Biology subjects

Daniel, S.

Publications and source records attributed to Daniel, S..

At least 19 recordsLinked to original sources

bioRxiv2026

An Inducible Model of RPE-Associated Hydroxyapatite Mineralization with Relevance to Drusen Formation in Age-Related Macular Degeneration

A cardinal feature of nonexudative age-related macular degeneration (AMD) is the accumulation of drusen between the retinal pigment epithelium (RPE) and Bruch's membrane, yet the mechanisms that initiate and promote drusen formation remain to be fully understood. Hydroxyapatite (HAP), a calcium-phosphate mineral identified within human drusen, has been proposed to contribute to drusen nucleation and is associated with increased likelihood of RPE atrophy. However, mechanistic studies providing insight into RPE-associated mineralization have been limited by a lack of easy-to-use and manipulatable culture models. Here, we established a rapid, inducible ARPE-19-based model of HAP mineralization. We found that ARPE-19 cells cultured in minimum essential media (MEM) supplemented with nicotinamide (NIC), sodium phosphate, and ascorbic acid (NaPAA) reproducibly formed HAP positive deposits, whereas mineralization was not observed while using standard DMEM/F12 medium, DMEM/F12 with NaPAA, MEM-NIC medium, or MEM-NIC medium with alternative osteogenic supplements (such as beta-glycerophosphate, ascorbic acid, and dexamethasone). Scanning electron microscopy with energy dispersive X ray spectroscopy demonstrated that the formed deposits were enriched in calcium (Ca) and phosphorus (P) with Ca/P ratios comparable to drusen-associated HAP deposits from AMD donor tissue. ARPE-19-based HAP deposits were also closely associated with neutral lipid-rich material, staining positive for BODIPY around their core structure. Bulk RNA sequencing of mineralized ARPE-19 cells revealed extracellular matrix, angiogenic, inflammatory, and metabolic transcriptional changes in the absence of strong enrichment of canonical osteogenic pathways. Co-treatment of mineralizing cells with either pyrophosphate, EDTA, or sodium citrate significantly reduced mineral deposition, but these approaches were not able to reverse it. Together, these findings establish a tractable RPE mineralization model that recapitulates key features of AMD-associated HAP and provides a platform for investigating mechanisms of drusen-associated mineral formation.

cell biology↗

bioRxiv2026

Cell-free membrane systems reveal electrostatic control of ion transport in TMEM165 and disease-associated CaCA2 variants

Ion transport across intracellular membranes is essential for cellular homeostasis, yet organellar transport mechanisms remain difficult to resolve in native cells. Here, we establish a cell-free membrane system to interrogate full-length intracellular transporters under defined chemical conditions. Using cell-free protein synthesis, human Golgi transporter TMEM165 and its yeast homolog GDT1 were synthesized in membranes and analyzed by fluorescence and electrochemical measurements. The platform controlled protein identity, ion composition, and transmembrane pH gradients. TMEM165 transport was regulated by pH gradients, consistent with proton-coupled transport shaped by the electrostatic environment of the transport pathway. Disruption of a conserved acidic residue decreased pH sensitivity, broadened ion permeability, and altered steady-state transport behavior, indicating impaired proton coupling and selectivity. These findings identify conserved acidic residues as key regulators of TMEM165 function. More broadly, this work establishes a strategy for reconstructing organellar membrane proteins, resolving disease mechanisms, and engineering transport function in defined synthetic systems.

biophysics↗

bioRxiv2026

Multimodal characterization of variation in neuronal types in the mouse basal ganglia

AbstractThe basal ganglia (BG) are a set of topographically organized, interconnected structures that are pivotal for regulating volitional movement and other aspects of cognitive, motivational, and affective behavior. Recently generated taxonomies of transcriptomically-defined cell types (T-types) have revealed both fine-grained distinctions in gene expression between neurons in these structures as well as continuous transcriptomic variation across similar T-types1-9, which are both related to location within a structure. However, it remains unclear to what extent these and other cellular properties co-vary with each other. Therefore, we performed Patch-seq experiments10,11 on over 900 neurons in mouse brain slices from BG to provide an integrated view of the co-variation between gene expression, location, physiology, and morphology measured from the same neurons. Medium spiny neurons (MSNs) from both the direct and indirect pathways across the dorsal and ventral striatum follow a gene expression gradient that varies in a dorsolateral to ventromedial direction; we find that this gradient also corresponds with systematic differences in action potential kinetics and dendritic arborization. Our analysis also characterizes additional multimodal dimensions of MSN variation, such as those between direct and indirect pathway neurons and between matrix and striosome neurons. Furthermore, through comparison with Patch-seq data from macaque, we demonstrate that the relationship between the transcriptomic/spatial gradient and electrophysiological and morphological properties is conserved across these two species. We also find that properties of striatal interneurons, such as action potential kinetics, vary across the striatum in a manner consistent with the MSN gradient. Outside the striatum, our multimodal Patch-seq dataset from the globus pallidus, subthalamic nucleus, and substantia nigra enabled us to characterize transcriptomically-defined types and link them to prior descriptions of cell types in these structures. Finally, we examined to what extent the MSN transcriptomic/spatial gradient persisted across different stages of the BG circuit by comparing Patch-seq neurons to reconstructed whole-neuron morphologies and the topography of their interareal projections, finding that the gradient is better preserved in GPe and GPi compared to SNr. Our study links transcriptomic variation across T-types in mouse BG to spatial localization and phenotypic differences at the level of individual cells, improving our understanding of cell type architecture in topographically organized circuits of the brain.

neuroscience↗

bioRxiv2026

A Ubiquitin network safeguards cell identity by continuously degrading stem-cell related translational machinery

How cell identity is maintained is a fundamental question, and loss of cell identity is a hallmark of aging that is associated with multiple age-related diseases. In the adult Drosophila midgut, we identified a post-transcriptional regulatory layer that supervises enterocyte (EC) identity and fails upon aging. Combining single-cell RNA-seq with lineage tracing in aging ECs and classical genetics we found that aging ECs express genes that unlock the differentiated state. Upon aging, the protein Rogue (CG13928), a translational repressor, orchestrates reactivation of a stem-cell-related translational repression machinery involving p-body-associated RNA-binding proteins that cancels the differentiated state. In young ECs, this machinery is continuously suppressed by the deubiquitinase Non-stop (dUSP22) and the ubiquitin E2 dUbcH8/Kdo and the E3 enzyme CTLH, together suppress the stem-cell related RNA binding proteins safeguarding EC identity. Upon aging, the levels of dUSP22 decline, dUbcH8/Kdo and the E3 CTLH complex are cleared via Rogue, and the stem cell-related p-bodies are reactivated, self-destroying EC identity.

cell biology↗

bioRxiv2026

Morphoelectric Diversity and Specialization of Neuronal Cell Types in the Primate Striatum

The basal ganglia are evolutionary ancient subcortical nuclei that form interconnected loops with the neocortex and limbic system to regulate movement, learning, habit formation, emotion, and motivation. Their dysfunction contributes to major neurological and psychiatric disorders, yet most cellular-level insights derive from rodent studies, leaving knowledge gaps in humans and translationally relevant primate species. To address this, we generated multi-modal Patch-seq data linking transcriptomic identity with morphological and electrophysiological properties in macaque striatum, the input nucleus of the basal ganglia. We found underappreciated diversity among medium spiny neurons, including non-canonical types, and variation aligned with functional gradients. Interneurons also exhibited spatial variation and even greater morphoelectric diversity, highlighting their functional modularity. Despite broad evolutionary conservation, we identified primate-specific features and key differences from rodent striatal neurons. By integrating molecular classification with cellular properties that shape network function, our findings provide insights into the functional organization of the primate striatum.

neuroscience↗

bioRxiv2025

Cross-species consensus atlas of the primate basal ganglia

The basal ganglia (BG) are conserved brain regions essential for motor control, learning, emotion, and cognition, and are implicated in neurological and psychiatric disease. Yet a unified cross-species taxonomy of BG cell types is lacking, limiting translation of BG circuit mechanisms, interpretation of human genetic risk, and development of cell type-targeted tools. We present a multiomic consensus atlas of 1.8 million nuclei from human, macaque, and marmoset spanning eight BG structures. Integrating cross-species gene expression, open chromatin, and spatial profiling enables definition of conserved and divergent cell types. Alignment to existing mouse and human atlases identifies 61 homologous cell types conserved over 80 million years. We identify a STRd D2 StrioMat Hybrid medium spiny neuron (MSN) type with molecular, electrophysiological, and morphological features that clarify hybrid MSN identities. Comparative cis-regulatory analysis reveals conserved sequence grammars that encode cell identity and inform viral targeting strategies, providing a foundational resource for BG evolution, function, and disease.

neuroscience↗

bioRxiv2025

Map of spiking activity underlying change detection in the mouse visual system

Visual behavior requires coordinated activity across hierarchically organized brain circuits. Understanding this complexity demands datasets that are both large-scale (sampling many areas) and dense (recording many neurons in each area). Here we present a database of spiking activity across the mouse visual system--including thalamus, cortex, and midbrain--while mice perform an image change detection task. Using Neuropixels probes, we record from >75,000 high-quality units in 54 mice, mapping area-, cortical layer-, and cell type-specific coding of sensory and motor information. Modulation by task-engagement increased across the thalamocortical hierarchy but was strongest in the midbrain. Novel images modulated cortical (but not thalamic) responses through delayed recurrent activity. Population decoding and optogenetics identified a critical decision window for change detection and revealed that mice use an adaptation-based rather than image-comparison strategy. This comprehensive resource provides a valuable substrate for understanding sensorimotor computations in neural networks.

neuroscience↗

bioRxiv2025

A Plasma Membrane Vesicle Imaging-Based Platform for Studying Membrane Fusion

Membrane fusion is central to biological processes such as viral entry, fertilization and cell-to-cell fusion. Gaining a mechanistic understanding of fusion requires the ability to visualize and quantify the dynamic interaction between two membranes and their associated protein machineries at high temporal and spatial resolution. However, studying these processes in live cells remains challenging due to the complexity of the cellular environment. Here we demonstrate a versatile cell-free platform based on giant plasma membrane vesicles (GPMVs) that enables controlled, quantitative analysis of receptor binding and membrane fusion kinetics in a native membrane context. As proof of concept, we reconstitute the SARS-CoV-1 Spike-ACE2 interaction, capturing specific receptor engagement and accumulation at the membrane interface using confocal microscopy and micropipette aspiration. Fusion was induced by proteolytic activation and quantified using both high-resolution microscopy and high-throughput Imaging Flow Cytometry. The platform also reveals the influence of membrane composition on fusion efficiency, demonstrated by the impact of cholesterol depletion. This approach provides a broadly applicable system for dissecting membrane fusion and protein-protein interactions across membranes, with compatibility for biophysical, imaging and structural analysis. It offers new opportunities for mechanistic studies and inhibitor screening in a biologically relevant yet experimentally accessible context.

biophysics↗

bioRxiv2025

Select azo compounds post-translationally modulate HTRA1 abundance and activity potentially through interactions at the trimer interface

High-temperature requirement protein A1 (HTRA1) is a secreted serine protease with diverse substrates, including extracellular matrix proteins, proteins involved in amyloid deposition, and growth factors. Accordingly, HTRA1 has been implicated in a variety of neurodegenerative diseases including a leading cause of blindness in the elderly, age-related macular degeneration (AMD). In fact, genome wide association studies have identified that the 10q26 locus which contains HTRA1 confers the strongest genetic risk factor for AMD. A recent study has suggested that AMD-associated risk alleles in HTRA1 correlate with a significant age-related defect in HTRA1 synthesis in the retinal pigmented epithelium (RPE) within the eye, possibly accounting for AMD susceptibility. Thus, we sought to identify small molecule enhancers of HTRA1 transcription and/or protein abundance using an unbiased high-throughput screening approach. To accomplish this goal, we used CRISPR/Sp.Cas9 engineering to introduce an 11 amino acid luminescent peptide tag (HiBiT) onto the C-terminus of HTRA1 in immortalized ARPE-19 cells. Editing was very efficient ([~]88%), verified by genomic DNA analysis, short interfering RNA (siRNA), and HiBiT blotting. Nineteen-hundred and twenty compounds from two libraries were screened. An azo compound with reported anti-amyloidogenic and cardioprotective activity, Chicago Sky Blue 6B (CSB), was identified as an enhancer of endogenous HTRA1 secretion (2.0 {+/-} 0.3 fold) and intracellular levels (1.7 {+/-} 0.2 fold). These results were counter-screened using HiBiT complement factor H (CFH) edited ARPE-19 cells, verified using HiBiT blotting, and were not due to HTRA1 transcriptional changes. Importantly, serine hydrolase activity-based protein profiling (SH-ABPP) demonstrated that CSB does not affect HTRA1s specific activity. However, interestingly, in follow-up studies, Congo Red, another azo compound structurally similar to CSB, also substantially increased intracellular HTRA1 levels (up to 3.6 {+/-} 0.3 fold) but was found to significantly impair HTRA1 enzymatic reactivity (0.45 {+/-} 0.07 fold). Computational modeling of potential azo dye interaction with HTRA1 suggests that CSB and Congo Red can bind to the non-catalytic face of the trimer interface but with different orientation tolerances and interaction energies. These studies identify select azo dyes as HTRA1 chemical probes which may serve as starting points for future HTRA1-centered small molecule therapeutics.

biochemistry↗

bioRxiv2025

Hebb's Vision: The Structural Underpinnings of Hebbian Assemblies

1In 1949, Donald Hebb proposed that groups of neurons that activate stereotypically form the organizational building blocks of perception, cognition, and behavior. Finding the structural underpinning of such assemblies has been technically challenging, due to a lack of large-scale structure-activity maps. Here, we analyze this relation using a novel dataset that links in vivo optical physiology to connectivity using postmortem elec-tron microscopy (EM). From the fluorescence traces, we extract neural assemblies from higher-order correlations in neural activity. Physiologically, we show that these assemblies exhibit properties consistent with Hebbs theory, including more reliable responses to repeated natural movie inputs than size-matched random ensembles and superior decoding of visual stimuli. Structurally, we find that neurons that participate in assemblies are significantly more integrated into the structural network than those that do not. Contrary to Hebbs original prediction, we do not observe a marked increase in the strength of monosynaptic excitatory connections between cells participating in the same assembly. However, we find significantly stronger indirect feed-forward inhibitory connections targeting cells in other assemblies. These results show that assemblies can be useful components of perception, and, surprisingly, they are delineated by mutual inhibition.

neuroscience↗

bioRxiv2025

Annotation Comparison Explorer (ACE): connecting brain cell types across studies of health and Alzheimer's Disease

BackgroundSingle-cell multiomic technologies have allowed unprecedented access to gene profiles of individual cells across species and organ systems, including the brain. The Allen Institute has created foundational atlases characterizing mammalian cell types in the adult mouse brain and the neocortex of humans with and without Alzheimers disease (AD). However, proliferation of public cell type classifications (or taxonomies) by us and others creates a challenge for knowledge integration. ResultsHere, we introduce Annotation Comparison Explorer (ACE), a web application for comparing cell type assignments and other cell-based annotations (e.g., donor demographics, anatomic locations, quality control metrics). ACE can filter cells and includes an interactive set of visualization tools, plot and data downloads, and statistics for comparing two or more taxonomy annotations alongside collected knowledge (e.g., cell type aliases, marker genes, abundance changes in disease). In this study we describe ACE functionality and present the following three ACE use cases. First, we demonstrate how a user can assign labels from the Seattle Alzheimers Disease Brain Cell Atlas (SEA-AD) taxonomy to their own cells and compare these mappings to user-defined cell type assignments and other cell metadata, using a previous cell type classification from the Allen Institute and two independent studies of different brain diseases as inputs. Second, we extend this approach for comparison of ten published human AD studies previously reprocessed through a common data analysis pipeline, and identify congruent cell type abundance changes in AD, including a decrease in certain somatostatin interneurons. Finally, ACE includes translation tables between different mouse and human brain cell type taxonomies on Allen Brain Map, from initial studies in neocortex to more recent studies spanning the whole brain, along with a human immune cell atlas focused on peripheral blood mononuclear cells. These use cases represent three of many possible applications for ACE. ConclusionsACE combines standard and custom visualizations into a user-friendly, open-source web tool for exploring categorical and numeric relationships and translating cell type classifications and knowledge across studies. ACE can be freely and publicly accessed at https://sea-ad.shinyapps.io/ACEapp/.

neuroscience↗

bioRxiv2024

Genetic removal of Nlrp3 protects against sporadic and R345W Efemp1-induced basal laminar deposit formation

Chronic, unresolved inflammation has long been speculated to serve as an initiating and propagating factor in numerous neurodegenerative diseases, including a leading cause of irreversible blindness in the elderly, age-related macular degeneration (AMD). Intracellular multiprotein complexes called inflammasomes in combination with activated caspases facilitate production of pro-inflammatory cytokines such as interleukin 1 beta. Specifically, the nucleotide-binding oligomerization (NOD)-like receptor protein 3 (NLRP3) has received heightened attention due to the wide range of stimuli to which it can respond and its potential involvement in AMD. In this study, we directly tested the role of Nlrp3 and its downstream effector, caspase 1 (Casp1) in mediating early AMD-like pathology (i.e., basal laminar deposits [BLamDs]) in wild-type (WT) mice and the Malattia Leventinese/Doyne honeycomb retinal dystrophy (ML/DHRD) mouse model (p.R345W mutation in Efemp1). Compared to aged-matched controls, R345W+/+ knockin mice demonstrated increased Muller cell gliosis, subretinal Iba-1+ microglial cells, higher Nlrp3 immunoreactivity in the retina, as well as significant transcriptional upregulation of complement component 3, Nlrp3, pro-Il1b, pro-caspase-1, and tissue inhibitor of matrix metalloproteinase 3 in the retinal pigmented epithelium (RPE)/choroid. These findings were accompanied by an age-related increase in BLamD formation in the R345W+/+ mice. Genetic elimination of either Nlrp3 or Casp1 significantly reduced both the size and coverage of BLamDs in the R345W+/+ background, highlighting an important and underappreciated pathway that could affect ML/DHRD onset and progression. Moreover, Nlrp3 knockout reduced spontaneous, idiopathic BLamDs in WT mice, suggesting translatability of our findings not only to rare inherited retinal dystrophies, but also potentially to AMD itself.

immunology↗

bioRxiv2024

Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits

We present an enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits. Best-in-class vectors were curated for accessing major striatal neuron populations including medium spiny neurons (MSNs), direct and indirect pathway MSNs, as well as Sst-Chodl, Pvalb-Pthlh, and cholinergic interneurons. Specificity was evaluated by multiple modes of molecular validation, three different routes of virus delivery, and with diverse transgene cargos. Importantly, we provide detailed information necessary to achieve reliable cell type specific labeling under different experimental contexts. We demonstrate direct pathway circuit-selective optogenetic perturbation of behavior and multiplex labeling of striatal interneuron types for targeted analysis of cellular features. Lastly, we show conserved in vivo activity for exemplary MSN enhancers in rat and macaque. This collection of striatal enhancer AAVs offers greater versatility compared to available transgenic lines and can readily be applied for cell type and circuit studies in diverse mammalian species beyond the mouse model.

neuroscience↗

bioRxiv2024

Raffinose induces autophagy to promote plant growth

Plant growth is governed by the integration of environmental cues and nutritional status. Under stress conditions, growth is usually attenuated in favor of stress response, creating a trade-off between growth and stress. Autophagy is a vital process in eukaryotes, maintaining cellular balance by degrading and recycling cellular components. It is triggered by various nutrient-deprivation conditions and both biotic and abiotic stresses in plants. Surprisingly, over-expressing autophagy-related genes across multiple plant species resulted in increased plant size, yield, and stress resistance, posing autophagy as a regulator of the stress-growth balance. Yet, the molecular mechanisms governing its induction remain partially understood. In the current work, we identified raffinose-a plant-derived sugar known for its role in stress responses-as a novel plant autophagy inducer. Raffinose treatment resulted in increased biomass and yield in an autophagy-dependent manner in several plant species. We also show that raffinose activates autophagy through the SnRK1 kinase complex, independent of TOR signaling, and that raffinose treatment results in increased expression of ATG5 and ATG7. We also point to possible downstream candidates operating autophagy-related biomass accumulation. Our findings offer new perspectives on the role of autophagy in maintaining a balance between plant growth and stress responses, underscoring the significance of raffinose in its regulation. SIGNIFICANCE STATEMENTThe intricate balance between plant growth and stress responses is crucial for agricultural productivity, particularly as climate change intensifies environmental stressors such as drought and extreme temperatures. Usually, there is a trade-off between growth and stress response. Autophagy--a cellular recycling process essential for maintaining cellular homeostasis--plays a pivotal role in this balance. Yet, the molecular mechanisms modulating it are partially understood. Raffinose treatment enhances biomass and yields in various plant species by inducing autophagy. By elucidating the molecular mechanisms of raffinose-mediated autophagy induction, our findings provide valuable insights into potential strategies for enhancing plant resilience against climate-induced stress.

plant biology↗

bioRxiv2024

Cell-free expression of Nipah virus transmembrane proteins for proteoliposome vaccine design

Membrane proteins expressed on the surface of enveloped viruses are potent antigens in a vaccine, yet are difficult to produce and present due to their instability without a lipid scaffold. Current vaccination strategies that incorporate viral membrane proteins, such as live attenuated viruses, inactivated viruses, or extracellular vesicles, have limitations including lengthy production time, poor immunogenicity, extensive processing steps, and/or poor stability. Cell-free protein synthesis of viral membrane proteins offers a rapid, one-step method to assemble vaccine nanoparticles via cotranslational folding of membrane proteins into nanoscale liposomes. Here, we develop a vaccine candidate for the deadly Nipah virus (NiV), a highly lethal virus listed by the World Health Organization as a priority pathogen, by cell-free expressing two full-length Nipah virus membrane proteins. We demonstrate that both NiV fusion protein (NiV F) and NiV glycoprotein (NiV G) can be expressed and cotranslationally integrated into liposomes and that they fold into their native conformation. We find the removal of a signal peptide sequence and alteration of liposome lipid composition improves viral membrane protein incorporation. Furthermore, a lipid adjuvant, monophosphoryl lipid A (MPLA), can be readily added to liposomes without disrupting protein-vesicle loading or protein folding conformations. Finally, we demonstrate that our generated liposomal formulations lead to enhanced humoral responses in mice compared to empty and single-protein controls. This work establishes a platform to quickly assemble and present membrane antigens as multivalent vaccines that will enable a rapid response to the broad range of emerging pathogenic threats.

synthetic biology↗

bioRxiv2024

The transcriptomic and spatial organization of telencephalic GABAergic neuronal types

The telencephalon of the mammalian brain comprises multiple regions and circuit pathways that play adaptive and integrative roles in a variety of brain functions. There is a wide array of GABAergic neurons in the telencephalon; they play a multitude of circuit functions, and dysfunction of these neurons has been implicated in diverse brain disorders. In this study, we conducted a systematic and in-depth analysis of the transcriptomic and spatial organization of GABAergic neuronal types in all regions of the mouse telencephalon and their developmental origins. This was accomplished by utilizing 611,423 single-cell transcriptomes from the comprehensive and high-resolution transcriptomic and spatial cell type atlas for the adult whole mouse brain we have generated, supplemented with an additional single-cell RNA-sequencing dataset containing 99,438 high-quality single-cell transcriptomes collected from the pre- and postnatal developing mouse brain. We present a hierarchically organized adult telencephalic GABAergic neuronal cell type taxonomy of 7 classes, 52 subclasses, 284 supertypes, and 1,051 clusters, as well as a corresponding developmental taxonomy of 450 clusters across different ages. Detailed charting efforts reveal extraordinary complexity where relationships among cell types reflect both spatial locations and developmental origins. Transcriptomically and developmentally related cell types can often be found in distant and diverse brain regions indicating that long-distance migration and dispersion is a common characteristic of nearly all classes of telencephalic GABAergic neurons. Additionally, we find various spatial dimensions of both discrete and continuous variations among related cell types that are correlated with gene expression gradients. Lastly, we find that cortical, striatal and some pallidal GABAergic neurons undergo extensive postnatal diversification, whereas septal and most pallidal GABAergic neuronal types emerge simultaneously during the embryonic stage with limited postnatal diversification. Overall, the telencephalic GABAergic cell type taxonomy can serve as a foundational reference for molecular, structural and functional studies of cell types and circuits by the entire community.

neuroscience↗

bioRxiv2024

Coexistence of self-compatible and self-incompatible alleles in a plant metapopulation via spatial rock-paper-scissors dynamics

Around 40% of flowering plants exhibit a preference for self-incompatibility systems (SI) on a macro-evolutionary scale. The dynamics of SI and self-compatible systems (SC) alleles can lead to the fixation of one genotype or coexistence, depending on factors like inbreeding depression and initial fractions. For the first time, we explore the dynamics of self-incompatible (SI) and self-compatible (SC) alleles in the presence of competitors, studying the relationship between population structure and SI frequency. Our numerical simulations consider non-instantaneous coupling between patches, focusing on a regime where the competitors fitness falls between inbred and outbred fitness. In this regime, SI, SC, and competitors exhibit repeating cycles of rock-paper-scissors dynamics both spatially and temporally. We find well-mixed environment leads to lower fractional population density of the focal species. Additionally in this regime, a paradoxical result emerges: in stress-free regions favorable to SI, the focal species may lose to the competitor.

ecology↗

bioRxiv2023

GSK3 inhibition reduces ECM production and prevents age-related macular degeneration-like pathology

Malattia Leventinese/Doyne Honeycomb Retinal Dystrophy (ML/DHRD) is an age-related macular degeneration (AMD)-like retinal dystrophy caused by an autosomal dominant R345W mutation in the secreted glycoprotein, fibulin-3 (F3). To identify new small molecules that reduce F3 production from retinal pigmented epithelium (RPE) cells, we knocked-in a luminescent peptide tag (HiBiT) into the endogenous F3 locus which enabled simple, sensitive, and high throughput detection of the protein. The GSK3 inhibitor, CHIR99021 (CHIR), significantly reduced F3 burden (expression, secretion, and intracellular levels) in immortalized RPE and non-RPE cells. Low-level, long-term CHIR treatment promoted remodeling of the RPE extracellular matrix (ECM), reducing sub-RPE deposit-associated proteins (e.g., amelotin, complement component 3, collagen IV, and fibronectin), while increasing RPE differentiation factors (e.g., tyrosinase, and pigment epithelium derived factor). In vivo, treatment of 8 mo R345W+/+ knockin mice with CHIR (25 mg/kg i.p., 1 mo) was well tolerated and significantly reduced R345W F3-associated AMD-like basal laminar deposit number and size, thereby preventing the main pathological feature in these mice. This is the first demonstration of small molecule-based prevention of AMD-like pathology in ML/DHRD mice and may herald a rejuvenation of interest in GSK3 inhibition for the treatment of neurodegenerative diseases, including, potentially AMD itself.

neuroscience↗