Biology subjects

Park, S.-Y.

Publications and source records attributed to Park, S.-Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Transforming clinical apheresis waste into a renewable source of patient-derived CD34+ hematopoietic stem cell biobank for beta-hemoglobinopathy research and therapeutic discovery

Background aimsThe development of next-generation therapies for sickle cell disease (SCD) and beta thalassemia (beta thal), including fetal globin-inducing small molecules and gene therapy approaches, depends on patient-derived CD34+ hematopoietic stem and progenitor cells (HSPCs) for discovery and preclinical validation, but commercial vendors stock only healthy donor material and disease-specific banks hold limited inventories. Recent US Food and Drug Administration and National Institutes of Health guidance favoring human cell-based methods over animal testing underscores the value of authentic patient cells. Methods: Over 14 months we recovered, purified, and biobanked CD34+ HSPCs from clinical apheresis product waste and mobilized peripheral blood (PB) otherwise discarded after clinical procedures, using immunomagnetic selection adapted for hemoglobinopathy specimens; a microfluidic technology was evaluated separately. We quantified yield and purity for bead-selected material and cell number and viability for the microfluidic pilot; engraftment was tested in NBSGW mice. Results: Immunomagnetic selection recovered a median of 4.71 x 106 CD34+ cells from just 1 to 2 mL of apheresis product waste, comparable to the 6.0 x 106 cells from a 10 to 40 fold larger volume of PB waste, with similar purity across sources and diagnoses. Because apheresis product waste is far more concentrated, it reaches equivalent yields without the density-gradient steps required for PB waste, approximately halving processing time. Recovered cells engrafted NBSGW mice, confirming preserved repopulating capacity. The microfluidic pilot (two patients, 11 specimens) recovered 2.17 x 106 CD34+ cells per specimen at greater than 90% viability and purity. Conclusions: A center with existing apheresis infrastructure can reproducibly recover, bank, and distribute research-grade patient CD34+ HSPCs, addressing a recognized gap in the hemoglobinopathy pipeline. HighlightsO_LIClinical apheresis waste is used to generate a single-center biobank of high-quality, research-grade CD34+ HSPCs from patients with sickle cell disease and beta-thalassemia. C_LIO_LIConcentrated apheresis waste matches large-volume PB waste in CD34+ yield and purity. C_LIO_LIMicrofluidic enrichment recovers CD34+ cells at >90% viability and purity across 2 patients. C_LIO_LIRecovered CD34+ HSPCs engraft mice and form erythroid cells, preserving function. C_LI

pharmacology and toxicology↗

bioRxiv2026

A pleiotropic EPAS1 enhancer mediating Tibetan adaptation to hypoxia is active in adipocytes

In response to hypoxic stress at high altitudes, variation at the EPAS1 locus has experienced strong selection in Tibetans. Functional dissection of the selection signals at this locus identified ENH5, an enhancer within the adaptive haplotype that has a blunted response to hypoxic stress in Tibetans. ENH5 was shown to be pleiotropic in several tissues related to hypoxia response, suggesting that a possible mechanism behind the strong selection signatures could be adaptive pleiotropy. Tibetans not only experience hypoxic conditions, but also cold temperatures due to the altitude and climate of the Tibetan Plateau. However, it is unclear whether cold temperatures affect ENH5 activity possibly contributing to the selective pressure at this locus. Here, we further characterized the role of ENH5 in subcutaneous white adipose tissue, an important tissue type that regulates body temperature in response to cold temperatures by releasing stored fat as heat through a process called thermogenesis. In this work, we investigated the role of ENH5 in adipocytes using ENH5 knockout mice (ENH5 KO), which phenocopy the reduced activity of the Tibetan allele. We show that ENH5 KO mice at normoxia and room temperature do not have significant differences in organismal phenotypes related to adiposity and metabolism compared to WT mice on a high fat diet. However, we detected effects of ENH5 conditional on thermogenic stimulation and hypoxia exposure, independently, in adipocytes cultured in vitro. Under either of these conditions, ENH5 KO has stronger differential expression of key genes involved in thermogenesis activity and adipocyte differentiation compared to WT. This differential response to thermogenic stimulation expands on the pleiotropic effects of the Tibetan ENH5 allele(s), in addition to those previously shown in well-established hypoxia-responsive tissues. Our results raise the possibility that pleiotropic effects of ENH5 may implicate unforeseen mechanisms, such as cellular energetics and thermogenesis, possibly contributing to the phenotypic adaptation to high altitude in Tibetans.

genetics↗

bioRxiv2026

Outbred Drosophila populations reveal diet-dependent genetic effects on development time

Metabolic effects of genetic variation often depend on diet, yet the loci underlying diet-dependent developmental responses remain incompletely defined. Here we combine multi-trait phenotyping of Drosophila Genetic Reference Panel lines with genome-wide mapping in newly developed Drosophila Recombinant Populations. High sugar causes genotype- and life-stage-dependent changes in metabolic and life-history traits, with development time emerging as a highly heritable, sugar-sensitive phenotype. Mapping in 16 outbred advanced intercross populations reveals distinct association landscapes under low- and high-sugar diets, with a concentrated low-sugar signal, a more distributed high-sugar pattern, and identified genotype-by-diet loci including tap, Eip75B and Cerk. Functional perturbation supports diet-dependent effects for several prioritized candidates. Allele-frequency analyses identify operationally defined thrifty-like variants associated with delayed development under high sugar and relatively earlier development under low sugar; these variants are enriched for cell-adhesion, neurodevelopmental, and morphogenetic processes. Together, these results establish an outbred Drosophila framework for dissecting how dietary sugar remodels the genetic architecture of development time.

genetics↗

bioRxiv2026

Gut Microbiota Mediates the Association between Diet Quality and Ectopic Adiposity: The Multiethnic Cohort Adiposity Phenotype Study

BackgroundHigher-quality diets have been associated with lower levels of ectopic fat deposited in the viscera and liver, which is hypothesized to be mediated in part by the gut microbiota. ObjectivesWe tested this hypothesis in a multi-ethnic imaging study using global (microbiome-wide) testing as well as a high-dimensional multiple-mediators regression framework to identify bacterial genera in the human gut that mediate the association between diet quality and ectopic adiposity. MethodsWe analyzed the cross-sectional data of 1,400 older adults (age 60-77) from five racial/ethnic groups in the Multiethnic Cohort Adiposity Phenotype Study (2013-2016). Overall diet quality was defined by adherence to the MIND diet. The relative abundance of 151 bacterial genera was quantified from 16S rRNA gene sequencing of the stool samples. Visceral fat, liver fat, and the presence of MASLD (metabolic dysfunction-associated steatotic liver disease) were determined based on magnetic resonance imaging (MRI). We used high-dimensional mediation analysis (HDMA) to estimate gut microbial mediation in the linear regression of visceral fat or liver fat, or in logistic regression of MASLD, on the MIND adherence score, adjusted for potential confounders. ResultsHigher diet quality was associated with lower ectopic adiposity: 12% less visceral fat area, 23% less liver fat, and a 49% less likelihood of having MASLD, comparing the highest to the lowest quartile of the MIND score. Using a distance-based global test, we confirmed overall significant microbial mediation of the inverse diet-ectopic fat association. From HDMA, four bacterial genera were identified as mediating the protective association with visceral fat, with the largest mediation conferred by Lachnospiraceae UCG.001 (12.2%). Two genera (Lachnoclostridium, Weissella) were shown to mediate the MIND association with both liver fat and MASLD. In particular, Lachnoclostridium mediated 13.6% of the liver fat association and 10.8% of the MASLD association, and Lachnospiraceae UCG.001 additionally mediated 12.1% of the liver fat association. ConclusionsOur results support the hypothesis that the gut microbiota contributes to conveying the effect of diet quality on preferred body fat distribution, e.g., involving bacteria that are known to produce short-chain fatty acids (Lachnospiraceae) or secondary bile acids (Lachnoclostridium).

microbiology↗

bioRxiv2025

A Doppler Ultrasound Method to Measure Vascular Responses to Walking

Measuring leg blood flow (LBF) in response to walking can offer unique insights regarding mechanical and physiological functions of the leg. However, current gold-standard methods of measuring LBF are invasive. Alternatively, Doppler ultrasound is a promising method to noninvasively measure LBF. The purpose of this study was to demonstrate the utility of a novel ultrasound scanning technique to measure vascular reactivity to walking. Participants walked on a 0{degrees} slope, followed by a -5{degrees} and 5{degrees} slope in random order. A Doppler ultrasound probe was fastened over the dominant-side common femoral artery using a custom 3D printed bracket. LBF was recorded immediately before and after each walking condition. Baseline LBF was not significantly different before each walking condition (p = .577), but there were significant differences in post-walking (p < .001), with uphill causing the greatest increase in LBF. These results suggest that our ultrasound technique is repeatable during quiet standing and can detect the differences in blood flow across different walking intensities. Our method may be valuable to understand how the circulatory system responds to various locomotion tasks, and how cardiovascular disease may impair locomotor functions.

physiology↗

bioRxiv2025

Regulatory mechanism of heme-regulated inhibitor through autophosphorylation-driven activation and heme-induced deactivation

Heme-regulated inhibitor (HRI) is a key modulator of hemoglobin synthesis, exerting such effects by sensing intracellular heme levels. Under heme-deficient conditions, HRI dissociates from heme, becomes activated, and phosphorylates the translation initiation factor eIF2. However, the precise regulatory mechanisms governing HRI activation remain incompletely understood. In this study, we delineate part of the regulatory mechanism involving autophosphorylation-dependent activation and heme-mediated deactivation of HRI. HRI formed a dimer in solution through its N-terminal domain, irrespective of its phosphorylation state. However, a mutant with deletion of the N-terminal domain retained autophosphorylation activity, indicating that N-terminal domain-mediated dimerization is not essential for activation. Phosphorylated HRI formed a stable complex with eIF2, whereas the dephosphorylated form failed to bind, indicating that autophosphorylation is required for eIF2 recognition. Biochemical analyses, together with modeling based on the predicted structure, revealed that the phosphate groups of Thr488 and Thr493 interact with adjacent basic residues. These interactions enhance eIF2 recognition and phosphorylation. Additionally, heme-induced deactivation selectively targeted the dephosphorylated kinase domain and suppressed autophosphorylation. These findings provide multiple mechanistic insights into regulation of the activity of HRI, highlighting distinct roles for autophosphorylation, structural elements, and heme responsiveness in controlling its function.

biochemistry↗

bioRxiv2025

Discovery of A Small Molecule non-IMiD Degrader of ZBTB7A for the Treatment of β-hemoglobinopathies

Sickle cell disease and {beta}-thalassemia, two major {beta}-hemoglobinopathies, pose significant clinical challenges globally. Current treatments often face limitations in efficacy and tolerability. The transcription factor ZBTB7A has emerged as a promising therapeutic target for reactivating fetal hemoglobin expression. Here, we report the discovery and characterization of SH6, a small molecule non-IMiD degrader of ZBTB7A. SH6 induces fetal hemoglobin in erythroid cell lines in a CRBN and ZBTB7A-dependent manner, and it is capable of inducing fetal hemoglobin expression in healthy donor, SCD and {beta}-thalassemia patient CD34+ cell derived erythroid cells. The efficacy of SH6 is confirmed in a xenotransplantation humanized mouse model. SH6 outperforms currently available therapeutic agents in vitro, and shows synergy with hypomethylating agents. SH6 exhibits a favorable in vivo toxicity profile. Our findings establish SH6 as a promising therapeutic lead candidate for further optimization towards clinical development for treatment of sickle cell disease and {beta}-thalassemia.

cell biology↗

bioRxiv2025

Deletion of the Saccharomyces cerevisiae RACK1 homolog, ASC1, enhances autophagy and counteracts TDP-43 toxicity

Cytoplasmic aggregation of nuclear proteins such as TDP-43 (TAR DNA-binding protein 43) and FUS (fused in sarcoma) is associated with several neurodegenerative diseases. Studies in higher cells suggest that these aggregates of TDP-43 and FUS sequester polysomes by binding RACK1 (receptor for activated C kinase 1), a ribosomal protein, thereby inhibiting global translation and contributing to toxicity. But RACK1 is also a scaffold protein with many other roles including a role in autophagy. Using yeast we find that deletion of the RACK1 ortholog, ASC1, reduces TDP-43 toxicity, but not FUS toxicity. TDP-43 foci remain liquid like in the presence asc1{Delta} but they become smaller. This is consistent with the findings in cell culture. However, using double label tags we establish that ASC1 does not co-localize with TDP-43 foci, arguing against the sequestration hypothesis. Instead, ASC1 appears to influence toxicity through autophagy. We previously showed that expression of TDP-43 inhibits autophagy and TOROID (TORC1 Organized in Inhibited Domains) formation and that modifiers that rescue yeast from TDP-43 toxicity reverse these inhibitions. Here we show that FUS does not inhibit autophagy. This autophagy enhanced by asc1{Delta} is non-canonical, marked by reduced TOROID formation, and effectively counteracts the autophagy inhibition caused by TDP-43. Our findings suggest that ASC1 influences TDP-43 toxicity through autophagy regulation rather than polysome sequestration, highlighting autophagy as a key therapeutic target. SummaryTDP-43 and FUS aggregates are linked to neurodegenerative diseases. RACK1, a ribosomal protein, was previously thought to contribute to toxicity by co-localizing with these aggregates and sequestering polysomes. In yeast, deletion of ASC1--the RACK1 homolog--reduces TDP-43 toxicity but not FUS toxicity. TDP-43 foci remain liquid-like, but ASC1 does not co-localize with them, challenging the sequestration hypothesis. Instead, asc1{Delta} enhances autophagy, rescuing cells from the autophagy inhibition caused by TDP-43. Unlike TDP-43, FUS does not inhibit autophagy. These findings highlight autophagy, rather than polysome sequestration, as the key mechanism of TDP-43 toxicity and its mitigation via ASC1/RACK1 reduction.

cell biology↗

bioRxiv2025

Bone Marrow Adipokine Mediates Hematopoietic Regeneration and Stem Cell Fitness

Bone marrow (BM) hematopoietic stem cells (HSCs) are exquisitely sensitive to cues from the BM microenvironment (ME), which is critical for their engraftment and regeneration following myeloablative stress. Retinoic acid signaling, acting on both HSCs and niche cells, has emerged as a central regulator of this process. Among ME components, BM adipocytes (BMAs), which can comprise up to 45% of BM volume and expand dramatically during the pancytopenic phase after myeloablation, play a previously underappreciated role in hematopoietic recovery. Here, we identify retinoid X receptor (RXR) signaling in BMAs as a key regulator of the adipokine Resistin, which promotes HSC self-renewal and functional fitness by activating NF-{kappa}B signaling. Conditional loss of RXR in adiponectin-expressing cells suppressed Resistin production, resulting in reduced NF-{kappa}B activity in HSCs, impaired self-renewal, and defective multilineage hematopoietic regeneration. Functionally, in vivo Resistin neutralization impaired hematopoietic reconstitution, whereas supplementation with either monomeric or dimeric Resistin enhanced HSC self-renewal and long-term lympho-hematopoietic reconstitution in an NF-{kappa}B-dependent manner. Together, these findings establish BMA-derived Resistin as an RXR-dependent, critical extrinsic regulator of HSC self-renewal and regenerative hematopoiesis, underscoring its essential role in lympho-myeloid reconstitution after myeloablation. Disclosures: The authors declare no relevant conflicts of interest.

physiology↗

bioRxiv2024

Accurate antibody loop structure prediction enables zero-shot design of target-specific antibodies

Protein loops, characterized by their versatile structures with varying sizes and shapes, can recognize a wide range of targets with high specificity and affinity. The variable loops of the antibody complementarity-determining region (CDR) are particularly crucial for immune responses and therapeutic applications due to their effective target recognition capabilities. Accurate structure prediction of these antibody loops is essential for the efficient in silico design of target-binding antibodies for therapeutic or industrial use. However, predicting antibody loop structures is challenging due to the lack of evolutionary information from related proteins. Thus, a successful ab initio structure prediction method, which operates without structural templates or related sequences, is crucial for the effective design of antibody loop-mediated interactions. This study demonstrates that highly accurate antibody loop structure prediction enables the effective zero-shot design of target-binding antibody loops. The performance of loop design has been shown to depend on the accuracy of ab initio loop structure prediction, as tested with two versions of our design model. The high affinity, diversity, novelty, and specificity of the antibody loops designed with these new methods were validated experimentally on four target proteins.

bioengineering↗

bioRxiv2024

Dual-mode action of scalable, high-quality engineered stem cell-derived SIRP alpha extracellular vesicles for treating acute liver failure

Acute liver failure (ALF) is a critical inflammatory condition characterized by rapid hepatocyte death, impaired liver regeneration due to the delayed removal of necroptotic cells, and high mortality rates. This study introduces a novel dual-mode action therapeutic approach using extracellular vesicles expressing Signal Regulatory Protein Alpha (SIRP-EVs) derived from genetically engineered mesenchymal stem cells (MSCs). These SIRP-EVs are designed to concurrently resolve necroptosis and promote liver regeneration. Our studies identified CD47 and SIRP as promising therapeutic targets for ALF. We developed a scalable 3D bioreactor-based process that produces high-purity SIRP-EVs, which preserve MSC properties and achieve significant production levels. SIRP-EVs target both macrophages and necroptotic hepatocytes in ALF models, enhancing macrophage phagocytic activity against necroptotic cells via CD47 blockade and promoting liver regeneration by reprogramming macrophages with MSC-derived cargo. Comprehensive in vitro and in vivo studies demonstrate that SIRP-EVs decrease CD47+ necroptotic cells and promote liver regeneration in ALF models, leading to reduced liver damage markers and enhanced survival rates. These findings highlight the potential of SIRP-EVs as a dual-mode action therapeutic for ALF, offering promising prospects for their application in other inflammatory diseases. Moreover, these results pave the way for advancing engineered EV-based therapies toward clinical implementation.

bioengineering↗

bioRxiv2024

PITPβ promotes COPI vesicle fission through lipid transfer and membrane contact formation

Intracellular transport among organellar compartments occurs in two general ways, by membrane-bound carriers or membrane contacts. Specific circumstances that involve the coordination of these two modes of transport remain to be defined. Studying Coat Protein I (COPI) transport, we find that phosphatidylcholine with short acyl chains (sPC) is delivered through membrane contact from the endoplasmic reticulum (ER) to sites of COPI vesicle formation at the Golgi to support the fission stage. Phosphatidylinositol transfer protein beta (PITP{beta}) plays a key role in this process, with the elucidation of this role advancing a new understanding of how PITP{beta} acts, providing a mechanistic understanding of a specific circumstance when vesicular transport requires membrane contact, and contributing to a basic understanding of how transport carriers in a model intracellular pathway are formed. SummarySpecific circumstances that membrane contact is needed for vesicular transport remain to be defined. We find that a critical lipid is delivered through membrane contact to support the fission stage of a model intracellular transport pathway.

cell biology↗

bioRxiv2024

Agrobacterium-mediated Cuscuta campestris transformation as a tool for understanding plant-plant interactions

Cuscuta campestris, a stem parasitic plant, has served as a valuable model plant for the exploration of plant-plant interactions and molecular trafficking. However, a major barrier to C. campestris research is that a method to generate stable transgenic plants has not yet been developed. Here, we describe the development of a Cuscuta transformation protocol using various reporter genes (GFP, GUS, or RUBY) and morphogenic genes (CcWUS2 and CcGRF/GIF), ultimately leading to a robust protocol for Agrobacterium-mediated C. campestris transformation. The stably transformed and regenerated RUBY C. campestris plants produced haustoria, the signature organ of parasitic plants, and these were functional in forming host attachments. The locations of T-DNA integration in the parasite genome were confirmed through TAIL-PCR. Transformed C. campestris also produced flowers and transgenic seeds exhibiting betalain pigment, providing proof of germline transmission of the RUBY transgene. Furthermore, the RUBY reporter is not only a useful selectable marker for the Agrobacterium-mediated transformation, but also provides insight into the movement of molecules from C. campestris to the host during parasitism. Thus, the protocol for transformation of C. campestris reported here overcomes a major obstacle to Cuscuta research and opens new possibilities for studying parasitic plants and their interactions with hosts.

plant biology↗

bioRxiv2023

Structural elucidation of how ARF small GTPases induce membrane tubulation for vesicle fission

The ADP-Ribosylation Factor (ARF) small GTPases have been found to act in vesicle fission through a direct ability to tubulate membrane. Here, we have used cryo-electron microscopy (EM) to solve the structure of an ARF6 protein lattice assembled on tubulated membrane to 3.9 [A] resolution. ARF6 forms tetramers that polymerize into helical arrays to form this lattice. We identify, and confirm functionally, protein contacts critical for this lattice formation. The solved structure also suggests how the ARF amphipathic helix is positioned in the lattice for membrane insertion, and how a GTPase-activating protein (GAP) docks onto the lattice to catalyze ARF-GTP hydrolysis in completing membrane fission. As ARF1 and ARF6 are structurally conserved, we have also modeled ARF1 onto the ARF6 lattice, which has allowed us to pursue the reconstitution of Coat Protein I (COPI) vesicles to confirm more definitively that the ARF lattice acts in vesicle fission. Our findings are notable for having achieved the first detailed glimpse of how a small GTPase bends membrane and having provided a molecular understanding of how an ARF protein acts in vesicle fission.

cell biology↗

bioRxiv2023

Allelic Imbalance Reveals Genetic and Epigenic Underpinnings of metabolic diseases

BackgroundObesity is a pivotal trigger for a spectrum of complex metabolic disorders. By colocalizing cis-eQTLs in adipose tissues from the GTEx consortium and trait-associated SNPs for complex traits from the GWAS Catalog within 3.6 million DNase I hypersensitive sites (DHSs), we systematically identify regulatory variants and genes that exhibit cis effects, as well as potential causal variants within the context of regulatory elements. ResultsOur analysis reveals that 229,504 (26.4%) cis-eQTLs located within DHS reside densely near the transcription start sites, contrasting with those outside of DHS. We observed that genes with higher allelic imbalance have shorter transcript lengths with larger number cis-eQTLs within DHS, and such imbalance genes are predominantly linked to signaling and immune response, whereas those with lower allelic imbalance tend to be involved in metabolism. Our composite colocalization score prioritizes 5,202 DHSs that encompass both cis-eQTLs and trait-associated SNPs, targeting 2,232 protein-coding genes and 523 lncRNAs across complex traits. We highlight the lncRNA SNHG5 as a prime example; it is associated with high-density lipoprotein levels and exhibits low allelic imbalance, and is also down-regulated in adipose tissue from patients with obesity. ConclusionsOur findings underscore the critical role of regulatory context in pinpointing causal variants and refining target genes, offering rich insights into the genetic mechanisms pertinent to obesity and providing valuable resources for the diagnosis and therapeutic targeting of metabolic diseases.

genomics↗

bioRxiv2023

A compact, ultrahigh-density headstage with high-fidelity hybrid integration for large-scale deep-brain opto-electrophysiology

Recent neuroscientific research seeks to comprehend the sophisticated deep-brain networks of neural circuits consisting of large scale neuronal ensembles across multiple brain regions. An ideal way to unveil the complex connectome might be stimulating individual neurons with high spatial resolution in a broad range of brain, while seamlessly monitoring the correspondent neuronal activities. Optogenetics is known as a key technology to enable such a goal thanks to its high spatial and temporal selectivity in neuromodulation. Existing silicon probe technologies have been able to partially achieve such a goal by recording broad region of brain activities through multiple electrodes per shank, but those cannot complete perfect coverage due to the limited channel counts for the optogenetic stimulation. Here, we present an high-channel-count optogenetic system with simultaneous 256 recoding and 128 optogenetic stimulation sites, exhibiting the highest channel density ever reported, enabled by a flexible polyimide cable-based hybrid-integration of a low-stimulation-artifact micro-LED ({micro}LED) opto-electrode with a low-power and -noise, area-efficient CMOS interfacing integrated-circuit (IC). The presented optogenetic system provides 256-neuron-size electrodes (11 x 15 {micro}m2) with a 40 {micro}m inter-electrode pitch for high spatial oversampling in recording and 128-soma-size {micro}LEDs (8 x 11 {micro}m2) with a 20 {micro}m inter-LED pitch for single-cell resolution in stimulation, resulting in a vertical span of 640 {micro}m and a horizontal span of 2,100 {micro}m with a total 8 shanks. For versatility in optogenetics-based experiments from small rodents to primates with user-preferable settings, the system base that provides programmability of recording and stimulation parameters and rest of signal processing, such as filtering, digitization, and data transmission including serial peripheral interface (SPI) has also been designed within small area of 23.8 x 28.8 mm2 with only 3.5-gram weight, resulting in the highest channel density both in size (0.56 channels/mm2) and weight (109.71 channels/gram) among the state-of-the-art optogenetics-based neuromodulation systems. To verify the system operation in vivo, a compact optogenetics headstage has been also fabricated. Using the prepared optogenetic headstage, 169 isolated neurons have been observed with various stimulation intensities. The results offered in this article indicate that the presented hybrid integrated ultrahigh-density, high-channel-count headstage can be used to realize the massive-scale in-depth brain studies with optogenetics.

bioengineering↗

bioRxiv2023

Genetic and transcriptomic analysis of hyphal constriction based on a novel assay method in the rice blast fungus

An ability of fungi to undergo hyphal constriction is important for fungal ecology and diseases. In the rice blast fungus, Magnaporthe oryzae, hyphal constriction is required to traverse host cell junctions through pit fields. However, little is known about genetic underpinnings of hyphal constriction, except the requirement of a mitogen-activated protein kinase, Pmk1. Here we demonstrate that a simple in vitro assay based on nitrocellulose membrane allows investigation of the genetic basis for hyphal constriction. Using the assay, we found that the constriction limit of M. oryzae hypha lies between 0.22 and 0.3 m, and that a histone modification might be involved in hyphal constriction. RNA-seq experiments combining our assay and {Delta}pmk1 showed that hyphal constriction relies on transcriptional changes of genes implicated primarily in membrane and cell wall-related cellular processes in Pmk1-dependent and/or Pmk1-independent manner. Furthermore, our assays with diverse fungal species suggest correlation between hyphal constriction and fungal lifestyles. Our study reveals that hyphal constriction can be induced without host-derived cues and provides molecular and evolutionary insights into a fundamental process to infection of host plant.

microbiology↗

bioRxiv2023

Dose-response relationship for the resistance of human insulin to degradation by insulin-degrading enzyme

Deeper understanding of the mechanism of the action of insulin and insulin-degrading enzyme (IDE) is a central theme in research into physiology and the pathophysiology of type 2 diabetes mellitus. Despite significant progress regarding the substrate recruitment, unfolding, digestion, and release by IDE, the structure and function of the insulin hexamer during the degradation cycle of IDE remain to be fully characterized. In the present study, we have characterized the behavior of human insulin hexamer in the absence of zinc. Using cryo-electron microscopy, we also observed that these hexamers represented a structure similar to that of T6 insulin. More interestingly, we also observed complexes in which some of their monomeric insulin components are partially distorted at their hexametric symmetry. This ensures that insulin determines the kinetics of its degradation by IDE without the requirement for zinc. These findings provide new information regarding the molecular events in insulin assembly and disassembly that permit its selective digestion by IDE.

biochemistry↗