Biology subjects

Kim, J.-H.

Publications and source records attributed to Kim, J.-H..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

A stepwise, modular design of building uniform brain assembloids representing the dynamic cellular interplay between neurons and glial cells

Current brain organoid technology fails to provide adequate patterning cues to induce a mature structure that represent the complexity of the human brain. Here, we developed a module-based cellular reconstitution technology to sequentially build uniform forebrain assembloids with mature cortical structures and functional connectivity. The uniformity and maturity of the newly-conceived forebrain assembloids were achieved by creating single-rosette-based organoids at the early stage, whose sizes were big and consistent with the treatment of Wnt and Hedgehog agonists, followed by spatial reconstitution with the Reelin-expressing neuronal layer and non-neuronal glial cells. The resulting single-rosette-based forebrain assembloids were highly uniform and reproducible without significant batch effects, solving major heterogeneity issues caused by difficulties in controlling the number and size of rosettes in conventional multi-rosette organoids. Furthermore, these forebrain assembloids structurally and functionally recapitulated the physiology of the human brain, including the six-layered cortical structure, functional connectivity, and dynamic cellular interplay between neurons and glial cells. Our study thus provided an innovative preclinical model to study a range of neurological disorders, understanding the pathogenesis of which requires an organoid system capable of representing the dynamic cellular interactions and the maturity of the human brain.

developmental biology↗

bioRxiv2024

Muscle Type-Specific Modulation of Autophagy Signaling in Obesity: Effects of Caloric Restriction and Exercise

BackgroundObesity causes metabolic dysregulation and contributes to various diseases, with autophagy playing a pivotal role in this process. Autophagy, a cellular recycling mechanism, is influenced by factors beyond obesity, like caloric restriction (CR) and CR combined with exercise (CR+Ex), which modulate autophagy in obesity management. However, the regulation of autophagy in skeletal muscle under conditions of obesity, CR, and CR+Ex remains poorly understood. MethodMice were divided into six groups: normal diet, normal diet CR, normal diet CR+Ex, high-fat diet, high-fat diet CR, and high-fat diet CR+Ex. All mice were fed ad libitum with either a normal or high-fat diet for the first four months, followed by the respective interventions for the subsequent four months. Body composition, motor function, and skeletal muscle autophagy signaling were assessed. ResultsObesity resulted in increased total mass, lean mass, fat mass, and fat percentage in tissue; decreased grip strength and endurance capacity. Notably, CR+Ex reduced total mass, lean mass, and fat mass in obese mice. In both normal and obese conditions, the expression of autophagy markers p62, LC3B-I, and LC3B-II is significantly higher in red muscle. Obesity leads to a reduction in cathepsin L expression, while CR further increased LC3B-I expression in red muscle. ConclusionCR+Ex proves to be an effective strategy for counteracting the adverse changes in body composition associated with obesity. Unlike red muscle, white muscle exhibits lower baseline autophagic levels and may necessitate elevated expression of autophagy-related proteins, such as cathepsin L, to mitigate the negative effects of obesity.

physiology↗

bioRxiv2024

The Impact of Frailty Syndrome on Skeletal Muscle Histology and the Preventive Effects of Exercise

Aging-induced frailty syndrome significantly impairs skeletal muscle health, yet its impact on muscle histology remains unclear. This study investigates the histological alterations in muscle associated with frailty syndrome and evaluates the preventive effects of exercise. Mice were divided into groups based on age and condition, including an exercised group. Evaluated variables include body weight, lean mass ratio, myofiber size and number, extracellular matrix (ECM) content, and myosin heavy chain isoforms. Findings indicate that frailty syndrome increases body weight and ECM content, while reducing myofiber size and number, highlighting its negative impact on skeletal muscle histology. Notably, exercise effectively mitigated these adverse changes, suggesting its potential role in preventing skeletal muscle dysfunction associated with frailty syndrome.

physiology↗

bioRxiv2024

Regulation of Ferroptosis in Obesity: Muscle Type-Specific Effects of Dietary Restriction and Exercise

BackgroundObesity is a significant global health issue and a risk factor for numerous diseases. Ferroptosis, an iron-dependent regulated cell death, is triggered by iron overload and the excessive accumulation of lipid peroxidation mediated by reactive oxygen species. Studies has identified a strong association between ferroptosis and obesity. Additionally, dietary restriction (DR) and DR combined with exercise (DR+Ex) are effective strategies for managing obesity and ferroptosis. However, the regulation of ferroptosis and its signaling pathways in skeletal muscle under conditions of obesity, DR, and DR+Ex remains poorly understood. MethodsMice were divided into four groups: normal diet, high-fat diet, high-fat DR, and high-fat DR+Ex. All mice were fed ad libitum with either a normal or high-fat diet for the first 14 weeks, followed by the respective interventions for the subsequent 8 weeks. Mice muscle ferroptosis were examined by immunohistochemistry, Hematoxylin & Eosin, Massons trichrome, Prussian blue staining, and Western-Immunoblot. ResultsThe high-fat diet resulted in increased inflammatory cell infiltration, fibrosis, and iron accumulation. Red and white muscle showed increased expression of 4-HNE, regulated by GPX4 and NCAO4, respectively. DR and DR+Ex reduced downstream 4-HNE expression by regulating GPX4 in red muscle. ConclusionDue to metabolic differences, obesity-induced ferroptosis in skeletal muscle and the regulation by DR+Ex exhibiting fiber type-specificity. Specifically, red and white muscle respond to obesity-induced ferroptosis through different pathways; red muscle can inhibit obesity-induced ferroptosis through DR+Ex by GPX4. This deepens the understanding of mechanisms related to skeletal muscle cell death and provides scientific data support for the personalized treatment of related diseases.

physiology↗

bioRxiv2024

A combinatorial neural code for long-term motor memory

Motor skill repertoire can be stably retained over long periods, but the neural mechanism underlying stable memory storage remains poorly understood. Moreover, it is unknown how existing motor memories are maintained as new motor skills are continuously acquired. Here we tracked neural representation of learned actions throughout a significant portion of a mouses lifespan, and we show that learned actions are stably retained in motor memory in combination with context, which protects existing memories from erasure during new motor learning. We used automated home-cage training to establish a continual learning paradigm in which mice learned to perform directional licking in different task contexts. We combined this paradigm with chronic two-photon imaging of motor cortex activity for up to 6 months. Within the same task context, activity driving directional licking was stable over time with little representational drift. When learning new task contexts, new preparatory activity emerged to drive the same licking actions. Learning created parallel new motor memories while retaining the previous memories. Re-learning to make the same actions in the previous task context re-activated the previous preparatory activity, even months later. At the same time, continual learning of new task contexts kept creating new preparatory activity patterns. Context-specific memories, as we observed in the motor system, may provide a solution for stable memory storage throughout continual learning. Learning in new contexts produces parallel new representations instead of modifying existing representations, thus protecting existing motor repertoire from erasure.

neuroscience↗

bioRxiv2024

GluN2B-mediated regulation of silent synapses for receptor specification and addiction memory

Psycho-stimulants including cocaine elicit stereotyped, addictive behaviors. Re-emergence of silent synapses containing only NMDA-type glutamate receptors (NMDARs) is a critical mediator of addiction memory and seeking behaviors. Despite the predominant abundance of GluN2B-containing NMDARs in silent synapses, their operational mechanisms are not fully understood. Using conditional depletion/deletion of GluN2B at D1-expressing accumbal medium spiny neurons, we examine the synaptic and behavioral actions that silent synapses incur after repeated exposure to cocaine. GluN2B ablation reduces the proportion of silent synapses, but some of them can persist by substitution to GluN2C, which drives the aberrantly-facilitated synaptic incorporation of calcium-impermeable AMPA-type glutamate receptors (AMPARs). The resultant precocious maturation of silent synapses impairs addiction memory but elevates locomotor activity, which can be normalized by blockade of calcium-impermeable AMPAR trafficking. Collectively, GluN2B supports the competence of cocaine-induced silent synapses for specifying subunit composition of AMPARs, and thereby expression of addition memory and the related behaviors.

neuroscience↗

bioRxiv2024

Muscle-resident mesenchymal progenitors sense and repair peripheral nerve injury via the GDNF-BDNF axis

Fibro-adipogenic progenitors (FAPs) are muscle-resident mesenchymal progenitors that can contribute to muscle tissue homeostasis and regeneration, as well as postnatal maturation and lifelong maintenance of the neuromuscular system. Recently, traumatic injury to the peripheral nerve was shown to activate FAPs, suggesting that FAPs can respond to nerve injury. However, questions of how FAPs can sense the anatomically distant peripheral nerve injury and whether FAPs can directly contribute to nerve regeneration remained unanswered. Here, utilizing single-cell transcriptomics and mouse models, we discovered that a subset of FAPs expressing GDNF receptors Ret and Gfra1 can respond to peripheral nerve injury by sensing GDNF secreted by Schwann cells. Upon GDNF sensing, this subset becomes activated and expresses Bdnf. FAP-specific inactivation of Bdnf (Prrx1Cre; Bdnffl/fl) resulted in delayed nerve regeneration owing to defective remyelination, indicating that GDNF-sensing FAPs play an important role in the remyelination process during peripheral nerve regeneration. In aged mice, significantly reduced Bdnf expression in FAPs was observed upon nerve injury, suggesting the clinical relevance of FAP-derived BDNF in the age-related delays in nerve regeneration. Collectively, our study revealed the previously unidentified role of FAPs in peripheral nerve regeneration, and the molecular mechanism behind FAPs response to peripheral nerve injury.

neuroscience↗

bioRxiv2024

Behavior can be decoded across the cortex when individual differences are considered

Group-level analyses have typically linked behavioral signatures to a constrained set of brain areas. Here we show that two behavioral metrics - reaction time (RT) and confidence - can be decoded across the cortex when each individual is considered separately. Subjects (N=50) completed a perceptual decision-making task with confidence. We built models decoding trial-level RT and confidence separately for each subject using the activation patterns in one brain area at a time after splitting the entire cortex into 200 regions of interest (ROIs). First, we developed a simple test to determine the robustness of decoding performance, which showed that several hundred trials per subject are required for robust decoding. We then examined the decoding performance at the group and subject levels. At the group level, we replicated previous results by showing that both RT and confidence could be decoded from a small number of ROIs (12.0% and 3.5%, respectively). Critically, at the subject level, both RT and confidence could be decoded from most brain regions even after Bonferroni correction (90.0% and 72.5%, respectively). Surprisingly, we observed that many brain regions exhibited opposite brain-behavior relationships across individuals, such that, for example, higher activations predicted fast RTs in some subjects but slow RTs in others. All results were replicated in a second dataset. These findings show that behavioral signatures can be decoded from a much broader range of cortical areas than previously recognized and suggest the need to study the brain-behavior relationship at both the group and subject levels.

neuroscience↗

bioRxiv2023

A mouse model of ZTTK syndrome reveals indispensable SON functions in organ development and hematopoiesis

Rare diseases are underrepresented in biomedical research, leading to insufficient awareness. Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome is a rare disease caused by genetic alterations that result in heterozygous loss-of-function of SON. While ZTTK syndrome patients suffer from numerous symptoms, the lack of model organisms hamper our understanding of both SON and this complex syndrome. Here, we developed Son haploinsufficiency (Son+/-) mice as a model of ZTTK syndrome and identified the indispensable roles of Son in organ development and hematopoiesis. Son+/- mice recapitulated clinical symptoms of ZTTK syndrome, including growth retardation, cognitive impairment, skeletal abnormalities, and kidney agenesis. Furthermore, we identified hematopoietic abnormalities in Son+/- mice, similar to those observed in human patients. Surface marker analyses and single-cell transcriptome profiling of hematopoietic stem and progenitor cells revealed that Son haploinsufficiency inclines cell fate toward the myeloid lineage but compromises lymphoid lineage development by reducing key genes required for lymphoid and B cell lineage specification. Additionally, Son haploinsufficiency causes inappropriate activation of erythroid genes and impaired erythroid maturation. These findings highlight the importance of the full gene dosage of Son in organ development and hematopoiesis. Our model serves as an invaluable research tool for this rare disease and related disorders associated with SON dysfunction.

genetics↗

bioRxiv2023

Cellular Calcium Activity at Depth Predicted from Surface Potential Recordings using Ultra-high Density Transparent Graphene Arrays

Recording brain activity with high spatial and high temporal resolution across deeper layers of cortex has been a long-sought methodology to study how neural information is coded, stored, and processed by neural circuits and how it leads to cognition and behavior. Electrical and optical neural recording technologies have been the key tools in neurophysiology studies toward a comprehensive understanding of the neural dynamics. The advent of optically transparent neural microelectrodes has facilitated multimodal experiments combining simultaneous electrophysiological recordings from the brain surface with optical imaging and stimulation of neural activity. A remaining challenge is to scale down electrode dimensions to single -cell size and increase the density to record neural activity with high spatial resolution across large areas to capture nonlinear neural dynamics at multiple spatial and temporal scales. Here, we developed microfabrication techniques to create transparent graphene microelectrodes with ultra-small openings and a large, completely transparent recording area. We achieved this by using long graphene microwires without any gold extensions in the field of view. To overcome the quantum capacitance limit of graphene and scale down the microelectrode diameter to 20 m, we used Pt nanoparticles. To prevent open circuit failure due to defects and disconnections in long graphene wires, we employed interlayer doped double layer graphene (id-DLG) and demonstrated cm-scale long transparent graphene wires with microscale width and low resistance. Combining these two advances, we fabricated high-density microelectrode arrays up to 256 channels. We conducted multimodal experiments, combining recordings of cortical potentials with high-density transparent arrays with two-photon calcium imaging from layer 1 (L1) and layer 2/3 (L2/3) of the V1 area of mouse visual cortex. High-density recordings showed that the visual evoked responses are more spatially localized for high-frequency bands, particularly for the multi-unit activity (MUA) band. The MUA power was found to be strongly correlated with the cellular calcium activity. Leveraging this strong correlation, we applied dimensionality reduction techniques and neural networks to demonstrate that single-cell (L2/3) and average (L1 and L2/3) calcium activities can be decoded from surface potentials recorded by high-density transparent graphene arrays. Our high-density transparent graphene electrodes, in combination with multimodal experiments and computational methods, could lead to the development of minimally invasive neural interfaces capable of recording neural activity from deeper layers without requiring depth electrodes that cause damage to the tissue. This could potentially improve brain computer interfaces and enable less invasive treatments for neurological disorders.

neuroscience↗

bioRxiv2023

Serum Lipidome Profiling Reveals a Distinct Signature of Ovarian Cancer in Korean Women

Distinguishing ovarian cancer (OC) from other gynecological malignancies remains a critical unmet medical need with significant implications for patient survival. However, non-specific symptoms along with our lack of understanding of OC pathogenesis hinder its diagnosis, preventing many women from receiving appropriate medical assistance. Accumulating evidence suggests a link between OC and deregulated lipid metabolism. Most studies, however, are limited by small sample size, particularly for early-stage cases. Furthermore, racial/ethnic differences in OC survival and incidence have been reported, yet most of the studies consist largely of non-Hispanic white women or women with European ancestry. Studies of more diverse racial/ethnic populations are needed to make OC diagnosis and prevention more inclusive. Here, we profiled the serum lipidome of 208 OC, including 93 patients with early-stage OC, and 117 non-OC (other gynecological malignancies) patients of Korean descent. Serum samples were analyzed with a high-coverage liquid chromatography high-resolution mass spectrometry platform, and lipidome alterations were investigated via statistical and machine learning approaches. Results show that lipidome alterations unique to OC were present in Korean women as early as when the cancer is localized, and those changes increase in magnitude as the diseases progresses. Analysis of relative lipid abundances revealed specific patterns for various lipid classes, with most classes showing decreased abundance in OC in comparison to other gynecological diseases. Machine learning methods selected a panel of 17 lipids that discriminated OC from non-OC cases with an AUC of 0.85 for an independent test set. This study provides a systemic analysis of lipidome alterations in human OC, specifically in Korean women, emphasizing the potential of circulating lipids in distinguishing OC from non-OC conditions.

cancer biology↗

bioRxiv2023

Somatosensory cortical representations of assimilation effect by vibrotactile stimulation

This study investigated neural activity related to the assimilation effect in the perception of vibrotactile stimuli. The assimilation effect refers to a tactile perceptual bias in which the perception of the vibrotactile frequency on one finger is biased towards a distracting vibrotactile stimulus targeting other types of mechanoreceptors on the different finger. The assimilation effect occurs not only between fingers on the same hand (in-hand) but also between fingers on different hands (across-hand). These behavioral aspects of the assimilation effect lead to an assumption that neural processes related to the assimilation effect would involve the integration of different tactile information mediated by the somatosensory cortex. We addressed this hypothesis by investigating brain responses using functional magnetic resonance imaging (fMRI) to vibrotactile stimuli that induced assimilation effect under in-hand and across-hand conditions. We first observed that the vibrotactile stimuli presented in this study activated primary (S1) and secondary (S2) somatosensory cortices. Yet, neural responses in these regions did not show correlations with individual assimilation effects, indicating that neural processing of vibrotactile signals in S1 and S2 would not be directly linked to the assimilation effect. Instead, we found that connectivity between S1 and medial prefrontal cortex (mPFC) was correlated with individual in-hand assimilation effects and that connectivity between S2 and posterior parietal cortex (PPC) was correlated with individual across-hand assimilation effects. These results suggest that the assimilation effect may be related to tactile information integration via functional connections between the somatosensory cortex and higher-order brain regions.

neuroscience↗

bioRxiv2023

Optimization of Shoot Regeneration and Application of CRISPR/Cas9 Gene Editing to Cultivated Strawberry

Efficient methods of plant transformation and tissue culture are essential to CRISPR/Cas-based gene editing of crops, but neither is well established in cultivated octoploid strawberry (F xananassa). In the present study, a method for shoot regeneration was established and optimized for two strawberry cultivars commercially grown in Florida, Sweet Sensation(R) Florida 127 FL127) and Florida Brilliance (FB). Runner segments at the tip, node, and petiole obtained from greenhouse-grown plants were used as explants for comparisons of shoot regeneration rate. FL127 showed the highest frequency of shoot regeneration to a basal Murashige and Skoog media (MS) containing 1 mg{middle dot}L-1 of TDZ, 0.05 mg{middle dot}L-1 of BA, and 0.05 mg{middle dot}L-1 of 2,4-D, while FB showed the best response to a lower concentration of BA (0.01 mg{middle dot}L-1) in the same media type. The average conversion frequencies of somatic embryos into shoot regenerations from the runner tips (RT) were 42.8% in FL127 and 56.9% in FB, respectively, with RT being the most prolific in shoot generation for both cultivars. Using these optimized tissue conditions, Agrobacterium-mediated CRISPR/Cas9 gene editing was conducted to evaluate the efficiency of transformation and knockout mutations in the phytoene desaturase (FaPDS) gene of FL127. A total of 234 explants treated with Agrobacterium resulted in an 80.3% regeneration efficiency, with 13.3% of regenerated plants exhibiting partial or complete albino phenotypes. Amplicon sequencing of edited progeny revealed substitutions, insertions, and deletions at the gRNA target sites or flanking regions of all FaPDS homoeologous copies. Our results provide effective methods of tissue culture and transformation for the efficient application of CRISPR-mediated gene editing in cultivated strawberry.

plant biology↗

bioRxiv2023

KoNA: Korean Nucleotide Archive as a New Data Repository for Nucleotide Sequence Data

During the last decade, generation and accumulation of petabase-scale high-throughput sequencing data have resulted in ethical and technical challenges, including access to human data, and transfer, storage, and sharing of enormous amount of data. To promote data-driven research in biology, the Korean government announced that all the biological data generated from government-funded research projects should be deposited in the Korea BioData Station (K-BDS), which consists of multiple databases for individual data types. We introduce the Korean Nucleotide Archive (KoNA), a repository for nucleotide sequence data. As of July 2022, the Korean Read Archive in KoNA has collected over 477 TB of raw next generation sequencing data from several national genome projects. To ensure data quality and prepare for international alignment, a standard operating procedure (SOP) was adopted, which is similar to the International Nucleotide Sequence Database Collaboration. The SOP includes quality control processes for submitted data and metadata using an automated pipeline followed by manual examination. To ensure fast and stable data transfer, a high-speed transmission system called GBox is used in KoNA. Furthermore, the data uploaded to or downloaded from KoNA through GBox can be readily processed in a cloud-computing service for genomic data analysis called Bio-Express. This seamless coupling of KoNA, GBox, and Bio-Express enhances data experience including submission, access, and analysis of raw nucleotide sequences. KoNA not only satisfies the unmet needs for a national sequence repository in Korea, but also provides datasets to researchers globally and contribute to advances in genomics. KoNA is available at https://www.kobic.re.kr/kona/.

genomics↗

bioRxiv2023

Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to vaccination

Single-cell RNA sequencing can to resolve transcriptional features from large numbers of individual immune cells, but techniques capable of resolving the variable regions of B cell receptors (BCR) - defining features that confer antigen specificity to B cells - remain limited, especially from widely-used 3'-barcoded libraries. Here, we report a method that for recovering paired, full-length variable region sequences of the BCRs from 3'-barcoded single-cell whole transcriptome libraries. We first verified this method could produce accurate, full-length BCR sequences. We then applied this method to profile antigen-specific B cell responses elicited against the capsular polysaccharide of Streptococcus pneumoniae serotype 3 (ST3) by glycoconjugate vaccines in infant rhesus macaques. Using our method, we defined features of the BCR associated with specificity for the ST3 antigen and showed that these sequence characteristics are present in multiple vaccinated monkeys, indicating a convergent response to vaccination. These results demonstrate the utility of our method to resolve key features of the B cell repertoire and for profiling antigen-specific responses elicited by vaccination.

immunology↗

bioRxiv2023

Multiple brain activation patterns for the same task

Meaningful variation in internal states that impacts cognition and behavior remains challenging to discover and characterize. Here we leveraged trial-to-trial fluctuations in the brain-wide signal recorded using functional MRI to test if distinct sets of brain regions are activated on different trials when accomplishing the same task. Across three different perceptual decision-making experiments, we estimated the brain activations for each trial. We then clustered the trials based on their similarity using modularity-maximization, a data-driven classification method. In each experiment, we found multiple distinct but stable subtypes of trials, suggesting that the same task can be accomplished in the presence of widely varying brain activation patterns. Surprisingly, in all experiments, one of the subtypes exhibited strong activation in the default mode network, which is typically thought to decrease in activity during tasks that require externally focused attention. The remaining subtypes were characterized by activations in different task-positive areas. The default mode network subtype was characterized by behavioral signatures that were similar to the other subtypes exhibiting activation with task-positive regions. These findings demonstrate that the same perceptual decision-making task is accomplished through multiple brain activation patterns.

neuroscience↗

bioRxiv2022

Npas4-mediated dopaminergic regulation of fear memory states

Amygdala circuitry encodes associations between conditioned stimuli and aversive unconditioned stimuli, and also controls fear expression (Pape and Pare, 2010). However, whether and how irrelevant information for unpaired conditioned stimuli (CS-) is discretely processed, and how it was influenced by stress remain unknown. CS- memory is retrievable immediately after fear conditioning, but then becomes silent after memory consolidation in mice. Synaptic pathway from the lateral to the anterior basal amygdala gates the expression of CS- memory, depending upon Npas4-mediated Drd4 synthesis. The upregulation of Npas4-Drd4 axis, which is precluded by corticosterone, shifts functional states of neural engrams for CS- memory toward silent states and limits its retrievability. In here, we demonstrate the cellular and molecular mechanisms regulating the functional states of neural engrams, which can be switched or maintained, supporting discriminative memory.

neuroscience↗

bioRxiv2022

Idiosyncratic relation between human brain activity and behavior

Research in neuroscience often assumes universal neural mechanisms, but increasing evidence points towards sizeable individual differences in brain activations. What remains unclear is the extent of the idiosyncrasy and whether different types of analyses are associated with different levels of idiosyncrasy. Here we develop a new method for addressing these questions. The method consists of computing the within-subject reliability and subject-to-group similarity of brain activations and submitting these values to a computational model that quantifies the relative strength of group- and subject-level factors. We apply this method to a perceptual decision-making task (N=50) and find that activations related to task, reaction time (RT), and confidence are influenced equally strongly by group- and subject-level factors. Both group- and subject-level factors are dwarfed by a noise factor, though higher levels of smoothing increases their contributions relative to noise. Overall, our method allows for the quantification of group- and subject-level factors of brain activations and thus provides a more detailed understanding of the idiosyncrasy levels in brain activations.

neuroscience↗