichment of NeoPBL to frequencies comparable to ex vivo cultured TIL over a 28-day period. Throughout this process, NeoPBL demonstrate specific reactivity against autologous tumor organoids and maintain memory-like features, including elevated expression of CD28 and TCF7. We additionally demonstrate that NeoPBL reactivity is polyclonal, encompassing multiple clonotypes that are detectable within in vivo TIL populations, underscoring physiological specificity for the targeted neoantigens. This streamlined process yields clinically relevant cell doses and enables identification and expansion of blood-derived neoantigen-specific TCRs. By potentially avoiding additional surgical risks and protracted delays of TIL and individualized TCR-engineered methods, the NeoPBL platform may have clinical and practical advantages. Ultimately, NeoPBL combines intrinsic cell fitness, minimal invasiveness and rapidity to potentially facilitate personalized adoptive cell therapy for cancer.

immunology↗

bioRxiv2025

Identification of modulated whole-brain dynamical models from nonstationary electrophysiological data

ObjectiveUnderstanding the mechanisms underlying brain dynamics is a long-held goal in neuroscience. However, these dynamics are both individualized and nonstationary, making modeling challenging. Here, we present a data-driven approach to modeling nonstationary dynamics based on principles of neuromodulation, at the level of individual subjects. ApproachPreviously, we developed the mesoscale individualized neural dynamics (MINDy) modeling approach to capture individualized brain dynamics which do not change over time. Here, we extend the MINDy approach by adding a modulatory component which is multiplied by a set of baseline, stationary connectivity weights. We validate this model on both synthetic data and publicly available EEG data in the context of anesthesia, a known modulator of neural dynamics. Main ResultsWe find that our modulated MINDy approach is accurate, individualized, and reliable. Additionally, we find that our models yield biologically interpretable inferences regarding the effects of propofol anesthesia on mesoscale cortical networks, consistent with previous literature on the neuromodulatory effects of propofol. SignificanceUltimately, our data-driven modeling approach is reliable and scalable, and provides insight into mechanisms underlying observed brain dynamics. Our modeling methodology can be used to infer insights about modulation dynamics in the brain in a number of different contexts.

neuroscience↗