Biology subjects

Park, J.

Publications and source records attributed to Park, J..

At least 307 records · Page 17Linked to original sources

bioRxiv2023

A 128-ch area-efficient neurochemical-sensing front-end for FSCV recordings of dopamine

Neurochemical recordings rely on electrochemical reactions of electroactive neurotransmitters such as dopamine, serotonin, and norepinephrine. This electrochemical technique allows for highly sensitive monitoring of neurotransmitters in the brain. Traditionally, single-channel carbon-fiber microelectrode recordings have been considered the gold standard method. However, an alternative approach involves the use of a microelectrode array, which enables high spatiotemporal resolution imaging of electroactive neurotransmitters. To enable neurochemical imaging using a microelectrode array, the development of a high-density current-sensing microchip is necessary. Here, a neurochemical microchip is introduced, featuring a 128-channel current sensing front-end capable of supporting 128 parallel neurochemical measurements. The designed amplifier array employs a highly scalable resistive feedback transimpedance amplifier design. This design allows for a large neurochemical dynamic range of {+/-}5{micro}A with a noise performance as low as 0.22nARMS. With the integration of this microchip, in vivo neurochemical imaging of dopamine can be achieved with high spatiotemporal resolution.

bioengineering↗

bioRxiv2023

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

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

neuroscience↗

bioRxiv2023

Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome

Membrane-bound particles in plasma are composed of exosomes, microvesicles, and apoptotic bodies and represent [~]1-2% of the total protein composition. Proteomic interrogation of this subset of plasma proteins augments the representation of tissue-specific proteins, representing a "liquid biopsy," while enabling the detection of proteins that would otherwise be beyond the dynamic range of liquid chromatography-tandem mass spectrometry of unfractionated plasma. We have developed an enrichment strategy (Mag-Net) using hyper-porous strong-anion exchange magnetic microparticles to sieve membrane-bound particles from plasma. The Mag-Net method is robust, reproducible, inexpensive, and requires <100 L plasma input. Coupled to a quantitative data-independent mass spectrometry analytical strategy, we demonstrate that we can collect results for >37,000 peptides from >4,000 plasma proteins with high precision. Using this analytical pipeline on a small cohort of patients with neurodegenerative disease and healthy age-matched controls, we discovered 204 proteins that differentiate (q-value < 0.05) patients with Alzheimers disease dementia (ADD) from those without ADD. Our method also discovered 310 proteins that were different between Parkinsons disease and those with either ADD or healthy cognitively normal individuals. Using machine learning we were able to distinguish between ADD and not ADD with a mean ROC AUC = 0.98 {+/-} 0.06.

biochemistry↗

bioRxiv2023

A Spatial Transcriptomics based Label-Free Method for Assessment of Human Stem Cell Distribution and Effects in a Mouse Model of Lung Fibrosis

Recently, cell therapy has emerged as a promising treatment option for various disorders. Given the intricate mechanisms of action (MOA) and heterogenous distribution in target tissues inherent to cell therapy, it is necessary to develop more sophisticated, unbiased approaches to evaluate the distribution of administered cells and the molecular changes at a microscopic level. In this study, we present a label-free approach for assessing the tissue distribution of administered human mesenchymal stem cells (hMSCs) and their MOA, leveraging spatially resolved transcriptomics (ST) analysis. We administered hMSCs to mouse model of lung fibrosis and utilized ST to visualize the spatial distribution of hMSCs within the tissue. This was achieved by capitalizing on interspecies transcript differences between human and mouse. Furthermore, we could examine molecular changes associated with the spatial distribution of hMSCs. We suggest that our method has the potential to serve as an effective tool for various cell-based therapeutic agents.

bioinformatics↗

bioRxiv2023

The Arabidopsis SWEET1 and SWEET2 uniporters recognize similar substrates despite differences in subcellular localization

Sugars Will Eventually be Exported Transporters (SWEETs) are central for sugar allocation in plants. The SWEET family is vast, with approximately 20 homologs in most plant genomes. Despite extensive research on their structures and molecular functions, it is still unclear how diverse SWEETs recognize their substrates. Previous work using SweetTrac1, a biosensor constructed by the intramolecular fusion of a conformation-sensitive fluorescent protein in the plasma membrane transporter SWEET1 from Arabidopsis thaliana, identified common features in the transporters substrates. Here, we report SweetTrac2, a new biosensor based on the Arabidopsis vacuole membrane transporter SWEET2 and use it to explore the substrate specificity of this second protein. Our results show that SWEET1 and SWEET2 recognize similar substrates but some with different affinities. Sequence comparison and mutagenesis analysis support the conclusion that the differences in affinity depend on non-specific interactions involving key residues in the binding pocket. Furthermore, SweetTrac2 can be an effective tool for monitoring sugar transport at vacuolar membranes that would be otherwise challenging to study.

biochemistry↗

bioRxiv2023

Single cell transcriptome analysis of cavernous tissues reveals the key roles of pericytes in diabetic erectile dysfunction

Erectile dysfunction (ED) affects a significant proportion of men aged 40-70 and is caused by cavernous tissue dysfunction. Presently, the most common treatment for ED is phosphodiesterase 5 inhibitors; however, this is less effective in patients with severe vascular disease such as diabetic ED. Therefore, there is a need for development of new treatment, which requires a better understanding of the cavernous microenvironment and cell-cell communications under diabetic condition. Pericytes are vital in penile erection; however, their dysfunction due to diabetes remains unclear. In this study, we performed single-cell RNA sequencing to understand the cellular landscape of cavernous tissues and cell type-specific transcriptional changes in diabetic ED. We found a decreased expression of genes associated with collagen or extracellular matrix organization and angiogenesis in diabetic fibroblasts, chondrocytes, myofibroblasts, valve-related lymphatic endothelial cells, and pericytes. Moreover, the newly identified pericyte-specific marker, Limb-bud and Heart (Lbh), in mouse and human cavernous tissues, clearly distinguishing pericytes from smooth muscle cells. Cell-cell interaction analysis revealed that pericytes are involved in angiogenesis, adhesion, and migration by communicating with other cell types in the corpus cavernosum; however, these interactions were highly reduced under diabetic conditions. Lbh expression is low in diabetic pericytes, and overexpression of LBH prevents erectile function by regulating neurovascular regeneration. Furthermore, the LBH-interacting proteins (Crystallin Alpha B and Vimentin) were identified in mouse cavernous pericytes through LC-MS/MS analysis, indicating that their interactions were critical for maintaining pericyte function. Thus, our study reveals novel targets and insights into the pathogenesis of ED in patients with diabetes. Impact statementSingle-cell RNA sequencing analysis of diabetic mouse cavernous tissue revealed that LBH as a novel pericyte marker and may interact with Crystallin Alpha B and Vimentin to promote neurovascular regeneration.

bioinformatics↗

bioRxiv2023

IAMSAM : Image-based Analysis of Molecular signatures using the Segment-Anything Model

Spatial transcriptomics is a cutting-edge technique that combines gene expression data with spatial information, allowing researchers to study gene expression patterns within tissue architecture. Here, we present IAMSAM, a user-friendly web-based tool for analyzing spatial transcriptomics data focusing on morphological features. IAMSAM accurately segments tissue images using the Segment-anything model, allowing for the semi-automatic selection of regions of interest based on morphological signatures. Furthermore, IAMSAM provides downstream analysis, such as identifying differentially expressed genes, enrichment analysis, and cell type prediction within the selected regions. With its simple interface, IAMSAM empowers researchers to explore and interpret heterogeneous tissues in a streamlined manner.

bioinformatics↗

bioRxiv2023

The Notch-Pdgfr beta axis suppresses brown adipocyte progenitor differentiation in early postnatal mice

De novo brown adipogenesis holds potential in combating the epidemics of obesity and diabetes. However, the identity of brown adipocyte progenitor cells (APCs) and their regulation have not been extensively studied. Here through in vivo lineage tracing, we observed that PDGFR{beta}+ pericytes give rise to developmental brown adipocytes, but not to those in adult homeostasis. In contrast, TBX18+ pericytes contribute to brown adipogenesis throughout both developmental and adult stages, though in a depot-specific manner. Mechanistically, Notch inhibition in PDGFR{beta}+ pericytes promotes brown adipogenesis through the downregulation of PDGFR{beta}. Furthermore, inhibition of Notch signaling in PDGFR{beta}+ pericytes mitigates HFHS (high-fat, high-sucrose) induced glucose and metabolic impairment in both developmental and adult stages. Collectively, these findings show that the Notch/PDGFR{beta} axis negatively regulates developmental brown adipogenesis, and its repression promotes brown adipose tissue expansion and improves metabolic health. HighlightsO_LIPDGFR{beta}+ pericytes act as an essential developmental brown APC. C_LIO_LITBX18+ pericytes contribute to brown adipogenesis in a depot-specific manner. C_LIO_LIInhibiting Notch-Pdgfr{beta} axis promotes brown APC adipogenesis. C_LIO_LIEnhanced postnatal brown adipogenesis improves metabolic health in adult stage. C_LI

developmental biology↗

bioRxiv2023

Ultra-wide angle neuroimaging: insights into immersive scene representation

While humans experience the visual environment in a panoramic 220{degrees} view, traditional functional MRI setups are limited to display images like postcards in the central 10-15{degrees} of the visual field. Thus, it remains unknown how a scene is represented in the brain when perceived across the full visual field. Here, we developed a novel method for ultra-wide angle visual presentation and probed for signatures of immersive scene representation. To accomplish this, we bounced the projected image off angled-mirrors directly onto a custom-built curved screen, creating an unobstructed view of 175{degrees}. Scene images were created from custom-built virtual environments with a compatible wide field-of-view to avoid perceptual distortion. We found that immersive scene representation drives medial cortex with far-peripheral preferences, but surprisingly had little effect on classic scene regions. That is, scene regions showed relatively minimal modulation over dramatic changes of visual size. Further, we found that scene and face-selective regions maintain their content preferences even under conditions of central scotoma, when only the extreme far-peripheral visual field is stimulated. These results highlight that not all far-peripheral information is automatically integrated into the computations of scene regions, and that there are routes to high-level visual areas that do not require direct stimulation of the central visual field. Broadly, this work provides new clarifying evidence on content vs. peripheral preferences in scene representation, and opens new neuroimaging research avenues to understand immersive visual representation.

neuroscience↗

bioRxiv2023

PPIAT:Target mass spectrometry based Protein-Protein interaction analytics tool

MotivationThe formation of protein networking is critical for understanding the biological functions of proteins and the underlying mechanisms of disease. To gain insights into target proteins that interact with a particular disease, we need to profiling all the proteins involved in the disease beforehand. However, the profiling results may not necessarily match with an experimental target protein. Therefore, it is necessary to identify physical protein-protein interactions (PPIs) using various methods. The cross-linking mass spectrometry (XL-MS) method is a representative approach to identify physical interactions between proteins, but there are many challenges in calculating theoretical mass values for application to target mass spectrometry. ResultsThe research team developed PPIAT, which integrates information on reviewed human proteins, protein-protein interactions, cross-linkers, enzymes, and modifications. All functions are available for free on the web application. Availability and implementationThe PPIAT is available at www.ppiat.cnu.ac.kr Contactkimlab@cnu.ac.kr

bioinformatics↗

bioRxiv2023

A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle

Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin-like proteins (PhLPs) to facilitate the folding of essential eukaryotic proteins. Using cryoEM and biochemical analyses, we determine the ATP-driven cycle of TRiC-PFD-PhLP2A interaction. In the open TRiC state, PhLP2A binds to the chambers equator while its N-terminal H3-domain binds to the apical domains of CCT3/4, thereby displacing PFD from TRiC. ATP-induced TRiC closure rearranges the contacts of PhLP2A domains within the closed chamber. In the presence of substrate, actin and PhLP2A segregate into opposing chambers, each binding to the positively charged inner surfaces formed by CCT1/3/6/8. Notably, actin induces a conformational change in PhLP2A, causing its N-terminal helices to extend across the inter-ring interface to directly contact a hydrophobic groove in actin. Our findings reveal an ATP-driven PhLP2A structural rearrangement cycle within the TRiC chamber to facilitate folding. Highlights- Structural analysis of TRiC-mediated folding cycle with cochaperones PhLP2A and PFD. - The interactions of PhLP2A and PFD with TRiC are mutually exclusive. - PhLP2A domains interact in a subunit-specific manner with the TRiC chamber. - PhLP2A domains are rearranged in ATP-closed TRiC to contact actin across the ring interface

biophysics↗

bioRxiv2023

READRetro: Natural Product Biosynthesis Planning with Retrieval-Augmented Dual-View Retrosynthesis

Elucidating the biosynthetic pathways of natural products has been a major focus of biochemistry and pharmacy. However, predicting the whole pathways from target molecules to metabolic building blocks remains a challenge. Here we propose READRetro as a practical bio-retrosynthesis tool for planning the biosynthetic pathways of natural products. READRetro effectively resolves the tradeoff between generalizability and memorability in bio-retrosynthesis by implementing two separate modules; each module is responsible for either generalizability or memorability. Specifically, READRetro utilizes a rule-based retriever for memorability and an ensemble of two dual-representation-based deep learning models for generalizability. Through extensive experiments, READRetro was demonstrated to outperform existing models by a large margin in terms of both generalizability and memorability. READRetro was also capable of predicting the known pathways of complex plant secondary metabolites such as monoterpene indole alkaloids, demonstrating its applicability in the real-world bio-retrosynthesis planning of natural products. A website (https://readretro.net) and open-source code have been provided for READRetro, a practical tool with state-of-the-art performance for natural product biosynthesis research.

bioinformatics↗

bioRxiv2023

A deep population reference panel of tandem repeat variation

Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3,550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.

genomics↗

bioRxiv2023

PPP1R3B is a metabolic switch that shifts hepatic energy storage from lipid to glycogen

Obesity is a growing worldwide epidemic that carries numerous metabolic complications including increased risk of type 2 diabetes (T2D), cardiovascular disease (CVD), and non-alcoholic fatty liver disease (NAFLD). Multiple genome-wide association studies (GWAS) have associated the PPP1R3B locus with cardiometabolic traits including fasting glucose and insulin levels (T2D traits), plasma lipids (CVD traits), and indications of hepatic steatosis and liver damage (NAFLD traits)1-5. The PPP1R3B gene encodes the glycogen regulatory protein PPP1R3B (also known as GL) which has an established role in liver glycogen metabolism and plasma glucose homeostasis6,7. The metabolic and NAFLD GWAS single nucleotide polymorphisms (SNPs) in this region, which are all in high linkage disequilibrium, result in increased liver PPP1R3B expression and hepatic glycogen accumulation, but have provided conflicting results on the impacts on hepatic steatosis and liver damage. Here we investigate the consequences of both Ppp1r3b overexpression and deletion in mouse and cell models and find that dysregulated Ppp1r3b expression in either direction promotes metabolic dysfunction and liver injury. Hepatocyte overexpression of Ppp1r3b increases hepatic glycogen storage, prolongs fasting blood glucose levels, and confers protection from hepatic steatosis, but increases plasma ALT in aged animals. Conversely, deletion of hepatocyte Ppp1r3b eliminates hepatic glycogen, causes impaired glucose disposal, and results in hepatic steatosis with age or high sucrose diet. We investigated the metabolic pathways contributing to steatosis and found that Ppp1r3b deletion and diminished glycogenesis diverts the storage of exogenous glucose to hepatic triglycerides (TG), and stored liver lipids are preferentially used for energy during fasting through lipid oxidation and ketogenesis. Further, we interrogated two large human biobank cohorts and found carriers of SNPs associated with increased PPP1R3B expression have increased plasma glucose, decreased hepatic fat, and lower plasma lipids, while putative loss-of-function (pLoF) variant carriers have increased hepatic fat and elevated plasma ketones and lipids, consistent with the results seen in our mouse models. These findings suggest hepatic PPP1R3B serves as a metabolic switch favoring hepatic energy storage as glycogen instead of TG.

molecular biology↗

bioRxiv2023

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↗

bioRxiv2023

Comparative Features of Calretinin, Calbindin and Parvalbumin Expressing Interneurons in Mouse and Monkey Primary Visual and Frontal Cortices

Much is known about differences in pyramidal cells across cortical areas and species, but studies of interneurons have focused on comparisons within single cortical areas and/or species. Here we quantified the distribution and somato-dendritic morphology of interneurons expressing one or more of the calcium binding proteins (CaBPs) calretinin (CR), calbindin (CB) and/or parvalbumin (PV) in mouse (Mus musculus) versus rhesus monkey (Macaca mulatta) in two functionally and cytoarchitectonically distinct regions- the primary visual and frontal cortical areas. The density, laminar distribution and morphology of interneurons were assessed in serial brain sections using immunofluorescent multi-labeling, stereological counting and 3D reconstructions. There were significantly higher densities of CB+ and PV+ neurons in visual compared to frontal areas in both species. The main species difference was the significantly greater density and proportion of CR+ interneurons and lower extent of CaBP co-expression in monkey compared to mouse cortices. Cluster analyses revealed that the somato-dendritic morphology of layer 2-3 inhibitory interneurons is more dependent on CaBP expression than on species and area. Only modest effects of species were observed for CB+ and PV+ interneuron morphologies, while CR+ neurons showed no difference. By contrast to pyramidal cells which show highly distinctive area- and species-specific features, here we found more subtle differences in the distribution and features of interneurons across areas and species. These data yield insight into how nuanced differences in the population organization and properties of neurons may underlie specializations in cortical regions to confer species and area-specific functional capacities. Key PointsO_LISomato-dendritic morphology of distinct interneurons did not substantially scale and vary across areas and species- differences were mainly dependent on CaBP expression. C_LIO_LICortical diversity in inhibitory function across areas and species is thus likely to be derived from differential laminar distribution and densities of distinct interneuron subclasses. C_LIO_LIIn contrast to pyramidal cells which differ widely in distribution and morphology across areas and species, the features of interneurons appears to be relatively more conserved across areas and species. C_LI

neuroscience↗

bioRxiv2023

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of Oxford Nanopore Technologies (ONT) PromethION sequencing, including those using proximity ligation and show that newer, higher accuracy ONT reads substantially improve assembly quality.

bioinformatics↗

bioRxiv2023

Clinically relevant concurrent BRAF and MEK inhibition alters differentiation states and sensitizes BRAF V600E-mutated high-grade gliomas to immune checkpoint blockade

Resistance to BRAF plus MEK inhibition (BRAFi+MEKi) in BRAFV600E-mutant gliomas drives rebound, progression, and high mortality, yet it remains poorly understood. This study addresses the urgent need to develop treatments for BRAFi+MEKi-resistant glioma in novel mouse models and patient-derived materials. BRAFi+MEKi reveals glioma plasticity by heightening cell state transitions along glial differentiation trajectories, giving rise to astrocyte- and immunomodulatory oligodendrocyte (OL)-like states. PD-L1 upregulation in OL-like cells links cell state transitions to tumor evasion, possibly orchestrated by Galectin-3. BRAFi+MEKi induces interferon response signatures, tumor infiltration, and suppression of T cells. Combining BRAFi+MEKi with immune checkpoint inhibition enhances survival in a T cell-dependent manner, reinvigorates T cells, and outperforms individual or sequential therapies in mice. Elevated PD-L1 expression in BRAF-mutant versus BRAF-wildtype glioblastoma supports the rationale for PD-1 inhibition in patients. These findings underscore the potential of targeting glioma plasticity and highlight combination strategies to overcome therapy resistance in BRAFV600E-mutant HGG. In briefXing et al. show that combined BRAF and MEK inhibitor (BRAFi+MEKi) treatment induces cell state transitions in BRAFV600E-mutant high-grade glioma cells linked with programmed death-ligand (PD-L1) upregulation and T cell suppression, potentially orchestrated through the secretion of galectin-3. These tumor-intrinsic adaptations may be overcome by concurrent immune checkpoint inhibition (ICI), as demonstrated in murine studies, offering novel therapeutic opportunities. HighlightsO_LIBRAFV600E-mutant HGG exhibits cell plasticity induced by BRAFi+MEKi, which links cell state transitions towards glial differentiation with immune evasion C_LIO_LIBRAFi+MEKi enhances anti-tumor immunity and simultaneously suppresses T cells via PD-L1 upregulation C_LIO_LIBRAF-mutant glioblastoma has elevated PD-L1 expression compared to BRAF-wildtype counterparts, providing a criterion for PD-1 inhibition therapy C_LIO_LIConcurrent BRAFi+MEKi and immune checkpoint inhibition enhance T cell-mediated anti-tumor activity and boost survival more effectively than sequential treatment in mice, guiding clinical translation C_LI

cancer biology↗