Biology subjects

Shao, L.

Publications and source records attributed to Shao, L..

At least 19 recordsLinked to original sources

bioRxiv2026

A genetic screen to identify novel interactions of the phosphatidylinositol phosphate signaling pathway in Drosophila spermatogenesis

Phosphatidylinositol (PI) phosphates (PIPs) are membrane lipids with crucial roles in intracellular signaling, membrane trafficking and cytoskeletal organization. To perturb PIP function in Drosophila melanogaster sperm development, we previously expressed the Salmonella PIP phosphatase SigD (also known as SopB) under control of a spermatocyte- specific promoter. SigD expression results in reduced levels of plasma membrane PI 4,5-bisphosphate [PI(4,5)P2; henceforth PIP2] and male sterility. Transgenic lines expressing high levels of SigD (SigD-high) exhibit defects in spermatocyte cytokinesis, ciliary transition zone maturation and spermatid elongation, whereas lines expressing low levels of SigD (SigD-low) have defects in nuclear shaping and spermatid cell polarization. To further investigate the role of PIPs during Drosophila sperm development, we conducted a sensitized genetic screen to identify suppressors and enhancers of SigD-low phenotypes. From a screen of 760 chromosomal deficiencies spanning 83.6% of chromosomes 2 and 3, we identified 80 interacting regions that were further narrowed down to 40 individual suppressors. Among the strongest interactors were genes involved in microtubule dynamics, nucleocytoplasmic transport and membrane trafficking. The novel genetic interactions identified by our screen pave the way for further investigation into molecular mechanisms underlying the affected aspects of sperm development.

genetics↗

bioRxiv2026

Cellular source and circuit context organize functional specificity in the Drosophila NPF system

Neuropeptides regulate diverse and sometimes opposing functions, yet how a single peptide achieves functional specificity remains unclear. Receptor diversity can provide specificity, but not in systems with only one receptor. Drosophila neuropeptide F (NPF) acts through a single receptor, providing a model to test whether specificity is organized by the peptide's cellular source. Using the whole-brain connectome, we defined four adult NPF cell types with no shared first-order synaptic partners and separate networks. These cell types made distinct and partly opposing contributions to reinforcement, feeding, mating, and energy storage. Most peptide-dependent effects were undetectable after population-level NPF reduction, showing that global perturbation can obscure source-specific functions. Changing neuronal activity and reducing NPF in the same cells produced different, sometimes opposing, phenotypes, so neuronal activation cannot be equated with peptide action. Thus, cellular source and circuit context generate functional specificity that population-level perturbation conceals.

neuroscience↗

bioRxiv2026

Dystrophic changes of nigrostriatal axons harboring a Synj1 Parkinson mutation suggest catastrophic failure of endocytic mechanisms

Synaptojanin 1 is a brain enriched phosphoinositide phosphatase implicated in endocytosis at the synapse. A mutation (R258Q) that selectively impairs its Sac1 phosphatase domain causes early onset familial Parkinsonism. Neurons of mice with this mutation display synaptic vesicle traffic defects across the brain, but selective dystrophic changes in a subset of dopaminergic axons in the dorsolateral striatum. Using correlative light microscopy-FIB-SEM of mutant mouse striata to visualize in 3D these abnormal structures we show that they represent clusters of focal axonal dilations harboring massive, onion-like DAT enriched plasma membrane infoldings, generally localized next to cell bodies of neighboring cells, often engulfing evaginations of such cells. This dysmorphia was associated with a deficit in dopamine release in the same striatal region. Given the involvement of Synj1 in endocytic mechanisms, these structures may reflect an imbalance between exocytosis and endocytosis. Their occurrence only in a subset of axons suggest a vulnerability threshold of these axons beyond which the expansion of the plasma membrane is not counteracted by compensatory mechanisms.

neuroscience↗

bioRxiv2026

T cell-specific loss of IRF1 results in defective CD8 T cell activation and antitumor immunity

Interferon regulatory factor 1 (IRF1) has long been recognized as a tumor suppressor; however, recent studies have revealed context-specific and sometimes opposing roles in cancer progression. Here, we describe a T cell-specific mechanism underlying the antitumor activity of IRF1. Unlike germline Irf1-deficient mice, T cell-specific loss of IRF1 does not lead to a deficiency in cytotoxic CD8 T cells. Nevertheless, tumor burden remains elevated in these mice, associated with reduced CD8 T cell infiltration driven by impaired activation and proliferation in the absence of IRF1. Transcriptomic analysis of activated Irf1-deficient T cells identified NFATc1 as a key gene significantly downregulated upon IRF1 loss. Analysis of human melanoma datasets further corroborated this finding, highlighting a previously unappreciated role for IRF1 in regulating T cell activation and antitumor immunity.

immunology↗

bioRxiv2026

Experience-Dependent Gain Modulation Drives Thermosensory Responses in Behavior

Sensory neurons must extract behaviorally relevant features from dynamic environments while maintaining sensitivity across wide stimulus ranges. To understand how sensory encoding adapts to experience during behavior, we combine long-duration calcium imaging in freely moving C. elegans with a temperature-trajectory playback paradigm to determine how the thermosensory neuron AFD extracts behaviorally relevant sensory features during navigation. We observe that AFD functions as a leaky integrator of recently experienced temperature changes, accumulating thermal inputs over a rolling window of tens of seconds, resulting in calcium levels that represent recent temperature dynamics during runs. Importantly, we determine that AFD selectively amplifies responses to temperature changes near its learned preferred temperature. This experience-dependent gain control aligns encoding with the navigational goal, providing a mechanism for representing temperature preference within a derivative-based sensory system. A minimal mathematical model incorporating derivative detection, leaky integration, and temperature-dependent gain captures the calcium dynamics over a range of stimuli, and a simulation based on the mathematical model predicts goal-oriented locomotor strategies across stimulus regimes. Together, these findings show how gain control allows a derivative-based sensory code to represent an absolute goal and guide locomotory strategies during navigation. HighlightsO_LIAFD encodes recent temperature changes over behaviorally relevant timescales. C_LIO_LIAFD amplifies temperature-change responses within a learned temperature-centered gain window. C_LIO_LIGain control provides a mechanism for representing distance to temperature preference within the derivative-based sensory system. C_LIO_LIA mathematical model and simulation of derivative sensing, leaky integration, and gain control predicts AFD calcium responses and goal-oriented locomotory strategies across stimulus regimes. C_LI

neuroscience↗

bioRxiv2026

Quantifying Drosophila melanogaster Feeding Behavior Using flyPAD and optoPAD

Quantifying feeding behavior with high temporal and spatial precision is critical for understanding how internal state, sensory cues, and neural activity shape food intake and dietary choice. Here, we describe a detailed protocol for performing consumption and dietary choice assays in Drosophila using the flyPAD/optoPAD system. This method enables simultaneous measurement of feeding events across multiple arenas while allowing precise control of gustatory stimuli and optogenetic stimulation. We provide step-by-step instructions for assay food preparation, flyPAD arena setup, data acquisition, and downstream data organization with suggested analyses. This approach is suitable for studying consumption, nutrient preference, learning, and state-dependent modulation of feeding behaviors, and can be readily adapted for optogenetic manipulations and comparative choice assays. HighlightsO_LIHigh throughput, quantitative measurement of Drosophila feeding behavior. C_LIO_LIEasy integration of optogenetic stimulation for precise control of neural circuits. C_LIO_LICompatible with both open-loop and closed-loop optogenetic stimulation paradigms. C_LIO_LIVersatile applications for consumption, nutrient preference, learning, and state-dependent feeding behaviors. C_LIO_LIStep-by-step guidance from arena acquisition and calibration through statistical modeling. C_LI

neuroscience↗

bioRxiv2026

A generalized synthetic control algorithm for sparse functional data

The Synthetic Control Method (SCM) and its interactive factor model generalizations (GSC) are powerful for estimating causal effects from panel data but are not easily applied when follow-up is irregular or sparse, common features of biomedical cohorts. We develop a Bayesian functional extension of GSC that treats each units outcome path as a smooth latent trajectory and accommodates unequally spaced measurements. Trajectories are approximated using Functional Principal Components Analysis (FPCA), providing a data-driven basis that captures dominant patterns with minimal shape assumptions while borrowing strength across individuals. Within this representation, we learn unit and time latent factors jointly with FPCA scores from the control data, construct counterfactual trajectories for treated units, and quantify uncertainty via the posterior. Identification relies on a latent-factor/weak-trend condition and overlap of controls and treated units in the functional score space. Simulation studies varying donor pool and treated unit size and sampling density show that the proposed approach (a.k.a GSC-FPCA) yields low bias when sampling is irregular or sparse, with well-calibrated interval coverage across a broad range of scenarios. We apply the method to longitudinal neuroimaging data from the National Consortium on Alcohol and Neurodevelopment in Adolescence - Adulthood (NCANDA-A) study to estimate the effect of adolescent binge drinking on subsequent brain volumes. Leveraging from 1 to 9 observed time points per participant, GSC-FPCA produces stable counterfactuals and detects a negative impact on gray-matter volumes with sustained high levels of binge drinking. Our results demonstrate that embedding GSC within a functional framework enables robust causal inference in biomedical applications characterized by irregularly-spaced visits, limited observations, and complex outcome dynamics.

neuroscience↗

bioRxiv2025

From perception to valence: a pair of interneurons that assign positive valence to sweet sensation in Drosophila

Assigning valence--appeal or aversion--to gustatory stimuli and relaying it to higher-order brain regions to guide flexible behaviors is crucial to survival. Yet the neural circuit that transforms gustatory input into motivationally relevant signals remains poorly defined in any model system. In Drosophila melanogaster, substantial progress has been made in mapping the sensorimotor pathway for feeding and the architecture of the dopaminergic reinforcement system. However, where and how valence is first assigned to a taste has long been a mystery. Here, we identified a pair of subesophageal zone interneurons in Drosophila, termed fox, that impart positive valence to sweet taste and convey this signal to the mushroom body, the flys associative learning center. We show that fox neuron activity is necessary and sufficient to drive appetitive behaviors and can override a tastants intrinsic valence without impairing taste quality discrimination. Furthermore, fox neurons transmit the positive valence to specific dopaminergic neurons that mediate appetitive memory formation. Our findings reveal a circuit mechanism that transforms sweet sensation into a reinforcing signal to support learned sugar responses. The fox neurons exhibit a convergent-divergent "hourglass" circuit motif, acting as a bottleneck for valence assignment and distributing motivational signals to higher-order centers. This architecture confers both robustness and flexibility in reward processing--an organizational principle that may generalize across species.

neuroscience↗

bioRxiv2025

Psilocybin triggers an activity-dependent rewiring of large-scale cortical networks

Psilocybin holds promise as a treatment for mental illnesses. One dose of psilocybin induces structural remodeling of dendritic spines in the medial frontal cortex in mice. The dendritic spines would be innervated by presynaptic neurons, but the sources of these inputs have not been identified. Here, using monosynaptic rabies tracing, we map the brain-wide distribution of inputs to frontal cortical pyramidal neurons. We discover that psilocybins effect on connectivity is network-specific: strengthening the routing of inputs from perceptual and medial regions (homolog of default mode network) to subcortical targets, while weakening inputs that are part of cortico-cortical recurrent loops. The pattern of synaptic reorganization depends on the drug-evoked spiking activity, because silencing a presynaptic region during psilocybin administration disrupts the rewiring. Collectively, the results reveal the impact of psilocybin on the connectivity of large-scale cortical networks and demonstrate neural activity modulation as an approach to sculpt the psychedelic-evoked neural plasticity.

neuroscience↗

bioRxiv2024

Assembling Ruthenium Complexes to Form Ruthenosome Unleashing Ferritinophagy-mediated Tumor Suppression

AbstactWe introduce ruthenosomes, a fusion of liposomal and reactive oxygen species (ROS)-generating properties meticulously engineered as potent ferroptosis inducers (FINs), marking a significant advancement in metallodrug design for cancer therapy. Formed through the self-assembly of oleate-conjugated ruthenium complexes, these ruthenosomes exhibit exceptional cellular uptake, selectively accumulating in mitochondria and causing substantial disruption. This targeted mitochondrial damage significantly elevates ROS levels, triggering autophagy and selectively activating ferritinophagy. Together, these processes sensitize cancer cells to ferroptosis. In vivo, ruthenosomes effectively suppress colorectal tumor growth, underscoring their therapeutic potential. Our study pioneers a design strategy that transforms ruthenium complexes into liposome-like structures capable of inducing ferroptosis independent of light activation. By leveraging ruthenosomes as multifunctional nanocarriers, this research offers a versatile and powerful platform for ROS-mediated, ferroptosis-driven cancer cell eradication.

biochemistry↗

bioRxiv2024

Evolutionarily divergent Mycobacterium tuberculosis CTP synthase filaments are under selective pressure

The final and rate-limiting enzyme in pyrimidine biosynthesis, CTP synthase (CTPS), is essential for the viability of Mycobacterium tuberculosis and other mycobacteria. Its product, CTP, is critical for RNA, DNA, lipid and cell wall synthesis, and is involved in chromosome segregation. In various organisms across the tree of life, CTPS assembles into higher-order filaments, leading us to hypothesize that M. tuberculosis CTPS (mtCTPS) also forms higher-order structures. Here, we show that mtCTPS does assemble into filaments but with an unusual architecture not seen in other organisms. Through a combination of structural, biochemical, and cellular techniques, we show that polymerization stabilizes the active conformation of the enzyme and resists product inhibition, potentially allowing for the highly localized production of CTP within the cell. Indeed, CTPS filaments localize near the CTP-dependent complex needed for chromosome segregation, and cells expressing mutant enzymes unable to polymerize are altered in their ability to robustly form this complex. Intriguingly, mutants that alter filament formation are under positive selection in clinical isolates of M. tuberculosis, pointing to a critical role needed to withstand pressures imposed by the host and/or antibiotics. Taken together, our data reveal an unexpected mechanism for the spatially organized production of a critical nucleotide in M. tuberculosis, which may represent a vulnerability of the pathogen that can be exploited with chemotherapy.

biochemistry↗

bioRxiv2024

Identifying Alzheimer's disease-related pathways based on whole-genome sequencing data

Alzheimers disease (AD) is a highly inheritable neurodegenerative disorder for which pathway-specific genetic profiling provides insights into its key biological mechanisms and potential treatment targets. Traditional disease-pathway analyses for AD have certain limitations, such as environmental interference and arbitrary sample division. We present a comprehensive framework that starts with genome data, avoiding these drawbacks and offering intrinsic pathway-specific genetic profiling for AD. Whole genome sequencing data from 173 individuals were used to quantify transcriptomes in 14 brain regions, estimate individual-level pathway variant scores, and analyze AD risk for each patient. These results were combined to identify AD-related pathways and quantify their interactions. The predicted expression levels were consistent with previous findings, and the estimated AD risk showed a significant correlation with Braak/Thal scores. A total of 3,798 pathways were identified as potentially associated with AD, with about 19.7% previously reported. Key pathways, including NF-{kappa}B signaling and GSK3{beta} activation, were linked to AD pathogenesis. The interactions among pathways highlighted shared gene functions in AD. In summary, we provided an effective framework for disease-pathway analysis, revealing the interdependence or compensatory effects of pathways in AD.

bioinformatics↗

bioRxiv2024

Genetic regulation of lncRNA expression in the whole human brain

Long non-coding RNAs (lncRNAs) play a key role in the human brain, and genetic variants regulate their expression. Herein, the expression quantitative trait loci (eQTL) of lncRNAs encompassing ten brain regions from 134 individuals was analyzed, and novel variants influencing lncRNA expression (eSNPs) and the respective affected lncRNAs (elncRNAs) were identified. The eSNPs are proximate to their corresponding elncRNAs, enriched in the non-coding genome, and have a high minor allele frequency. The elncRNAs exhibit a high-level and complex pattern of expression. The genetic regulation is more tissue-specific for lncRNAs than for protein-coding genes, with notable differences between cerebrum and cerebellum. However, it shows relatively similar patterns across the cortex regions. Furthermore, we observed a significant enrichment of eSNPs among variants associated with neurological disorders, especially insomnia, and identified insomnia-related lncRNAs involved in immune response functions. Moreover, the present study offers an improved tool for lncRNA quantification, a novel approach for lncRNA function analysis, and a database of lncRNA expression regulation in the human brain. These findings and resources will advance the research on non-coding gene expression regulation in neuroscience.

bioinformatics↗

bioRxiv2024

A quantitative ultrastructural timeline of nuclear autophagy reveals a role for dynamin-like protein 1 at the nuclear envelope

Autophagic mechanisms that maintain nuclear envelope homeostasis are bulwarks to aging and disease. By leveraging 4D lattice light sheet microscopy and correlative light and electron tomography, we define a quantitative and ultrastructural timeline of nuclear macroautophagy (nucleophagy) in yeast. Nucleophagy begins with a rapid accumulation of the selective autophagy receptor Atg39 at the nuclear envelope and finishes in [~]300 seconds with Atg39-cargo delivery to the vacuole. Although there are several routes to the vacuole, at least one pathway incorporates two consecutive membrane fission steps: inner nuclear membrane (INM) fission to generate an INM-derived vesicle in the perinuclear space and outer nuclear membrane (ONM) fission to liberate a double membraned vesicle to the cytosol. ONM fission occurs independently of phagophore engagement and instead relies surprisingly on dynamin like 1 (Dnm1), which is recruited to sites of Atg39 accumulation by Atg11. Loss of Dnm1 compromises nucleophagic flux by stalling nucleophagy after INM fission. Our findings reveal how nuclear and INM cargo are removed from an intact nucleus without compromising its integrity, achieved in part by a non-canonical role for Dnm1 in nuclear envelope remodeling.

cell biology↗

bioRxiv2023

Spatial segregation and aging of metabolic processes underlie phenotypic heterogeneity in mycobacteria

Individual cells within clonal populations of mycobacteria vary in size, growth rate, and antibiotic susceptibility. Heterogeneity is, in part, determined by LamA, a protein found exclusively in mycobacteria. LamA localizes to sites of new cell wall synthesis where it recruits proteins important for polar growth and establishing asymmetry. Here, we report that in addition to this function, LamA interacts with complexes involved in oxidative phosphorylation (OXPHOS) at a subcellular location distinct from cell wall synthesis. Importantly, heterogeneity depends on a unique extension of the mycobacterial ATP synthase, and LamA mediates the coupling between ATP production and cell growth in single cells. Strikingly, as single cells age, concentrations of proteins important for oxidative phosphorylation become less abundant, and older cells rely less on oxidative phosphorylation for growth. Together, our data reveal that central metabolism is spatially organized within a single mycobacterium and varies within a genetically identical population of mycobacteria. Designing therapeutic regimens to account for this heterogeneity may help to treat mycobacterial infections faster and more completely.

microbiology↗

bioRxiv2022

Membrane remodeling properties of the Parkinson's disease protein LRRK2

Mutations in Leucine-rich repeat kinase 2 (LRRK2) are responsible for late-onset autosomal dominant Parkinsons disease (PD). LRRK2 has been implicated in a wide range of physiological processes including membrane repair in the endolysosomal system. Here, using cell free systems, we report that purified LRRK2 directly binds acidic lipid bilayers with a preference for highly curved bilayers. While this binding is nucleotide independent, LRRK2 can also deform low curvature liposomes into narrow tubules in a guanylnucleotide-dependent but ATP-independent way. Moreover, assembly of LRRK2 into scaffolds at the surface of lipid tubules can constrict them. We suggest that an interplay between the membrane remodeling and signaling properties of LRRK2 may be key to its physiological function. LRRK2, via its kinase activity, may achieve its signaling role at sites where membrane remodeling occurs. Significance StatementLRRK2 is one of the most frequently mutated gene in familial Parkinsons disease. While much has been learned about its molecular properties, upstream regulators and protein substrates of its kinase activity, its precise function remains unclear. Recent evidence has pointed to a role of LRRK2 in membrane repair in the endo/lysosomal system. Here we show that purified LRRK2 has membrane remodeling properties. We suggest that its ability to sense and induce membrane curvature may be key to its function in membrane dynamics. These properties may help coordinate a direct role of LRRK2 at the membrane interface with its the signaling role of its kinase domain.

cell biology↗

bioRxiv2022

Three-dimensional structured illumination microscopy with enhanced axial resolution

We present two distinct, complementary methods for improving axial resolution in three-dimensional structured illumination microscopy (3D SIM) with minimal or no modification to the optical system. First, we show that placing a mirror directly opposite the sample enables 4-beam interference with higher spatial frequency content than 3D SIM illumination, offering near-isotropic imaging with [~]120 nm lateral and 160 nm axial resolution. Second, we develop an improved deep learning method that can be directly applied to 3D SIM data, obviating the need for additional hardware. This procedure results in [~]120 nm isotropic resolution and can be combined with denoising to facilitate volumetric imaging spanning dozens of time points. We demonstrate the potential of these advances by imaging a variety of cellular samples, delineating the nanoscale distribution of vimentin and microtubule filaments, observing the relative positions of caveolar coat proteins and lysosomal markers, and visualizing rich cytoskeletal dynamics within T-cells in the early stages of immune synapse formation.

cell biology↗

bioRxiv2022

Downregulating PTBP1 fails to convert astrocytes into hippocampal neurons and to alleviate symptoms in Alzheimer's mouse models

Conversion of astroglia into functional neurons has been considered as a promising therapeutic strategy for neurodegenerative diseases. Recent studies reported that downregulation of the RNA binding protein, PTBP1, converts astrocytes into neurons in situ in multiple mouse brain regions, consequently improving pathological phenotypes associated with Parkinsons disease, RGC loss, and aging. Here, we demonstrate that PTBP1 downregulation using antisense oligonucleotides or an astrocyte specific AAV-mediated shRNA system fails to convert hippocampal astrocytes into neurons in WT, and {beta}-amyloid (5xFAD) and tau (PS19) Alzheimers disease (AD) mouse models, and fails to reverse synaptic/cognitive deficits and AD-associated pathology. Similarly, PTBP1 downregulation cannot convert astrocytes into neurons in the striatum and substantia nigra. Together, our study suggests that cell fate conversion strategy for neurodegenerative disease therapy through manipulating one single gene, such as PTBP1, warrants more rigorous scrutiny.

neuroscience↗