Biology subjects

Shin, J.

Publications and source records attributed to Shin, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Fluorogenic Covalent Probes for RNA

Sequence-generalized fluorescent labels and stains for RNA can enable imaging, tracking and analysis of the biopolymer. However, current non-covalent RNA dyes are poorly selective for RNA over DNA, interact weakly with their target, and can show limited utility in cellular RNA staining due to poor selectivity and high background signals. Here we report a fluorogenic covalent labeling approach based on acylimidazole-mediated reaction of donor-acceptor fluorophores with 2'-hydroxyl (2'-OH) groups of RNA, providing a wavelength-tunable, sequence-independent strategy for selective labeling of the biopolymer. This reactive probe design enables labeling and imaging under mild aqueous conditions, providing up to 390-fold fluorescence enhancement and 970-fold selectivity for RNA over DNA, with four emission colors documented. The covalent fluorophore platform enables improved new tools for RNA-specific analysis and imaging in gels, in solution, and in living cells.

biochemistry↗

bioRxiv2025

A comparison of adiponectin-deficient mice reveals the fundamental role of intracellular adiponectin

Adiponectin is an important adipokine with insulin-sensitizing, anti-inflammatory, and anti-fibrotic properties. The physiological roles of adiponectin have been studied using global adiponectin knockout (KO) mice. However, the reported phenotypes of adiponectin KO mice vary based on the mouse lines generated by different strategies and investigators. We performed a head-to-head comparison of the adiponectin KO mice that were generated in Dallas, Houston and Osaka. RNAseq revealed that the expression of the bioactive domain of adiponectin - the globular domain - was preserved in the Houston and Osaka KO mice. A complete adiponectin KO model, such as the Dallas KO mouse, exhibits a lower body weight, the highest adipocyte mitochondrial function and displays a susceptibility to DNA damage-mediated lung fibrosis. The reconstitution of globular adiponectin into the Dallas KO mice prompted an increase in body weight and a partial recapitulation of the Osaka KO model transcriptome signature. The intracellular globular adiponectin form is important, as we found that globular adiponectin enhances PPAR{gamma} activity by modulating the coregulators interacting with PPAR{gamma}. Overall, the residual expression of globular adiponectin regulates adipose tissue metabolism by altering PPAR{gamma} activity, highlighting an important novel role of intracellular adiponectin.

physiology↗

bioRxiv2025

Laminar Shear Stress Increases the Cytosolic Pool of PINK1 in Endothelial Cells and Enhances Mitophagic Sensitivity Toward Dysfunctional Mitochondria

Phosphatase and tensin homolog (PTEN)-induced putative kinase 1 (PINK1) is an essential molecule in mitophagy process in mammalian cells. Mutation or deficiency of PINK1 has been closely related to several disease conditions. The purpose of this study was to determine PINK1 expression levels and subcellular localization under exercise-mimic laminar shear stress (LSS) condition in human aortic endothelial cells (HAECs) or in exercising mice, and its implication on endothelial homeostasis and cardiovascular disease (CVD) prevention. First, LSS significantly elevated both full-length PINK1 (FL-PINK1) mRNA and protein expressions in ECs. Mitochondrial fractionation assays and confocal microscopic analysis showed reduced FL-PINK1 accumulation on mitochondria with an increase in a cytosolic pool of FL-PINK1 under LSS. Mitophagy flux, determined by a mtKeima probe, decreased with intact mitochondrial morphology and membrane potential under LSS, suggesting that elevated cytosolic PINK1 is not utilized for immediate mitophagy inductions. However, increased cytosolic PINK1 seems to elevate mitophagic sensitivity toward dysfunctional mitochondria in pathological conditions. LSS-preconditioned ECs showed lower angiotensin II (AngII)-induced mtDNA lesions and displayed rapid Parkin recruitment and mitophagy induction in response to mitochondrial uncoupler (CCCP) treatment. Exercise-preconditioned mice, a physiological LSS-enhanced model, showed elevated PINK1 expression in ECs of the thoracic aorta compared to sedentary control. In addition, exercise enhanced AngII-induced mitophagy induction in ECs and reduced AngII-induced mtDNA lesion formation in the mouse aorta. Taken together, LSS increases a cytosolic pool of FL-PINK1, which may elevate the mitophagic sensitivity toward dysfunctional mitochondria in ECs.

physiology↗

bioRxiv2025

Regulation of the Yolk Microtubule and Actin Cytoskeleton by Dachsous Cadherins during Zebrafish Epiboly

Epiboly is a crucial morphogenetic process during early animal embryogenesis that expands surface area of embryonic tissues while thinning them. During zebrafish development, epiboly spreads the superficial enveloping layer (EVL), germ layers, and yolk syncytial layer to cover the yolk cell. Here we investigated functions of the three zebrafish dchs genes, dchs1a, dchs1b and dchs2 that encode large atypical cadherins and report that they have partially overlapping functions in epiboly progression. We have inserted GFP at the C-terminal Dchs1b intracellular domain of the endogenous dchs1b locus using homologous recombination. We observed the resulting Dchs1b-GFP fusion protein localized in both the cell membrane and the cytoplasm of EVL and embryonic cells during gastrulation. The dynamic microtubule and actin cytoskeleton of the yolk cell are essential for epiboly. Our studies of the yolk microtubule network demonstrate that these microtubules are more bundled and show faster polymerization during epiboly in dchs triple loss-of-function mutant embryos than in wild-type embryos, indicating that dchs genes are required for limiting microtubule polymerization and promoting dynamics during epiboly. The epiboly progression defects of dchs1b deficient mutants were suppressed by mutations in the tetratricopeptide repeat protein 28 (ttc28) gene encoding a cytoplasmic protein previously shown to bind to Dchs1b intracellular domain and alter microtubule dynamics during early cleavages. We further demonstrate that MZdchs1b mutants exhibit abnormal organization and dynamics of yolk cell actin cytoskeleton during epiboly. Together, these lines of evidence as well as our transcriptomic analyses support the notion that like during early embryonic cleavages, Dchs1b plays a major role, while Dchs1a and Dchs2 proteins have supporting roles in regulating microtubule dynamics and organization of both microtubule and actin cytoskeleton to ensure normal epiboly.

developmental biology↗

bioRxiv2025

Growth Factor-Independent mTORC1 Signaling Promotes Primary Cilia Length via Suppression of Autophagy

ABSTRACT/SUMMARYThe mechanistic target of rapamycin (mTOR) complex 1 (mTORC1), as a sensor of growth signals that subsequently controls cell growth, has been predominantly studied in actively proliferating cells. Primary cilia are sensory organelles present on most quiescent cells, where they play essential roles in receiving environmental and developmental signals. Given that ciliated cells are non-proliferative, we investigated whether mTORC1 signaling influences the growth of primary cilia. Here, we show that mTORC1 promotes primary cilia elongation, without effects on ciliogenesis or cell growth, by suppressing autophagy. Inhibition of mTORC1 signaling through pharmacological, nutritional, or genetic interventions gave rise to shortened primary cilia, while activation of the pathway resulted in elongation. Furthermore, pharmacological or genetic inhibition of autophagy, a key downstream process blocked by mTORC1, also elongated primary cilia and rendered them resistant to mTORC1 inhibition. Notably, these mTORC1-mediated effects on primary cilia extend to mouse neurons ex vivo and in vivo. These findings highlight a previously unrecognized role for mTORC1 signaling in the control of primary cilia length that may contribute to diseases where ciliary function is altered, referred to as ciliopathies.

cell biology↗

bioRxiv2025

Neural dynamics in superior colliculus of freely moving mice

Vision is an active process that depends on head and eye movements to explore the visual environment. Superior colliculus (SC) is known for its role in generating these movements, as well as processing visual information, but has not been studied extensively during free movement in complex visual environments. To determine the impact of active vision, we recorded neural activity across the depth of SC during free movement while simultaneously recording eye and head position. We find that superficial SC (sSC) neurons respond to visual input following gaze-shifting saccadic movements, whereas deep SC (dSC) neurons respond to the movements themselves, as demonstrated by their sustained response in darkness. Additionally, we find motor responses in dSC are more correlated to head movements rather than eye movements. Furthermore, we compared sSC gaze shift responses to known gaze shift responses in primary visual cortex (V1), finding similarities in key response types, although the temporal sequences following gaze shifts differ between the regions. Our results demonstrate distinct visual processing differences between SC and V1 as well as highlighting the various roles SC plays during active vision. HighlightsO_LIWe recorded neural activity across the depths of superior colliculus (SC) in freely moving mice while measuring head and eye movements. C_LIO_LINeurons in mouse SC respond strongly to gaze shifts, and these responses differ between superficial (sSC) and deep (dSC) layers. C_LIO_LIsSC neurons respond primarily to the visual input during a saccadic movement. C_LIO_LIdSC neurons generally represent the head movement more than the eye movement, independent of visual input. C_LIO_LIWhile sSC gaze shift responses share similarities with V1 there are unique response profiles in SC that suggest differences in the role of visual processing between SC and V1 during free movement. C_LI

neuroscience↗

bioRxiv2025

Evaluating the Limitations of Bayesian Metabolic Control Analysis

Bayesian Metabolic Control Analysis (BMCA) has emerged as a promising framework for inferring metabolic control coefficients in data-limited scenarios by integrating Bayesian inference with linlog rate laws. However, its predictive accuracy and limitations remain underexplored. This study systematically evaluates BMCAs ability to infer elasticity values, flux control coefficients (FCCs), and concentration control coefficients (CCCs) under varying data availability conditions using three synthetic metabolic network models. Our findings highlight the strengths and weaknesses of BMCA, guiding its application in metabolic engineering and emphasizing the need for methodological refinements. Author summaryUnderstanding how enzymes control metabolic pathways is crucial for optimizing biomanufacturing and synthetic biology applications. Bayesian Metabolic Control Analysis (BMCA) is a promising computational method that integrates Bayesian inference with metabolic control analysis to estimate key control parameters, even in cases with limited experimental data. However, the accuracy and limitations of BMCA remain unclear. In this study, we systematically evaluate BMCA using three synthetic metabolic networks to determine how different types of physiological data impact its predictive performance. We find that BMCA requires flux and enzyme concentration data for accurate predictions, while external metabolite concentrations contribute little. Additionally, BMCA fails to predict elasticity values beyond a magnitude of 1.5 and reliably infer allosteric regulation, even when strong regulatory interactions exist. In addition, BMCA does not accurately rank metabolic control points, which may limit its utility in identifying key enzymes in engineered pathways. Our work provides practical insights into when and how BMCA can be applied, guiding future research in metabolic modeling and control analysis.

systems biology↗

bioRxiv2025

3D Bioprinting of Kidney Tissue Using a Photocrosslinkable Hydrogel Derived from Decellularized Extracellular Matrix

Three-dimensional bioprinting has emerged as a promising strategy in tissue engineering, aiming to fabricate functional tissue constructs for organ regeneration. A critical challenge in this field is the development of organ-specific bioinks that can provide a microenvironment conducive to cellular growth and differentiation. In this study, we successfully developed a photocrosslinkable bioink by methacrylating decellularized porcine kidney extracellular matrix. The decellularization process effectively removed all cellular components while preserving the native kidney extracellular matrix composition. The resulting methacrylated decellularized extracellular matrix bioink exhibited optimal rheological properties, making it well-suited for digital light processing based stereolithography and piston-driven extrusion bioprinting. Human embryonic kidney cells encapsulated in the bioink showed high viability and a strong proliferative capacity, indicating potential for tissue-specific maturation over time. This work demonstrates the feasibility of utilizing kidney-specific decellularized extracellular matrix-based bioinks, providing a platform for engineering renal tissue constructs for therapeutic applications.

bioengineering↗

bioRxiv2025

Long-term innovative potential of genetic research and its suppression

Long-term innovation depends not only on discovering new elements but also on facilitating new recombination at the time of their co-availability. This notion of combinatorial innovation raises the question about whether scientific exploration and industry research persist over similar time horizons to meet innovative opportunities. Here, we analyze about 20 million papers and US, Chinese, and European patents to compare the courses of scientific and industrial activities in genetic research, a domain of far-reaching societal importance. We observe that research on new genes has declined since the early 2000s, but the exploration of novel gene combinations remains active for biotechnology innovation. Yet, fields of highly practical or commercial focus are less likely to test novel gene combinations. Furthermore, industry R&D on each gene tends to decline earlier than scientific interest in that gene. After this decline of the industrial momentum, continuous scientific research still sustains exploratory and innovative opportunities, involving novel gene combinations, clinical trials, and technologically-impactful work. Based on a hypothetical scenario of over-aligned science and industry, we estimate that up to 42.2-74.4% of the combinational opportunities would be unexplored if scientific research becomes hindered due to industrys retreat. This study suggests the potential complementary roles of scientific and industrial research with different temporal modes in innovation cycles, calling for balanced policies to foster innovation ecosystems.

scientific communication and education↗

bioRxiv2025

Spatiotemporal Patterns Differentiate Hippocampal Sharp-Wave Ripples from Interictal Epileptiform Discharges in Mice and Humans

Hippocampal sharp-wave ripples (SPW-Rs) are high-frequency oscillations critical for memory consolidation in mammals. Despite extensive characterization in rodents, their application as biomarkers to track and treat memory dysfunction in humans is limited by coarse spatial sampling, interference from interictal epileptiform discharges (IEDs), and lack of consensus on human SPW-R localization and morphology. We demonstrate that mouse and human hippocampal ripples share spatial, spectral and temporal features, which are clearly distinct from IEDs. In 1024-channel hippocampal recordings from APP/PS1 mice, SPW-Rs were distinguishable from IEDs by their narrow localization to the CA1 pyramidal layer, narrowband frequency peaks, and multiple ripple cycles on the unfiltered local field potential. In epilepsy patients, ripples showed similar narrowband frequency peaks and visible ripple cycles in CA1 and the subiculum but were absent in the dentate gyrus. Conversely, IEDs showed a broad spatial extent and wide-band frequency power. We introduce a semi-automated, human ripple detection toolbox ("ripmap") selecting optimal detection channels and separating event waveforms by low-dimensional embedding. Our approach improves ripple detection accuracy, providing a firm foundation for future human memory research.

neuroscience↗

bioRxiv2025

Predictive acoustical processing in human cortical layers

In our dynamic environments, predictive processing is vital for auditory perception and its associated behaviors. Predictive coding formalizes inferential processes by implementing them as information exchange across cortical layers and areas. With laminar-specific blood oxygenation level dependent we measured responses to a cascading oddball paradigm, to ground predictive auditory processes on the mesoscopic human cortical architecture. We show that the violation of predictions are potentially hierarchically organized and associated with responses in superficial layers of the planum polare and middle layers of the lateral temporal cortex. Moreover, we relate the updating of the brains internal model to changes in deep layers. Using a modeling approach, we derive putative changes in neural dynamics while accounting for draining effects. Our results support the role of temporal cortical architecture in the implementation of predictive coding and highlight the ability of laminar fMRI to investigate mesoscopic processes in a large extent of temporal areas.

neuroscience↗

bioRxiv2025

Isoform-level discovery, quantification and fusion analysis from single-cell and spatial long-read RNA-seq data with Bambu-Clump

Single cell and spatial transcriptomics have dramatically changed how we can profile RNA from heterogenous biological samples. Combining single cell and spatial profiling with long read RNA-Seq promises to enable the discovery and quantification of individual RNA isoforms at the single-cell level. However, highly multiplexed data such as from a single cell experiment only generates a limited number of reads for each cell, constituting a major challenge for transcript discovery and quantification with existing approaches that usually have limited power for samples with low sequencing depth. Here we present Bambu-Clump, a computational method that performs transcript discovery and quantification from single cell and spatial long read RNA-Seq data using information from both each cell and the cell cluster. Using this approach, Bambu-Clump provides the most accurate transcript discovery compared to other existing methods, and improves transcript quantification compared to methods that rely on estimates derived from single cells. We apply Bambu-Clump to identify fusion transcripts in single-cells, compare 5 and 3 selection protocols, and identify novel isoform cell-type markers in spatial mouse brain data. Together, Bambu-Clump provides an easy-to-use, efficient, and accurate method for analysing individual isoform expression for single cells and cell clusters across multiple datasets and replicates from long read RNA-Seq.

bioinformatics↗

bioRxiv2024

Transcriptomic analysis reveals vector attraction to potato virus Y is mediated through temporal regulation of TERPENE SYNTHASE 1 (TPS1)

Virus-plant dynamics change over time, influencing interactions between plants and insect vectors. However, the signaling pathways and regulators that control these temporal responses remain largely unknown. In this study, we used insect performance and preference bioassays, RNA-Seq, and genetic tools to identify underlying mechanisms mediating temporal variation in plant-virus-vector interactions. We show that settlement and fecundity of the aphid vector, Myzus persicae, is increased on potato virus Y (PVY)-infected Nicotiana benthamiana plants two weeks after inoculation but not after six weeks. RNA-Seg analysis revealed transcripts related to plant defense and amino acid biosynthesis are upregulated in response to PVY infection and down regulated in response to aphid herbivory, and these patterns changed over time. Based on this analysis we identified a sesquiterpene synthase gene, terpene synthase 1 (NbTPS1), that is upregulated early in PVY infection, but not at later infection time points. Using virus-induced gene silencing and transient overexpression in N. benthamiana we demonstrate that PVY induction of NbTPS1 is required for increased aphid attraction to PVY-infected plants in the early stages of infection. Taken together, PVY temporally regulates transcriptional pathways related to plant defense responses and volatile organic compounds that influence aphid vector performance and preference.

plant biology↗

bioRxiv2024

The CoREST-complex regulates MYC stability and promotes post-transcriptional mRNA splicing in melanoma

The CoREST complex is a multi-subunit epigenetic regulator implicated in histone modification and transcriptional repression, but its role in tumorigenesis is not well-defined. Here, we show that the CoREST complex directly interacts with and stabilizes the MYC oncoprotein in cancer cells through site-specific deacetylation of lysine residues, primarily mediated by HDAC1/2. These modifications protect MYC from proteasomal degradation independently of transcriptional regulation, maintaining high MYC protein levels in cancer cells. Transcriptomic analysis reveals that the CoREST-mediated MYC stabilization activates transcription of genes critical for DNA replication and mitotic chromosome segregation, and enhances melanoma cell viability. These findings suggest that the CoREST complex maintains cancer cell genome stability and promotes survival by sustaining MYC oncogenic activity, highlighting it as a potential therapeutic target in MYC-driven malignancies.

cancer biology↗

bioRxiv2024

Meta-prediction extends human cortical and subcortical reward learning

Environmental conditions affect human reward prediction. Stable environments foster accurate prediction but constrain learning opportunities, whereas uncertain environments diminish predictability. This stability-uncertainty dilemma complicates task design. We conceptualize this challenge as a task learning paradigm termed meta-prediction - predicting human prediction itself. The meta-prediction entwines two Bellman equations: one emulating human reward learning while the other generates new tasks by predicting the prediction error arising from the first. The meta-prediction with 82 subjects data generated subject-independent tasks across four distinct scenarios. These tasks orchestrate foraging and uncertainty conditions, confirming our frameworks task design ability. Moreover, their mechanistic interpretability provides insight into human reward learning. An independent fMRI study with 49 individuals validated that these tasks effectively modulated behavior and neural activities in prediction error encoding regions, including ventral striatum and lateral prefrontal cortex. Lastly, we demonstrated its compositional capacity to generate complex tasks, uncovering intrinsic biases in human reward learning.

neuroscience↗

bioRxiv2024

Anatomical Region-Specific Transcriptomic Signatures and the Role of Epithelial Cells in Pterygium Inflammation: A Multi-Omics Analysis

BackgroundThe anatomy of pterygium consists of the head, neck, and body. Prior studies have examined the three parts collectively, yet the treatment methods and their success rates differ based on the anatomical characteristics. In this study, we divide the pterygium tissue into Main (head and neck) and Acc (body) to investigate its pathogenesis across regions. PurposesThis study aims to understand the pathogenesis and identify potential therapeutic targets of pterygium. Through a robust multi-omics analysis of bulk and single-cell RNA sequencing (RNA-seq) data from pterygium patients, we focus on the expression of inflammatory and mitochondrial energy pathways and identify potential genes responsible for the upregulated pathways in pterygium. MethodsWe collected bulk RNA-seq data from six pterygium patients and single-cell RNA-seq data from two pterygium patients. We then investigated the pathway enrichment, pathway correlation, differential gene expressions, protein-protein interactions, and cell-cell communications of pterygium. ResultsFrom the analysis of bulk RNA-seq data, the distribution of sample points from the principal component analysis plot and the pathways enriched from the Gene Ontology analysis showed distinct expression patterns in the Acc group compared to the Main and control groups. This suggested the need to separate the Main and Acc regions within pterygium samples and utilize single-cell RNA-seq data to understand the differences between the Main and control groups that the bulk data could not capture. The annotation of integrated single-cell data revealed a cluster of epithelial cells containing only pterygium samples. Cells from this cluster exhibited significant contributions to the ANGPTL, IL1, and KLK signaling networks in the cell-cell communication analysis. We also observed significant upregulation of the cells in the inflammatory pathways related to integrated stress response and the renin-angiotensin-aldosterone system, both of which showed high correlations with energy metabolism pathways. Significant changes in the expression of multiple pro-inflammatory, antioxidant, and immune-related genes were also identified. ConclusionThe different expression patterns between the Main and Acc groups suggest the need to consider different anatomical regions separately in future studies of pterygium. Additionally, the significant role epithelial cells from the Main group play in the inflammation of pterygium presents a potential clinical approach to the disease.

bioinformatics↗

bioRxiv2024

DeFrND: detergent-free reconstitution into native nanodiscs with designer membrane scaffold peptides

Membrane scaffold proteins-based nanodiscs (NDs) have facilitated unprecedented structural and biophysical analysis of membrane proteins in a near-native lipid environment. However, successful reconstitution of membrane proteins in NDs requires prior solubilization and purification in detergents, which may impact their physiological structure and function. Furthermore, the detergent-mediated reconstitution of NDs is unlikely to recapitulate the precise composition or asymmetry of native membranes. To circumvent this fundamental limitation of traditional ND technology, we herein describe the development of membrane-solubilizing peptides to directly extract membrane proteins from native cell membranes into nanoscale discoids. By systematically protein engineering and screening, we created a new class of chemically modified Apolipoprotein-A1 mimetic peptides to enable the formation of detergent-free NDs (DeFrNDs) with high efficiency. NDs generated with these engineered membrane scaffold peptides are suitable for obtaining high-resolution structures using single-particle cryo-EM with native lipids. To further highlight the versatility of DeFrNDs, we directly extract a sampling of membrane signaling proteins with their surrounding native membranes for biochemical and biophysical interrogations.

biophysics↗

bioRxiv2024

Structure, dynamics and evolution of the Candida albicans multi-drug resistance ABC transporter CDR1

The pleiotropic drug resistance transporter Cdr1 from Candida albicans plays a crucial role in antifungal resistance. Here, we present high-resolution cryo-electron microscopy structures of C. albicans Cdr1 in multiple functional states: nucleotide-bound, substrate-bound, and apo forms. The 3.5 [A] resolution structure of Cdr1 in complex with ATP and ADP reveals the molecular details of its asymmetric nucleotide-binding sites (NBS), with ATP bound to the deviant NBS1 and ADP to the canonical NBS2. Structures of Cdr1 bound to rhodamine 6G (3.4 [A]) and Oregon Green 488 (3.5 [A]) in complex with these nucleotides elucidate the pleiotropic substrate-binding pocket and highlight how nucleotide exchange drives conformational change required for transport. Additionally, we determined a 3.7 [A] resolution structure of Cdr1 in the detergent LMNG without nucleotides, as well as a 3.5 [A] resolution structure with nucleotides but no substrate, representing an apo state. We complemented these structural insights with molecular dynamics simulations to understand substrate binding dynamics, ancestral sequence reconstruction to trace the evolution of key functional motifs, and analysis of clinical isolates from sequence databases to identify potential resistance-associated variations. Comparison of these structures provides new insights into the conformational changes associated with the transport cycle of this asymmetric ABC transporter, revealing how ATP binding at the deviant NBS1 allosterically regulates the canonical NBS2, driving ATPase activity. This work significantly advances our understanding of the molecular mechanisms underlying multidrug resistance in pathogenic fungi and provides a structural and evolutionary framework for the rational design of Cdr1 inhibitors to combat antifungal resistance.

microbiology↗