Biology subjects

Son, S.

Publications and source records attributed to Son, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Bead-based RNA Detection with Cas13a: Multi-scale Design and Validation

CRISPR-based assays offer sensitive and specific nucleic acid detection for a broad range of diagnostic and surveillance applications. While standard solution-based assays are simple, they typically lack the ability to detect multiple targets individually without the need for more complex instrumentation and multi-step workflows. Surface-based strategies offer greater potential for multiplexing since the identity of a target can be associated with a location on a slide or a specific bead, as in the case of DNA arrays or Luminex bead assays. However, the design principles for optimizing surface-based CRISPR assays have yet to be developed. Here we present a multi-scale analytical framework integrating nanoscale enzyme kinetics, microscale diffusion constraints, and macroscale assay parameters that we use to develop a bead-based Cas13a assay where the bead becomes fluorescent when the target RNA for that bead is detected. The assay, which we call SurfCas, uses surface-bound guide RNAs and reporter RNAs to detect one or more soluble target RNAs in a one-pot assay. We show that SurfCas has a sensitivity approaching bulk reactions, and we demonstrate multiplexed detection of target RNAs in a complex biological matrix. The design principles we establish for surface-based CRISPR assays offer guidance on how to further improve SurfCas sensitivity and scale multiplexed detection of target RNAs in a single reaction.

bioengineering↗

bioRxiv2025

Selective Observation Under Limited Resources Biases Social Inference Through Hysteresis

Despite limited access to others actions and outcomes, humans excel at inferring hidden intentions. Given only partial access, how do they decide what to observe, and how does selective observation shape inference? Here, we examined how choosing what to observe can bias the inference about others intentions. Participants played a game where they pursued a fleeing target while a computerized opponent acted competitively or cooperatively. Participants overestimated the opponents competitiveness after the opponent acted more competitively than expected, whereas no such bias occurred when the opponent was more cooperative than expected. This asymmetry depended on the sequence of events, resembling hysteresis, a form of path dependence observed in physical systems. We found that these biases became stronger when participants chose to observe the opponent instead of their own avatar, and this choice came at the cost of losing precise control over their avatar. Our findings highlight the trade-off in selecting what to observe, as the resulting inference biases propagate differently depending on the interaction history.

neuroscience↗

bioRxiv2025

Inertial sensing of water content in tumor spheroids

Cellular water content governs the concentration of all biomolecules inside a cell, thereby influencing the physical and functional properties of the cell. However, measurements of water content in physiologically relevant cell culture models remain largely unavailable, particularly in 3D models such as tumor spheroids and organoids. Here, we achieve such measurements using a commercially available, industrial-grade, steel tube. The steel tube functions as a mechanical resonator that inertially senses the buoyant mass of particles. For microgram-scale particles [≥]400 {micro}m in diameter, we achieve <1% precision error in buoyant mass with a 5-minute acquisition interval. By sequentially measuring the buoyant mass of individual, glioblastoma patient-derived tumor spheroids in media of different densities and cell permeabilities, we determine the absolute and fractional (v/v) water content of the spheroids, along with their dry mass, volume, and density properties. We achieve ~0.4% precision error in fractional water content with a throughput of 3 spheroids per hour. This enables us to detect both inter-spheroid variability in fractional water content and acute responses to kinase inhibition. Overall, we establish a simple and accessible technique for quantifying water content in living 3D cell culture models, opening new avenues for studying biophysical regulation in multicellular systems.

bioengineering↗

bioRxiv2025

A characterization of mouse retinal ganglion cell types labeled with AAV tools

The mouse retina is made-up of approximately 150 types of neurons each with unique characteristics and functions in interpreting visual information. Recent efforts to categorize cell types using molecular markers, morphology, and electrophysiological response properties have provided a wealth of information and a host of tools for studying specific cell types. AAV-based approaches have several advantages over transgenic mouse lines, including ease of application to many different animal models without extensive crossing and their amenability to intersectional approaches. Here, we provide an in-depth characterization of retinal ganglion cell types labeled by two AAV vectors drawn from a recent panel of constructs with synthetic promoters. Each promoter analyzed here was derived from a gene expressed in a cell type specific manner. Using a combination of morphology, molecular markers, and electrophysiological measurement of light responses, we found that each vector labeled distinct subsets of RGCs. However, both labeled more cell types than expected from the expression pattern of the promoters endogenous gene. We then characterized the projection patterns of these RGC types to the brain, finding that each AAV type labeled distinct axonal populations. These tools provide new access to a unique subset of cells and will be instrumental to future studies analyzing their functions and connectivity.

neuroscience↗

bioRxiv2025

Reduced neuronal self-avoidance in mouse starburst amacrine cells with only one Pcdhg isoform

The clustered protocadherins (cPcdhs) are a family of [~]60 homophilic cell adhesion molecules expressed across three gene clusters (Pcdha, Pcdhb, and Pcdhg) with a variety of essential roles in the developing nervous system. Some of these roles rely on specific isoforms, while others are more consistent with a model of isoform redundancy or a requirement for diversity. The {gamma}-Pcdhs (expressed from the Pcdhg gene cluster) are particularly important for neuronal self-avoidance in starburst amacrine cells in the mouse retina. Here, we used mouse mutants to test two of the C-type isoforms - {gamma}C4 and {gamma}C5 - and found that neither was required for normal self-avoidance. Conversely, when we analyzed a mutant with only {gamma}C4 intact, we found significant failures in self-avoidance that could not be completely rescued by overexpression of this isoform from a transgene. We have recently found that this isoform is essential for normal neuronal survival during development, and our new findings here support the hypothesis that {gamma}C4 is specialized for the survival function at the expense of a significant role in self-avoidance.

neuroscience↗

bioRxiv2025

Neural Gain Modulation Propagates from Posterior to Anterior Brain Regions to Optimize Orientation Perception in Chronic Astigmatism

While visual impairments commonly occur daily, many individuals fail to recognize these distortions. Yet, the brains role in adapting to distorted sensory inputs remains largely unknown. In this study, we focused on how the brain recalibrates physical orientation-specific blur after chronic exposure to astigmatism. By reconstructing the population orientation tuning response from electroencephalogram activity patterns and estimating neural gain modulation using an optics-based computational model (data from 42 participants, including 15 females), we found enhanced neural gain for underrepresented orientations and reduced gain for overrepresented ones, especially in individuals with long-term astigmatism. The strength of the gain modulation correlated with the optimization of orientation perception in these participants. Furthermore, this push-pull neural gain modulation dynamically propagated from the posterior brain regions to others, and the strength of the propagation correlated with the degree of perceptual optimization. In contrast, short-term exposure resulted in transient and short-lived neural optimization, characterized by a relatively stronger anterior-to-posterior transference pattern. These results show how feature-specific information is modified across the entire brain in response to systematic visual distortion, revealing duration-dependent strategies the brain employs to handle sensory impairments.

neuroscience↗

bioRxiv2025

A Chlorinated Diketopiperazine Antibiotic Targets Mycobacterium Tuberculosis DNA Gyrase

We describe a novel macrocyclic peptide, speirobactin, produced by Photorhabdus that selectively kills Mycobacterium tuberculosis. A non-ribosomal peptide synthase (NRPS) containing two linear modules codes for the synthesis of speirobactin. The biosynthetic operon contains a pentapeptide-repeat protein as a resistance gene. Genomic analysis of speirobactin-resistant mutants of M. tuberculosis led to identification of DNA gyrase as the molecular target. The mutations were recreated by allelic replacement and show that DNA gyrase is the only target. Transcriptome analysis of M. tuberculosis treated with antibiotics shows that speirobactin clusters close to fluoroquinolones, supporting its action against the DNA gyrase.

cell biology↗

bioRxiv2024

Cell surface crowding is a tunable biophysical barrier to cell-cell fusion

Cell-cell fusion is fundamental to developmental processes such as muscle formation, as well as to viral infections that cause pathological syncytia. An essential step in fusion is close membrane apposition, but cell membranes are crowded with proteins, glycoproteins, and glycolipids, all of which must be cleared before a fusion pore can be nucleated. Here, we find that cell surface crowding drastically reduces fusogenicity in multiple systems, independent of the method for driving fusion. We estimate that cell surface crowding presents an energetic barrier to membrane apposition on the scale of [~]100kBT, greater than that of bare membrane fusion. We show that increasing cell surface crowding reduces fusion efficiency of PEG-mediated and fusogen-mediated cell-cell fusion, as well as synthetic membranes under force. Interestingly, we find that differentiating myoblasts naturally decrease cell surface crowding prior to fusion. Cell surface crowding presents an underappreciated biophysical barrier that may be tuned developmentally and could be targeted externally to control tissue-specific cell-cell fusion.

biophysics↗

bioRxiv2024

Targeted Degradation of MYC2 through MPK6 Phosphorylation Reveals Mechanisms and Implications for JA Signaling

MYC2 is a key regulator in the Jasmonic acid (JA) signaling pathway, yet the mechanisms governing its stability remain unclear. In this study, we demonstrate that MYC2 is degraded by MPK6 under JA signaling. Through yeast two-hybrid and co-immunoprecipitation assays, and in vitro kinase assay, we show that MPK6 directly interacts with and phosphorylates MYC2. Additionally, MYC2 transcriptional activity is enhanced in the mpk6 mutant. Further, MPK6 phosphorylates MYC2 at threonine 328, leading to its degradation. These findings suggest that MPK6 drives MYC2 degradation by specifically phosphorylating threonine 328 within the JA signaling pathway.

plant biology↗

bioRxiv2024

Brain-wide connectivity and novelty response of the dorsal endopiriform nucleus in mice

The dorsal endopiriform nucleus (EPd) is an enigmatic cortical subplate structure located inside the piriform cortex that shares a similar developmental origin with the claustrum. Although the EPd has been previously implicated in epilepsy and olfactory processing, its anatomical organization, connectivity patterns, and function remain largely unclear due to a lack of specific molecular markers. Our previous mapping study serendipitously identified that the Oxt receptor (Oxtr) is densely expressed in the EPd. Subsequent immunohistochemical and spatial transcriptomic analyses confirmed that Oxtr expression is enriched in the EPd, revealing distinct molecular organization compared to the neighboring claustrum. Whole brain input-output mapping of EPd Oxtr-positive neurons unveils extensive bidirectional connections to the ventral half of the brain, orchestrating functional circuits regulating olfaction, internal state, and emotion. Furthermore, our in-vivo miniscope recordings show that EPd Oxtr neurons exhibit high baseline activity during exploratory behavior, with a sharp decrease in activity in response to novel stimuli. This suggests that the EPd regulates interoceptive states and likely plays a role in adapting to novel exteroceptive cues.

neuroscience↗

bioRxiv2024

State-dependent Online Reactivations for Different Learning Strategies in Foraging

Reactivation of neural responses associated with navigation is thought to facilitate learning. We wondered whether reactivation is subject to contextual control, meaning that different types of learning promote different reactivation patterns. We trained macaques to forage in a first-person virtual maze and identified two distinct learning states prioritizing reward and information using unsupervised ethogramming based on low-level features. In orbitofrontal (OFC) and retrosplenial (RSC) cortices, representations of the goal, the path towards it, and recently traveled paths were strongly reactivated - online - during reward-prioritizing choices. During learning, reactivation of optimal paths increased in RSC after reward-prioritizing choices, and reactivation of uninformative paths decreased in RSC and OFC after information-prioritizing choices. Reactivation in OFC selectively covaried with ongoing RSC activity when prioritizing information; vice versa during prioritizing reward. These results highlight that cognitive states can drive learning and reactivation patterns can be tailored to the needs of the moment.

neuroscience↗

bioRxiv2024

Biogenesis of circular RNAs in vitro and in vivo from the Drosophila Nk2.1/scarecrow gene

scarecrow (scro) encodes a fly homolog of mammalian Nkx2.1 that is vital for early fly development as well as for optic lobe development. Interestingly, scro was reported to produce a circular RNA (circRNA). In this study, we identified 12 different scro circRNAs, which are either mono- or multi-exonic forms. The most abundant forms are circE2 carrying the second exon only and bi-exonic circE3-E4. Levels of circE2 show an age-dependent increase in adult heads, supporting a general trend of high accumulation of circRNAs in aged fly brains. Aligning sequences of introns flanking exons uncovered two pairs of intronic complementary sequences (ICSs); one pair residing in introns 1 and 2 and the other in introns 2 and 4. The first pair was demonstrated to be essential for the circE2 production in cell-based assays; furthermore, deletion of the region including potential ICS components in the intron-2 reduced in vivo production of circE2 and circE3-E4 by 80%, indicating them to be essential for the biogenesis of these isoforms. Besides the ICS, the intron regions immediately abutting exons seemed to be responsible for a basal level of circRNA formation. Moreover, the replacement of scro-ICS with those derived from laccase2 was comparably effective in scro-circRNA production, buttressing the importance of the hairpin-loop structure formed by ICS for the biogenesis of circRNA. Lastly, overexpressed scro affected outcomes of both linear and circular RNAs from the endogenous scro locus, suggesting that Scro plays a direct or indirect role in regulating expression levels of either or both forms.

genetics↗

bioRxiv2023

Exuberant de novo dendritic spine growth in mature neurons

Dendritic spines are structural correlates of excitatory synapses maintaining stable synaptic communications. However, this strong spine-synapse relationship was mainly characterized in excitatory pyramidal neurons (PyNs), raising a possibility that inferring synaptic density from dendritic spine number may not be universally applied to all neuronal types. Here we found that the ectopic expression of H-Ras increased dendritic spine numbers regardless of cortical cell types such as layer 2/3 pyramidal neurons (PyNs), parvalbumin (PV)- and vasoactive intestinal peptide (VIP)-positive interneurons (INs) in the primary motor cortex (M1). The probability of detecting dendritic spines was positively correlated with the magnitude of H-Ras activity, suggesting elevated local H-Ras activity is involved in the process of dendritic spine formation. H-Ras overexpression caused high spine turnover rate via adding more spines rather than eliminating them. Two-photon photolysis of glutamate triggered de novo dendritic spine formation in mature neurons, suggesting H-Ras induced spine formation is not restricted to the early development. In PyNs and PV-INs, but not VIP-INs, we observed a shift in average spine neck length towards longer filopodia-like phenotypes. The portion of dendritic spines lacking key excitatory synaptic proteins were significantly increased in H-Ras transfected neurons, suggesting that these increased spines have other distinct functions. High spine density caused by H-Ras did not result in change in the frequency or the amplitude of miniature excitatory postsynaptic currents (mEPSCs). Thus, our results propose that dendritic spines possess more multifaceted functions beyond the morphological proxy of excitatory synapse.

neuroscience↗

bioRxiv2023

S-nitrosylation-mediated unfolded protein response maintains hematopoietic progenitors

The Drosophila lymph gland houses blood progenitors that give rise to myeloid-like blood cells. Initially, blood progenitors proliferate, but later become quiescent to maintain multipotency before differentiation. Despite the identification of various factors involved in multipotency maintenance, the cellular mechanism regulating blood progenitor quiescence remains elusive. Here, we reveal the expression of nitric oxide synthase in blood progenitors, generating nitric oxide for post-translational S-nitrosylation of protein cysteine residues. S-nitrosylation activates the Ire1-Xbp1-mediated unfolded protein response, leading to G2 cell cycle arrest. Specifically, we identify the epidermal growth factor receptor as a target of S-nitrosylation, resulting in its retention within the endoplasmic reticulum and blockade of its receptor function. Collectively, our findings highlight developmentally programmed S-nitrosylation as a critical mechanism that induces protein quality control in blood progenitors, maintaining their undifferentiated state by inhibiting cell cycle progression and rendering them unresponsive to paracrine factors.

developmental biology↗

bioRxiv2023

Hypothalamic neuronal activation in primates drives naturalistic goal-directed eating behavior

Eating addiction is the primary cause of modern obesity. Although the causal role of the lateral hypothalamic area (LHA) for eating is demonstrated in rodents, there is no evidence in primates regarding naturalistic eating behaviors. We investigated the role of LHA GABAergic (LHAGABA) neurons in eating by chemogenetics in three macaques. LHAGABA neuron activation significantly increased naturalistic goal-directed behaviors and food motivation, which was specific for palatable food. PET and MRS validated the chemogenetic activation. Rs-fMRI result revealed that functional connectivity (FC) between the LHA and frontal areas was increased, while the FC between the frontal cortices was decreased after the LHAGABA neuron activation. Thus, our study elucidates the role of LHAGABA neurons in eating and obesity therapeutics for primates and humans.

neuroscience↗

bioRxiv2022

Engineered molecular sensors of cell surface crowding

Cells mediate interactions with the extracellular environment through a crowded assembly of transmembrane proteins, glycoproteins and glycolipids on their plasma membrane. The extent to which surface crowding modulates the biophysical interactions of ligands, receptors, and other macromolecules is poorly understood due to the lack of methods to quantify surface crowding on native cell membranes. In this work, we demonstrate that physical crowding on reconstituted membranes and live cell surfaces attenuates the effective binding affinity of macromolecules such as IgG antibodies in a surface crowding-dependent manner. We combine experiment and simulation to design a crowding sensor based on this principle that provides a quantitative readout of cell surface crowding. Our measurements reveal that surface crowding decreases IgG antibody binding by 2-20 fold in live cells compared to a bare membrane surface, resulting in a cell surface osmotic pressure opposing binding of 1 - 4 kPa. Our sensors show that sialic acid, a negatively charged monosaccharide, contributes disproportionately to red blood cell surface crowding via electrostatic repulsion, despite occupying only ~1% of the total cell membrane by mass. We also observe significant differences in surface crowding for different cell types and find that expression of single oncogenes can both increase and decrease crowding, suggesting that surface crowding may be an indicator of both cell type and state. Our high-throughput, single-cell measurement of cell surface osmotic pressure may be combined with functional assays to enable further biophysical dissection of the cell surfaceome. Significance StatementCells interact with each other and the extracellular environment through a crowded assembly of polymers on their plasma membranes. The high density of these surface polymers can generate physical crowding that impacts cell function. However, tools to quantify the extent and effect of surface crowding on live cell membranes are lacking. In this work, we design macromolecular sensors that act as direct reporters of cell surface crowding. We combine experiments on reconstituted and live cell surfaces with molecular dynamics simulations to provide a mechanistic understanding of how cell surface crowding reduces binding of soluble molecules, and we show that crowding varies significantly with cell type and is affected by oncogene expression.

biophysics↗

bioRxiv2022

dach-1, a cytochrome P450 gene, regulates synaptic and developmental plasticity during the diapause of Caenorhabditis elegans

Animals exhibit phenotypic plasticity through the interaction of genes with the environment, and little is known about the genetic factors that change synaptic function at different developmental stages. Here, we investigated the genetic determinants of how developmental stages alter synaptic transmission using the free-living nematode Caenorhabditis elegans. C. elegans enters the stress-resistant dauer larval stage under harsh conditions. Although dauer is known to have reduced permeability and increased resistance to most known exogenous chemicals, we discovered that dauer is hypersensitive to a cholinesterase inhibitor, aldicarb. To investigate genes regulating dauer-specific acetylcholine transduction, we first screened for aldicarb-resistant mutations in dauer and then performed a secondary screen to rule out aldicarb-resistant mutations that also affect adults. We isolated two different mutations of a single gene called cyp-34A4 or dach-1 encoding a cytochrome P450. In the non-dauer stages, dach-1 is mainly expressed in the intestine, but its expression is robustly increased in the epidermis of dauers. By tissue-specific rescue experiments, we found that dach-1 modulates aldicarb sensitivity in a cell non-autonomous manner. In addition, dach-1 plays pleiotropic functions in dauers by regulating quiescence and surviving heat shock and hyperosmolar stress. Our study reveals novel functions of the cytochrome P450 in synaptic and physiological changes during developmental plasticity.

genetics↗

bioRxiv2021

Effect of spatiotemporally changing environment on serial dependence in ensemble representations

The recent visual past has a strong impact on our current perception. Recent studies of serial dependence in perception show that low-level adaptation repels our current perception away from previous stimuli1-5 whereas post-perceptual decision attracts perceptual report toward the immediate past6-12. In their studies, these repulsive and attractive biases were observed with different task demands perturbing ongoing sequential process. Therefore, it is unclear whether the opposite biases arise naturally in navigating complex real-life environments. Here we only manipulated the environmental statistics to characterize how serially dependent perceptual decisions unfold in spatiotemporally changing visual environments. During sequential mean orientation adjustment task on the array of Gabor patches, we found that the repulsion effect dominated only when ensemble variance increased across consecutive trials whereas the attraction effect prevailed when ensemble variance decreased or remained the same. The observed attractive bias by high- to-low-variance stimuli and repulsive bias by low-to-high-variance stimuli were reinforced by the repeated exposure to the low and the high ensemble variance, respectively. Further, this variance-dependent differential pattern of serial dependence in ensemble representation remained the same regardless of whether observers had a prior knowledge of environmental statistics or not. We used a Bayesian observer model constrained by visual adaptation13,14 to provide a unifying account of both attractive and repulsive bias in perception. Our results establish that the temporal integration and segregation of visual information is flexibly adjusted through variance adaptation.

neuroscience↗