Biology subjects

Peng, C.

Publications and source records attributed to Peng, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Sex-specific Genetic Regulatory Effects in Chickens

Sexual dimorphism is a defining vertebrate feature, yet its sex-specific molecular architecture remains poorly understood. Here we established a sex-balanced, uniformly reared chicken cohort to map this landscape, integrating individual whole-genome sequencing with 7,969 bulk and 779,380 single nucleus transcriptomes across 32 tissues from 280 birds. We identified 495,098 independent expression quantitative trait loci for 20,194 genes, including 10,937 loci modulated by cell-type composition. Notably, 340 genes were regulated by 449 loci in a sex-dependent manner, significantly enrichment in endocrine tissues like adipose and the adrenal gland. Furthermore, we fine-mapped 1,219 structural variants, demonstrating their unique roles to tissue- and sex-specific expression beyond SNPs. Ultimately, we showed the utility of these regulatory effects in elucidating the molecular basis of metabolism and complex traits in both chickens and humans. This comprehensive atlas of regulatory effects provides profound insights into the genomic and molecular basis of sexual dimorphism in vertebrates.

genomics↗

bioRxiv2026

HDAC11 Regulates RNA Splicing via De-Fatty Acylation of SF3B2

Histone deacetylase 11 (HDAC11) is a lysine de-fatty acylase whose cellular substrates and mechanisms remain incompletely defined. Here, using metabolic labeling, mass spectrometry, click chemistry, and standard molecular biology, we show that SF3B2 is modified by lysine myristoylation at K10 and that HDAC11 efficiently removes this modification in cells, establishing SF3B2 as a direct enzymatic substrate. A de-myristoylation mimetic mutant (SF3B2 K10R) exhibits altered pre-mRNA binding activity in a context-dependent manner. In HCC cells, loss of SF3B2 lysine myristoylation enhances SF3B2 association with androgen receptor (AR) splice variant loci and promotes alternative splicing towards the AR-v7 variant. Consistently, HDAC11 overexpression increases, and HDAC11 knockdown decreases, the AR-v7/AR-FL splice isoform ratio in HCC cells in a manner requiring HDAC11 catalytic activity and recapitulated by SF3B2 K10R. In contrast, modulation of HDAC11 does not alter AR splicing in prostate cancer cells, indicating cell type specific regulation. Together, these findings establish lysine myristoylation as a reversible regulatory modification on a spliceosomal component and reveal HDAC11-catalyzed de-myristoylation of SF3B2 as a mechanism that can tune alternative splicing in liver cancer cells. In BriefClements et al. utilize metabolic labelling, mass spectrometry, click chemistry, and protein and RNA biochemistry to establish that a histone deacetylase enzyme, HDAC11, can influence RNA splicing through de-fatty acylation of the RNA splicing factor SF3B2. De-fatty acylation of SF3B2 at K10 by HDAC11 modulates SF3B2s pre-mRNA binding to AR splice variant loci, thereby driving alternative splicing of the AR-v7 variant in a cell type dependent manner. This work provides direct mechanistic evidence linking an HDAC to RNA splicing, identifies a reversible lipid modification on SF3B2, and expands current understanding of post-translational regulation of spliceosomal proteins and HDAC11 de-fatty acylation substrates. HighlightsO_LIHDAC11 de-fatty-acylates SF3B2 at K10, revealing a previously unrecognized modification on SF3B2. C_LIO_LISF3B2 de-fatty acylation enhances alternative splice-site binding in liver cancer cells. C_LIO_LIHDAC11 regulates RNA splicing through enzymatic de-fatty acylation of a spliceosomal protein. C_LI

molecular biology↗

bioRxiv2026

Monocyte reprogramming by nociceptors impedes T cell-mediated tumor immunity

Nociceptors - peripheral nervous system neurons that trigger the sensation of pain or itch in response to noxious stimuli - can communicate with leukocytes and modulate immune responses in a context-dependent manner1,2. Here, we demonstrate that nociceptors rapidly induce monocytes to adopt an immunosuppressive phenotype, reminiscent of myeloid-derived suppressor cells (MDSCs), which have been linked to impaired anti-tumor immunity. MDSCs are abundant in human bladder cancer, a malignancy where survival is negatively correlated with expression of pro-neurogenic cytokines. Accordingly, in an orthotopic mouse model of urinary bladder carcinoma, incipient tumors promoted dense innervation by nociceptors and infiltration by monocytes that differentiated rapidly into MDSCs. Nociceptors did not affect the development of tumor-specific T cells in draining lymph nodes, but they were essential during the early stages of tumor formation to establish an immunosuppressive tumor microenvironment. Ablation or chemogenetic inhibition of nociceptors prevented the formation of immunosuppressive MDSCs and markedly increased the rate of bladder tumor rejection by T cells. Conversely, monocyte depletion in nociceptor-sufficient mice enabled tumor rejection. Collectively, these findings demonstrate that urothelial tumors co-opt an immunosuppressive neuro-immune axis to evade anti-tumor immunity and identify nociceptors as potential targets for bladder cancer treatment.

immunology↗

bioRxiv2026

ANKS1B in the Nucleus Accumbens controls escalated cocaine self-administration via regulating CBP-FoxO3 complex

The transition from controlled to escalated drug intake is a core feature of cocaine use disorder (CUD), yet the molecular mechanisms underlying this behavioral escalation remain poorly defined. Our prior genome-wide association study (GWAS) identified ANKS1B as a significant shared genetic risk factor for heroin, methamphetamine, and alcohol dependence, suggesting a broad role in addiction vulnerability. However, the specific function of ANKS1B in cocaine addiction and its associated neural mechanisms were unknown. Here, we found that ANKS1B expression level in the Nucleus Accumbens (NAc) was downregulated after extended cocaine use, and manipulating ANKS1B could selectively influence the escalation of cocaine intake and the subsequent cocaine-seeking behavior in the long-access cocaine self-administration rat model. Molecular experiments reveal that ANKS1B interacts with the histone acetyltransferase CBP to control H3K27 acetylation and extended cocaine intake, via epigenetically repressing the transcription factor FoxO3. Overall, these findings suggest that ANKS1B is a crucial factor influencing the escalation of cocaine use. The ANKS1B-CBP-FoxO3 signaling pathway presents a promising target for potential therapeutic interventions for controlling extended cocaine use.

neuroscience↗

bioRxiv2026

On-virion structural dynamics reveal temperature- and receptor-coordinated activation of an alphacoronavirus spike

Human alphacoronaviruses primarily infect the human upper respiratory tract, yet how physiological temperature and receptor-binding coordinate viral spike (S) protein activation remain unclear. Using cryo-electron tomography and subtomogram averaging, we directly visualized the structural dynamics of S on human coronavirus 229E (HCoV-229E) virions under physiologically relevant temperatures and in the presence of the host receptor human aminopeptidase N (hAPN). We identified two prefusion S2 conformations, compact and loose, that interconvert reversibly by temperature, revealing intrinsic S2 "breathing" on virions. Receptor-binding domain (RBD)-up conformations are rare on apo virions but are promoted at physiological temperature and stabilized upon receptor binding. hAPN can bind bivalently to neighboring S, forming Gemini S-hAPN complexes. Receptor incubation further promotes conversion from prefusion to postfusion S, an effect enhanced at 33. Together, our results demonstrate an optimized temperature for the HCoV-229E viral fitness, establish temperature and receptor binding as synergistic regulators of alphacoronavirus S activation and define an integrated, on-virion model of S conformational transitions during viral entry. These findings provide a structural framework for understanding alphacoronavirus infectivity.

microbiology↗

bioRxiv2026

Predicting TCR-pMHC Binding by Reinforcement Learning

The binding between T cell receptors (TCRs) and peptide-major histocompat-ibility complexes (pMHCs) is fundamental to the immune systems ability to recognize and eliminate pathogens. Accurate prediction of TCR-pMHC inter-actions holds significant promise for advancing cancer immunotherapy, vaccine design, and autoimmune disease research. However, existing approaches often treat the sequences, structures, and functions of TCRs, peptides, and MHC molecules in isolation, neglecting their interdependencies and hence limiting the prediction accuracy. In this study, we present ProTCR, a novel approach that integrates sequence, structural, and functional information within a reinforce-ment learning framework, offering a new paradigm for predicting TCR-pMHC binding. The reinforcement learning optimization enables ProTCR to generate TCR-pMHC sequences with enhanced binding propensity, thereby improving prediction accuracy. On benchmark datasets such as IEDB and VDJdb, ProTCR achieves an AUROC of 0.75, outperforming state-of-the-art methods by 32.7%, while offering interpretable insights into the structural and sequence determi-nants of binding. We further validate ProTCR using TCRs and neoantigens derived from a cervical cancer patient via proteogenomic profiling. Our analysis reveals a strong correlation between T cell clonal expansion and ProTCR-predicted TCR-peptide binding scores, supporting the biological relevance of the model. Additionally, ProTCR demonstrates robust performance in predict-ing SARS-CoV-2 TCR-pMHC complexes and generating MHC-specific peptides with potential applications in peptide-based immunotherapies. Collectively, these findings establish ProTCR as a powerful and interpretable tool for TCR-pMHC binding prediction, with broad utility across immunology research and translational applications.

bioinformatics↗

bioRxiv2025

Evolutionary Decoding of the Bacillus subtilis Secretome: Insights from Pan-Genomics and Deep Learning

Bacillus subtilis serves as a crucial host for industrial protein production, where the efficiency and regulation of its secretion system represent a central focus of applied research. Despite substantial genomic diversity among strains, current understanding of signal peptides, which are key elements in the secretion process, remains largely based on single model strains, lacking systematic investigation from a pan-genomic perspective. This study integrates pan-genomics and deep learning to construct a pan-secretome profile of 287 B. subtilis strains. Our analysis reveals an open repertoire of signal peptides in B. subtilis. Our results reveal an open pan-signal peptidome in B. subtilis. Core signal peptides exhibit high sequence conservation and primarily direct the localization of housekeeping proteins, whereas accessory signal peptides govern the extracellular secretion of environment-responsive proteins, forming a functional "housekeeping-adaptive" dichotomy. We demonstrated for the first time at a broad scale the widespread evolutionary decoupling between signal peptides and their corresponding mature peptides, uncovering a modular evolutionary mechanism in protein evolution. While the deep learning model achieved high accuracy (88.0%) in discriminating core and accessory gene-encoded full-length proteins, its performance was considerably limited when using signal peptide sequences alone (69.7% accuracy), reflecting the information constraints inherent to short sequences. This study provides a systematic portrayal of the signal peptide evolutionary landscape in B. subtilis at the pan-genome scale, advancing our understanding of the evolutionary principles governing bacterial secretion systems and establishing a theoretical foundation for optimizing industrial protein production through rational signal peptide design.

bioinformatics↗

bioRxiv2025

Flexible Skull-Conformal Phased Array for Aberration-Corrected Transcranial Focused Ultrasound Therapy

Transcranial focused ultrasound (tFUS) is a promising non-invasive tool for precise deep-brain interventions, including neuromodulation, blood-brain barrier opening, and drug delivery. However, conventional rigid tFUS arrays suffer from poor skull conformity, compromising patient comfort and targeting precision, while skull-induced aberrations degrade focal accuracy and efficiency. To address these challenges, we present the first flexible, skull-conformal aberration-corrected phased array (F-SCAPA), a transformative solution integrating mechanical adaptability with advanced acoustic correction. The 0.5-MHz array--comprising 8x8 elements--features an optimized fabrication process that enhances material efficiency, ensures flexibility and stretchability, and maintains uniform electrical performance. Coupled with CT-based skull modeling and time-reversal aberration correction, F-SCAPA dynamically conforms to cranial anatomy while compensating for phase distortions. Transcranial validation in a human skull demonstrates precise focusing at 36 mm depth, achieving an axial full width at half maximum (FWHM) of 8.9 mm. This breakthrough overcomes existing limitations by combining mechanical adaptability with high-resolution transcranial focusing, establishing F-SCAPA as a robust, patient-compatible platform for next-generation non-invasive brain therapies.

bioengineering↗

bioRxiv2025

A Stretchable Wearable Doppler Ultrasound Patch for Continuous Vascular Monitoring

Continuous blood flow monitoring is crucial for the diagnosing and preventing cardiovascular diseases, but existing techniques have several limitations that hinder widespread clinical use, such as invasiveness, operator dependency and lack of continuous measurement. In this paper, we present a wearable ultrasound patch designed for continuous blood flow monitoring. The patch integrates six ultrasonic transducers arranged symmetrically along the central axis. A baseplate with a specific angle (30 degrees) is used to form a 60-degree Doppler incident angle. We have simplified and improved the fabrication process of the serpentine electrodes, avoiding the cumbersome traditional steps such as transfer printing and spin-coating of Cu/PI. The fabricated wearable ultrasound patch exhibits a center frequency of 5.05 MHz, a -6 dB bandwidth of 42.58%, and an elastic stretchability of up to 30%. Based on pulsed-wave (PW) Doppler, it calculates the Doppler frequency shift using a slow-time sampling algorithm. In vitro studies showed an absolute percentage error of 4.1% to 12% for constant flow velocity measurements, with actual flow velocities varying between 20 and 100 cm/s. The mean absolute error (MAE) was 3.56 cm/s, and the mean absolute percentage error (MAPE) was 5.99%. In pulsatile flow experiments, the patch was also able to capture the changing peaks of the velocity waveform, demonstrating its feasibility for continuous blood flow monitoring.

bioengineering↗

bioRxiv2025

A BCG toxic effector induces mitochondrial DNA compaction to refrain protective immunity

Innate immune memory typically emphasizes nuclear chromatin remodeling that determines transcriptional memory in monocytes and macrophages. Here, we show that compaction of mitochondrial DNA (mtDNA), governed by mitochondrial transcription factor A (TFAM) abundance and mtATP-dependent remodeling, defines the transcriptional and functional state of trained macrophages. While typical pathogen-associated molecular pattern (PAMPs) triggered mtDNA accessibility, Bacillus Calmette-Guerin (BCG) effector PE18 directly interacted with and activated SLC25A5 to reduce mtATP levels, thereby inhibiting TFAM degradation by AFG3L2. Accumulated TFAM restricts mtDNA accessibility, suppressing the transcription of the mtNd1 and thereby reducing mtNd1-mediated mtROS production, which diminishes the trained capacity of macrophages against secondary infections. Notably, BCG{Delta}pe18 maintains macrophages cytokine transcriptional capacity independent of classical nuclear histone modifications. Moreover, BCG{Delta}pe18 provides robust and lifelong protective immunity against Mycobacterium tuberculosis (Mtb) infection. These findings reveal mitochondrial genome as a regulatory entity in trained immunity, and suggest a potential strategy for improving vaccine performance.

immunology↗

bioRxiv2025

StoPred: Accurate Stoichiometry Prediction for ProteinComplexes Using Protein Language Models and GraphAttention

Proteins often function as part of complexes, and the specific stoichiometry of these assemblies is critical for their biological roles, but experimental determination of assembly composition remains challenging and existing computational methods for stoichiometry prediction are limited. Existing approaches rely on template-based searches or require predefined stoichiometry for structure prediction, hampering their applicability to proteins without close homologs or known assembly states. Recent advances using protein language models (pLM) have enabled sequence-based prediction of homo-oligomer stoichiometry, but these methods are not applicable to hetero-oligomeric complexes and do not fully leverage inter-subunit relationships. Here, we present StoPred, a method that predicts the stoichiometry of protein complexes by integrating pLM embeddings with a graph attention network to model subunit-level interactions. StoPred infers stoichiometry directly from sequence or structure features for both homo-and hetero-oligomers, without requiring template assemblies or predefined composition. We benchmark StoPred against deep learning-based and template-based methods, and show that it achieves improved accuracy and efficiency across curated and blind datasets, with up to 16% and 41% higher top-1 accuracy for homomeric and heteromeric complexes, respectively, compared to the strongest prior method on our held-out test dataset. More importantly, StoPred is the first deep learning-based method capable of accurately predicting the stoichiometry of hetero-oligomeric complexes.

bioinformatics↗

bioRxiv2025

ARHGEF17 Deficiency Induces Endothelial Dysfunction and Intracranial Aneurysm Formation via RhoA/ROCK2/MLC Signaling Pathway

BACKGROUNDGenetic susceptibility is a major determinant in intracranial aneurysm (IA) formation and rupture, yet the underlying mechanisms linking genetic variation to vascular dysfunction remain largely unknown. We have identified mutations in ARHGEF17, a guanine nucleotide exchange factor that regulates RhoA activation and cytoskeletal organization, as potential risk variants for IA. Given ARHGEF17s regulatory role in endothelial barrier integrity and actin remodeling, we hypothesized that ARHGEF17 deficiency promotes IA pathogenesis through dysregulation of the RhoA/ROCK2/MLC signaling axis, leading to endothelial dysfunction and vascular wall instability. METHODSCRISPR-Cas9-mediated ARHGEF17 knockout (ARHGEF17-/-) mice and morpholino-based ARHGEF17-deficient zebrafish were established to assess the in vivo vascular effects of ARHGEF17 loss. An intracranial aneurysm model combining elastase injection and deoxycorticosterone acetate (DOCA)-induced hypertension was used to evaluate aneurysm incidence, rupture rate, and survival. Structural remodeling of the Circle of Willis (CoW) was assessed by Victoria Blue, EVG, and Picrosirius Red staining, as well as immunofluorescence for -SMA, OPN, CD31, and inflammatory markers. Complementary in vitro studies were performed in HUVECs using lentiviral ARHGEF17 silencing (three shRNAs of varying efficiency) to examine endothelial proliferation, migration, tube formation, and barrier function (TEER). Activation of RhoA/ROCK2/MLC signaling was quantified by G-LISA and Western blotting. The ROCK inhibitor Y-27632 (10 M) was applied to determine pathway dependence. RESULTSARHGEF17-/- mice exhibited a significantly higher incidence and rupture rate of intracranial aneurysms, accompanied by fragmentation of elastic fibers, loss of collagen organization, vascular smooth muscle cell dedifferentiation, and robust inflammatory activation in the CoW. Zebrafish lacking ARHGEF17 showed frequent intracranial hemorrhage and compromised vascular wall integrity, further confirming ARHGEF17s role in cerebrovascular stability. In ECs, ARHGEF17 knockdown impaired proliferation, migration, tube formation, and barrier integrity in a silencing-efficiency-dependent manner. Mechanistically, ARHGEF17 deficiency activated the RhoA/ROCK2/MLC pathway, leading to increased phosphorylation of MLC and MYPT1 and disorganization of F-actin and junctional proteins. Pharmacological inhibition with Y-27632 restored endothelial function, normalized cytoskeletal structure, and re-established junctional continuity, indicating a ROCK2-dependent mechanism. CONCLUSIONSOur findings establish ARHGEF17 as a critical regulator of cerebrovascular integrity and identify RhoA/ROCK2/MLC mediated cytoskeletal remodeling as the mechanistic link between ARHGEF17 deficiency and aneurysm pathogenesis. Loss of ARHGEF17 compromises endothelial barrier function, triggers vascular inflammation, and promotes aneurysm formation and rupture. Importantly, ROCK inhibition rescues endothelial dysfunction, highlighting the RhoA/ROCK2/MLC axis as a promising therapeutic target for ARHGEF17 mutation-associated intracranial aneurysms.

neuroscience↗

bioRxiv2025

Cross-species analysis identifies genotype-driven vulnerabilities in lung adenocarcinoma

While three major genetic alteration subsets, characterized by mutations in STK11, KRAS, and EGFR, are seminal in driving tumorigenesis in LUAD, their distinct effects on tumor cells and the tumor microenvironment are not fully understood. Here, we map critical oncogenic subset-specific vulnerabilities by identifying conserved cell-type-specific reprogrammings between human and mouse LUAD. Through harmonized scRNA-seq analysis of 57 human and 18 mouse specimens, we unveil that genetic alterations impose genotype-specific immune imprints on the tumor microenvironment: KRAS is associated with a transitional immune state, whereas STK11 and EGFR mutations define discrete and contrasting immune phenotypes. We find that STK11-mutant tumors exhibit complement and interferon-rich immune microenvironments while EGFR-mutant tumors harbor a naive T cell-rich phenotype accompanied by a global HLA downregulation, stress-responsive alveolar macrophages marked by MARCO. In the epithelial compartments, cross-species analysis reveals metabolic dependencies, including OGDH in EGFR- and PDE4D in STK11-mutant cells. Statement of SignificanceThis study delineates oncogenotype-specific molecular and immune imprints in lung adenocarcinoma, revealing STK11-, KRAS-, and EGFR-mutated tumors as transcriptionally and immunologically discrete ecosystems. By mapping epithelial vulnerabilities alongside immune imprints, we unveil genotype-imposed dependencies that inform the rational development of precision therapies with direct translational relevance.

cancer biology↗

bioRxiv2025

Mid-zone hepatocytes trade proliferation for survival via Atf4-Chop axis in early acute liver injury

Hepatocytes undergo extensive proliferation to facilitate liver repair after injury, yet early adaptive changes prior to proliferation remain unclear. Here, we report that during early acetaminophen (APAP)-induced liver injury, hepatocytes exhibit transient proliferation suppression that is most pronounced in mid-zone hepatocytes, consistent with zonal APAP metabolism. While spatial transcriptomics (ST) provided robust evidence for this arrest in the mid-zone, support for a similar arrest in pericentral hepatocytes was limited. Integrating ST with immunohistochemistry and functional studies, we identified a unique mid-zone stress-response program centered on the Atf4-Chop axis, which suppresses proliferation via the cell cycle inhibitor Btg2. Together, our findings support a model in which mid-zone hepatocytes transiently prioritize stress adaptation over proliferation, thereby preserving regenerative capacity for subsequent liver repair.

pharmacology and toxicology↗

bioRxiv2025

C9orf72/SMCR8 complex maintains microglial homeostasis via RAB8A-ESCRT-mediated lysosomal repair

Microglia are critical regulators of neuroinflammation and neurodegeneration. Haploinsufficiency of C9orf72, the most common genetic cause of ALS and FTD, has been mainly linked to autophagy-lysosomal pathway defects, but its precise role in microglial lysosomal function remains unclear. Here we identify the C9orf72/SMCR8 complex as a key regulator of microglial homeostasis through lysosomal repair. Loss of C9orf72 and SMCR8 in mice causes age-dependent neuroinflammation and microgliosis, with microglia adopting a disease-associated state. In aged CNS tissue, microglia display lysosomal damage, marked by galectin-3 upregulation and its accumulation on lysosomes. To model this process, we applied the lysosomotropic agent LLOMe to microglia, which recapitulated lysosomal damage and revealed defective recruitment of phosphorylated RAB8A and the ESCRT machinery in C9orf72/SMCR8-deficient cells. Notably, mutant microglia accumulate GTP-bound RAB8A, which becomes aberrantly hyperphosphorylated and mislocalized to non-lysosomal vesicles. We further show that the GAP activity of the C9orf72/SMCR8 complex is essential for lysosomal repair. These findings uncover a previously unrecognized role for the C9orf72/SMCR8 complex in coordinating RAB8A-ESCRT-mediated lysosomal repair, thereby safeguarding microglial homeostasis and limiting neuroinflammation.

cell biology↗

bioRxiv2025

Cortical α-synuclein pathology induces cell autonomous neuronal hypoactivity and compensatory circuit changes in a model of early Lewy Body Dementia

Posterior cortical impairments in visuospatial/perceptual function are common non-motor symptoms of the Lewy Body Dementias (LBD) and are relatively specific for LBDs compared to other dementias. Across populations, cognitive impairments correlate with the presence of -synuclein (-syn) pathology in limbic and neocortical brain regions. However, the specific role that -syn pathology plays in driving cortical circuit dysfunction and cognitive impairment remains controversial. We hypothesized that inducing -syn pathology in primary visual cortex (V1) in mice would impair neuronal activity and encoding of visual information, leading to visuoperceptual impairments. To test this, we injected -syn pre-formed fibrils (PFF) into V1, causing the formation of sparse Lewy-like pathology. Using longitudinal in vivo two-photon (2P) calcium imaging over 6 months, we recorded visually evoked activity of pyramidal cells in layer 2/3 (L2/3) and quantified -syn pathology using C05-05, a fluorescent ligand that binds aggregated -syn. Measuring population activity, we found a greater percentage of neurons in PFF-injected mice were responsive to visual stimuli with lower direction selectivity compared to controls at 4-5 months post-injection (MPI). Neurons with somatic Lewy-like inclusions showed reduced activity compared to neighboring neurons without inclusions. Conversely, neurons without somatic inclusions showed increased activity, positively correlated with the local burden of -syn pathology. Using a coherent motion discrimination task, we found no impairments in visuoperceptual ability in PFF-injected mice. Our results demonstrate that -syn pathology leads to reductions in neuronal activity in cells with somatic inclusions and reciprocal changes in local population activity but does not impair visuoperceptual function. Reflecting the early stages of neocortical -syn pathology, our model provides a framework for future studies to better understand the heterogeneity of cognitive symptoms and -syn pathology across patients.

neuroscience↗

bioRxiv2025

FlyTomo: A streamlined software for on-the-fly cryo-ET data processing and diagnosis

Cryo-electron tomography (Cryo-ET) combined with subtomogram averaging (STA) enables the structural elucidation of macromolecular assemblies in their native environments. However, the widespread adoption of cryo-ET has been limited by its labor-intensive, expertise-dependent data processing workflow. Here we present FlyTomo, a software that streamlines data processing from frame alignment to STA with high-throughput for authentic cryo-ET scenarios. During data acquisition, FlyTomo performs real-time diagnosis, enabling prompt feedback on sample quality, microscope performance and structural features. After acquisition, it aggregates diagnostic metrics into an interactive overview, guiding users through data review and refinement. FlyTomo also curates raw and processed data into structured directories to simplify data management and archiving. We validated FlyTomo across a diverse set of authentic cryo-ET samples, including purified enveloped viruses and cryo-lamellae, on multiple microscopes and cameras, achieving structures at resolutions ranging from 3.4 to 5.7 [A]. Collectively, by integrating accuracy, scalability and usability, FlyTomo reduces the technical barrier for in situ structural biology using cryo-ET.

biophysics↗

bioRxiv2025

Identification of Pesticides Associated with an Increased Risk of Parkinson's Disease using a Multi-Screen Approach

Parkinsons Disease (PD) is a progressive neurodegenerative disease characterized by aggregation and transmission of alpha-synuclein (-syn) protein and loss of dopaminergic neurons. The etiology of PD is multifactorial involving both genetic and environmental factors. Pesticide exposure has been associated with PD, but it is still unclear which of the hundreds of chemically and structurally diverse pesticides confer this association. While there are numerous pesticides currently registered for use in the United States, in this study, we focused on 62 pesticides used in the California Central Valley. We used 2 cell-based screens and a recently developed pesticide-wide association study (PWAS) analysis to identify candidates that increase the risk of PD. One cell-based screen tested for pesticides that alter autophagy and the other tested for their effect on -syn transmission. To establish biological plausibility, pesticides that were positive in all 3 screens were tested for dopaminergic neurotoxicity in an in vivo zebrafish (ZF) model. The autophagy screen resulted in a total of 22 hits for alterations to either autophagosomes (16 hits) and lysosomes (14 hits) out of the 62 pesticides tested. The -syn transmission screen resulted in 29 hits, and the PWAS resulted in 34 hits. Six pesticides were positive in all 3 screens and four of these pesticides induced aminergic neuron loss in ZF larvae. The majority of the pesticides identified in our screens have not previously been implicated as risk factors for PD but should be considered in future studies.

pharmacology and toxicology↗