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Jeong, H.

Publications and source records attributed to Jeong, H..

At least 55 records · Page 3Linked to original sources

Selective engagement of prefrontal VIP neurons in reversal learning

To gain insights into neural mechanisms enabling behavioral adaptations to complex and multidimensional environmental dynamics, we examined roles of VIP neurons in mouse medial prefrontal cortex (mPFC) in probabilistic reversal learning. Behaviorally, manipulating VIP neuronal activity left probabilistic classical conditioning unaffected but severely impaired reversal learning. Physiologically, conditioned cue-associated VIP neuronal responses changed abruptly after encountering an unexpected reward. They also conveyed strong reward prediction error signals during behavioral reversal, but not before or after, unlike pyramidal neurons which consistently conveyed error signals throughout all phases. Furthermore, the signals persistence across trials correlated with reversal learning duration. These results suggest that mPFC VIP neurons play crucial roles in rapid reversal learning, but not in incremental cue-outcome association learning, by monitoring significant deviations from ongoing environmental contingency and imposing error-correction signals during behavioral adjustments. These findings shed light on the intricate cortical circuit dynamics underpinning behavioral flexibility in complex, multifaceted environments.

neuroscience↗

Mesolimbic dopamine ramps reflect environmental timescales

Mesolimbic dopamine activity occasionally exhibits ramping dynamics, reigniting debate on theories of dopamine signaling. This debate is ongoing partly because the experimental conditions under which dopamine ramps emerge remain poorly understood. Here, we show that during Pavlovian and instrumental conditioning, mesolimbic dopamine ramps are only observed when the inter-trial interval is short relative to the trial period. These results constrain theories of dopamine signaling and identify a critical variable determining the emergence of dopamine ramps.

neuroscience↗

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↗

Hidden route of protein damage through confined oxygen gas

Oxidative modifications can severely impair protein structure, fold, and function, closely linked to human aging and diseases. Conventional oxidation pathways typically involve the free diffusion of reactive oxygen species (ROS), followed by chemical attacks on the protein surface. Here, we report a hidden route of protein oxidative damage, which we refer to as O2-confinement oxidation pathway. This pathway starts with the initial trapping of dissolved molecular oxygen (O2) within protein cavity spaces, followed by interaction with photosensitizing tryptophan residues. The trapped O2 is then converted to singlet oxygen (1O2), a powerful ROS, through spin-flip electron transfer mechanism under blue light. The generated 1O2 within the protein ultimately attacks the protein core residues through constrained diffusion, accelerating the oxidative damage. This alternative photooxidation pathway through the initial O2 trapping would bypass the antioxidant defense systems which target freely-diffusing ROS, constituting an additional layer of protein oxidative damage in cells and tissues.

biochemistry↗

Tight junction component protein claudin-1 deficiency in retinal pigment epithelium leads to early and intermediate age-related macular degeneration phenotypes in mice.

The early and intermediate age-related macular degeneration (AMD) is characterized by the presence of drusen and pigmentary abnormalities in the retinal pigment epithelial (RPE) cells which form the outer blood retinal barrier (oBRB). Fluid leakage through the disrupted oBRB from the choroid to the neural retina has been implicated in the pathogenesis of AMD, however; the molecular mechanisms still remain unclear. The family of four transmembrane proteins, claudins are known to form tight junctions (TJs) in the oBRB. Nonetheless, there are few reports showing how they function in the oBRB in vivo. We found that claudin-1 is dominantly expressed in TJs of the mouse RPE. To investigate the role of claudin-1 in the RPE, we generated RPE-specific Cldn1 conditional knockout mice (Best1-Cre+/- Cldn1flox/flox mice: Cldn1 cKO mice). Deficiency of Cldn1 led to age-related lipid deposits such as subretinal drusenoid deposits (SDD), increased lipid droplets in the RPE, basal lamellar deposits (BlamD) and membranous debris in the Bruchs membrane. In addition, pigmentary abnormalities such as RPE hypertrophy, multilayered-RPE cells, and ectopic pigment granules outside the RPE were observed in Cldn1 cKO mice. Our study provides new insights into the possible association of the TJ protein claudin-1 with lipid metabolism and cellular ageing in the RPE contributing to the early onset of AMD.

molecular biology↗

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

Apes possess two sex chromosomes--the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility1. The X chromosome carries genes vital for reproduction and cognition2. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosomes. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies allowed us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the Xs, the ape Ys vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements, and satellites. Our analysis of Y chromosome genes revealed expansions of multi-copy gene families and signatures of purifying selection. Thus, the Y exhibits dynamic evolution, while the X is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of >100 great ape individuals. These reference assemblies are expected to inform human evolution and conservation genetics of nonhuman apes, all of which are endangered species.

genomics↗

GraphMHC: neoantigen prediction model applying the graph neural network to molecular structure

Neoantigens are biomarkers that can predict the prognosis associated with immune checkpoint inhibition by estimating the binding potential of candidate peptides to somatic mutation and major histocompatibility complex (MHC) proteins. Although deep neural networks have been primarily used for these prediction models, it is difficult to consider the models reported thus far as accurately representing the interactions between biomolecules. In this study, we propose the GraphMHC model, which utilizes a graph neural network model through molecular structure to simulate the binding between MHC proteins and peptide sequences. Amino acid sequences sourced from the immune epitope database (IEDB) undergo conversion into molecular structures. Subsequently, atomic intrinsic informations and inter-atomic connections are extracted and structured as a graph representation. Bindings are classified by feeding them into the GraphMHC network, comprising stacked graph attention and convolution layers. The prediction results from the test set using the GraphMHC model showed a high performance with an area under the receiver operating characteristic curve of 92.2% (91.9-92.5%), surpassing the baseline model. Moreover, by applying the GraphMHC model to melanoma patient data from the Cancer Genome Atlas project, we found a borderline difference in overall survival and a significant difference in stromal score between the high and low neoantigen load groups. This distinction was not present in the baseline model. This study presents the first feature-intrinsic method based on biochemical molecular structure for modeling the binding between MHC protein sequences and neoantigen candidate peptide sequences. The model can provide highly accurate suitability information for cancer patients who want to apply immune checkpoint inhibitors. Author summary

bioinformatics↗

Structure of C. elegans TMC-2 complex suggests roles of lipid-mediated subunit contacts in mechanosensory transduction

Mechanotransduction is the process by which a mechanical force, such as touch, is converted into an electrical signal. Transmembrane channel-like (TMC) proteins are an evolutionarily-conserved family of ion channels whose function has been linked to a variety of mechanosensory processes, including hearing and balance sensation in vertebrates and locomotion in Drosophila. The molecular features that tune homologous TMC ion channel complexes to diverse mechanical stimuli are unknown. Caenorhabditis elegans express two TMC homologs, TMC-1 and TMC-2, both of which are the likely pore-forming subunits of mechanosensitive ion channels but differ in their expression pattern and functional role in the worm. Here we present the single particle cryo-electron microscopy structure of the native TMC-2 complex isolated from C. elegans. The complex is composed of two copies each of the pore-forming TMC-2 subunit, the calcium and integrin binding protein CALM-1 and the transmembrane inner ear protein TMIE. Comparison of the TMC-2 complex to the recently published cryo-EM structure of the C. elegans TMC-1 complex reveals differences in subunit composition and highlights conserved protein-lipid interactions, as well as other structural features, that together suggest a mechanism for TMC-mediated mechanosensory transduction. Significance StatementOne mechanism by which organisms sense their environment is through the perception of mechanical stimuli such as sound, touch, and vibration. Transmembrane channel-like (TMC) proteins are ion channels whose function has been linked to a variety of mechanosensitive processes, including hearing and balance in vertebrates and touch sensation in worms. The molecular mechanisms by which TMCs respond to mechanical stimuli are unknown. Here we present the structure of the TMC-2 complex isolated from worms. Comparison of the TMC-2 complex to the recently solved structure of the worm TMC-1 complex highlights common structural features that are likely important for sensing mechanical stimuli yet also illuminates key differences that may explain the distinct functional roles of TMC-1 and TMC-2 in the worm.

biochemistry↗

Blood-based Nano-QuIC: Accelerated and Inhibitor-resistant Detection of Misfolded Alpha-synuclein

A hallmark of -synucleinopathies (e.g. Parkinsons disease) is the misfolding and aggregation of -synuclein in tissues and biological fluids. Protein amplification assays like real-time quaking-induced conversion (RT-QuIC) are sensitive yet currently limited to semi-invasive sample types such as cerebrospinal fluid because more accessible samples, such as blood, contain inhibitors. Here, we show that Nanoparticle-enhanced Quaking-induced Conversion (Nano-QuIC) can double the speed of reactions spiked with misfolded -synuclein while increasing sensitivity 100-fold in human plasma. Nano-QuIC detected spike concentrations down to 90 pg/ml in lysed whole blood, while reactions without nanoparticles (RT-QuIC) failed to have any detection due to the presence of strong inhibitors. Moreover, Nano-QuIC showed increased seeding activity in plasma samples from Parkinsons patients (n=4) versus healthy controls (n=4). This sets the groundwork for the noninvasive diagnostic use of Nano-QuIC, potentially enabling early disease detection and management through blood-based testing. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/552630v2_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1141573org.highwire.dtl.DTLVardef@18c63d6org.highwire.dtl.DTLVardef@1ee9524org.highwire.dtl.DTLVardef@81af13_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

Cell type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells

The functional impact and cellular context of mosaic structural variants (mSVs) in normal tissues is understudied. Utilizing Strand-seq, we sequenced 1,133 single cell genomes from 19 human donors of increasing age, revealing a heterogeneous mSV landscape in hematopoietic stem and progenitor cells (HSPCs). While mSV clonal expansions are confined to individuals over 60, de novo mSV formation occurs consistently across age, frequently leading to megabase-scale segmental aneuploidies. Cells harboring subclonal mosaicism show evidence for increased mSV formation. To enable high-resolution cell-typing of each Strand-seq library, we generated single-cell MNase-seq reference datasets for eight distinct HSPCs. Subclonal mSVs frequently exhibit enrichment in myeloid progenitors, and single-cell multiomic analysis suggests that these mSVs result in recurrent dysregulation of pathways related to proliferation and metabolism, including Ras signaling and lipid metabolism. The comprehensive mSV landscape identified in this study implicates mSVs in cell type-specific molecular phenotypes, establishing a foundation for deciphering links between mSVs, aging, and disease risk.

genomics↗

The orientation of choroidal macrophage polarization significantly influences the development of myopia in murine models

Myopia is a primary contributor to visual impairment and has emerged as a global public health concern. Evidence indicates that one of the main structural features of myopia is the corresponding decrease in choroidal thickness, and choroidal macrophages play an important role in maintaining the choroidal thickness. Nevertheless, the effect of choroidal macrophages on myopia remains unclear. Here, we discovered that the continuous intraperitoneal injection of clodronate liposomes depleted choroidal macrophages and leads to myopia, which confirmed that the presence of choroidal macrophages plays an important role in myopia development. Subsequently, based on the phenotypic characteristics of macrophages, experiments were designed to study the effects of different polarization directions of macrophages on myopia development. We found that lipopolysaccharides (LPS) injection can induce the polarization of choroidal M1 macrophages, thinning the choroidal thickness and resulting in myopia. Conversely, IL-4 or IL-13 injection causes choroidal M2 macrophage polarization, thickens the choroid, and suppresses the progression of myopia. Additionally, we demonstrated that the opposite effects of M1 and M2 macrophages on myopia development may be related to their impacts on choroidal thickness, inflammation, and oxidative stress response. These findings establish that choroidal macrophages are critically important in the development of myopia and provide new strategies for the development of myopic therapies.

immunology↗

Mesostriatal dopamine is sensitive to specific cue-reward contingencies

Learning causal relationships relies on understanding how often one event precedes another. To gain an understanding of how dopamine neuron activity and neurotransmitter release change when a retrospective relationship is degraded for a specific pair of events, we used outcome-selective Pavlovian contingency degradation in rats. Two cues were paired with distinct food rewards, one of which was also delivered in the absence of either cue. Conditioned approach was attenuated for the cue-reward contingency that was degraded. Dopamine neuron activity in the midbrain and dopamine release in the ventral striatum showed a profile of changes in cue- and reward-evoked responding that was not easily explained by a standard reinforcement learning model. An alternative model based on learning causal relationships was better able to capture evoked dopamine responses during contingency degradation, as well as conditioned behavior following optogenetic manipulations of dopamine during noncontingent rewards. Our results suggest that mesostriatal dopamine encodes the contingencies between meaningful events during learning.

neuroscience↗

Few-shot learning: temporal scaling in behavioral and dopaminergic learning

Learning the causes of rewards is necessary for survival. Thus, it is critical to understand the mechanisms of such a vital biological process. Cue-reward learning is controlled by mesolimbic dopamine and improves with spacing of cue-reward pairings. However, whether a mathematical rule governs such improvements in learning rate, and if so, whether a unifying mechanism captures this rule and dopamine dynamics during learning remain unknown. Here, we investigate the behavioral, algorithmic, and dopaminergic mechanisms governing cuereward learning rate. Across a range of conditions in mice, we show a strong, mathematically proportional relationship between both behavioral and dopaminergic learning rates and the duration between rewards. Due to this relationship, removing up to 19 out of 20 cue-reward pairings over a fixed duration has no influence on overall learning. These findings are explained by a dopamine-based model of retrospective learning, thereby providing a unified account of the biological mechanisms of learning.

neuroscience↗

Sensory cortical ensembles exhibit differential coupling to ripples in distinct hippocampal subregions

Cortical neurons activated during recent experiences often reactivate with dorsal hippocampal CA1 sharp-wave ripples (SWRs) during subsequent rest. Less is known about cortical interactions with intermediate hippocampal CA1, whose connectivity, functions, and SWRs differ from those of dorsal CA1. We identified three clusters of visual cortical excitatory neurons that are excited together with either dorsal or intermediate CA1 SWRs, or suppressed before both SWRs. Neurons in each cluster were distributed across primary and higher visual cortices and co-active even in the absence of SWRs. These ensembles exhibited similar visual responses but different coupling to thalamus and pupil-indexed arousal. We observed a consistent activity sequence: (i) suppression of SWR-suppressed cortical neurons, (ii) thalamic silence, and (iii) activation of the cortical ensemble preceding and predicting intermediate CA1 SWRs. We propose that the coordinated dynamics of these ensembles relay visual experiences to distinct hippocampal subregions for incorporation into different cognitive maps.

neuroscience↗

The fingering patterns in the epithelial layer control the gap closure rate via curvature-mediated force

Closing gaps in cellular monolayers is a fundamental aspect of both morphogenesis and wound healing. This closure can be achieved through leader cell crawling or actomyosin-based contraction, depending on the size of the gap. Here, we focus on wounds whose closure is driven by interfacial instabilities, featuring both leader cell-driven fingers and actin-mediated contraction. Our proposed model predicts a positive correlation between the frequency of fingering and the overall speed of boundary closure. This fingering frequency is precisely regulated through the orchestration of cell density-driven pressure, cell-cell repulsions, and the initial curvature of the wound boundary. Our findings demonstrate an inverse correlation between fingering frequency and boundary curvatures, indicating a "self-control" mechanism for closure rates independent of the initial curvatures of the wound periphery. Notably, changes in curvature caused by fingering formation generate force that aids in the healing process.

biophysics↗

Structurally divergent and recurrently mutated regions of primate genomes

To better understand the pattern of primate genome structural variation, we sequenced and assembled using multiple long-read sequencing technologies the genomes of eight nonhuman primate species, including New World monkeys (owl monkey and marmoset), Old World monkey (macaque), Asian apes (orangutan and gibbon), and African ape lineages (gorilla, bonobo, and chimpanzee). Compared to the human genome, we identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. Across 50 million years of primate evolution, we estimate that 819.47 Mbp or ~27% of the genome has been affected by SVs based on analysis of these primate lineages. We identify 1,607 structurally divergent regions (SDRs) wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (CARDs, ABCD7, OLAH) and new lineage-specific genes are generated (e.g., CKAP2, NEK5) and have become targets of rapid chromosomal diversification and positive selection (e.g., RGPDs). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species for the first time.

genomics↗

Multifunctional Materials Strategies for Enhanced Safety of Wireless, Skin-Interfaced Bioelectronic Devices

Many recently developed classes of wireless, skin-interfaced bioelectronic devices rely on conventional thermoset silicone elastomer materials, such as poly(dimethylsiloxane) (PDMS), as soft encapsulating structures around collections of electronic components, radio frequency antennas and, commonly, rechargeable batteries. In optimized layouts and device designs, these materials provide attractive features, most prominently in their gentle, noninvasive interfaces to the skin even at regions of high curvature and large natural deformations. Past work, however, overlooks opportunities for developing variants of these materials for multimodal means to enhance the safety of the devices against failure modes that range from mechanical damage to thermal runaway. This paper presents a self-healing PDMS dynamic covalent matrix embedded with chemistries that provide thermochromism, mechanochromism, strain-adaptive stiffening, and thermal insulation, as a collection of attributes relevant to safety. Demonstrations of this materials system and associated encapsulation strategy involve a wireless, skin-interfaced device that captures mechanoacoustic signatures of health status. The concepts introduced here can apply immediately to many other related bioelectronic devices.

bioengineering↗

High-resolution assessment of multidimensional cellular mechanics using label-free refractive-index traction force microscopy

A critical requirement for studying cell mechanics is three-dimensional (3D) assessment of cellular shapes and forces with high spatiotemporal resolution. Traction force microscopy (TFM) with fluorescence imaging enables the measurement of cellular forces, but it is limited by photobleaching and a slow 3D acquisition speed. Here, we present refractive-index traction force microscopy (RI-TFM), a high-speed volumetric technique that simultaneously quantifies the 3D morphology and traction force of cells. RI-TFM reconstructs a 3D tomogram of single cells on a planar hydrogel elastomer using a high-speed illumination scheme with 0.5-Hz temporal resolution. This allows for quantitative analyses of 3D dry-mass distributions and shear (in-plane) and normal (out-of-plane) tractions of single cells on the extracellular matrix without labelling. When combined with a constrained total variation-based deconvolution algorithm, the proposed method provides 0.55-Pa shear (in-plane) and 1.59-Pa normal (out-of-plane) traction sensitivity for a 1-kPa hydrogel substrate. We demonstrate the utility of RI-TFM by assessing the effects of compromised intracellular stress due to actin disruption or low temperature and capturing the rapid dynamics of cellular junction formation in the spatiotemporal changes in non-planar traction components.

biophysics↗