Biology subjects

Bae, Y.

Publications and source records attributed to Bae, Y..

32 records · Page 2Linked to original sources

bioRxiv2023

Operator model for evolutionary dynamics

Drift, selection, and mutation are integral evolutionary factors. In this article, operator model is newly suggested to intuitively represent those evolutionary factors into mathematical operators, and to ultimately offer unconventional methodology for understanding evolutionary dynamics. To be specific, each of the drift, selection, and mutation was respectively interpreted as operator which in essence is a random matrix that acts upon the vector which contains population distribution information. The simulation results from the operator model coincided with the previous theoretical results for beneficial mutation accumulation rate in concurrent and successional regimes for asexually reproducing case. Furthermore, beneficial mutation accumulation in strong drift regime for asexually reproducing case was observed from the simulation while allowing the interactions of mutations with diverse selection coefficients. Lastly, methods to justify, reinforce, apply, and expand the operator model were discussed to scrutinize the implications of the model. With its unique characteristics, the operator model is expected to broaden perspective and to offer effective methodology for understanding the evolutionary process.

evolutionary biology↗

bioRxiv2023

Global gene expression of human malaria parasite liver stages throughout intrahepatocytic development

Plasmodium falciparum (Pf) is causing the greatest malaria burden, yet the liver stages (LS) of this most important parasite species have remained poorly studied. Here, we used a human liver-chimeric mouse model in combination with a novel fluorescent PfNF54 parasite line (PfNF54cspGFP) to isolate PfLS-infected hepatocytes and generate transcriptomes that cover the major LS developmental phases in human hepatocytes. RNA-seq analysis of early Pf LS trophozoites two days after infection, revealed a central role of translational regulation in the transformation of the extracellular invasive sporozoite into intracellular LS. The developmental time course gene expression analysis indicated that fatty acid biosynthesis, isoprenoid biosynthesis and iron metabolism are sustaining LS development along with amino acid metabolism and biosynthesis. Countering oxidative stress appears to play an important role during intrahepatic LS development. Furthermore, we observed expression of the variant PfEMP1 antigen-encoding var genes, and we confirmed expression of PfEMP1 protein during LS development. Transcriptome comparison of the late Pf liver stage schizonts with P. vivax (Pv) late liver stages revealed highly conserved gene expression profiles among orthologous genes. A notable difference however was the expression of genes regulating sexual stage commitment. While Pv schizonts expressed markers of sexual commitment, the Pf LS parasites were not sexually committed and showed expression of gametocytogenesis repression factors. Our results provide the first comprehensive gene expression profile of the human malaria parasite Pf LS isolated during in vivo intrahepatocytic development. This data will inform biological studies and the search for effective intervention strategies that can prevent infection.

microbiology↗

bioRxiv2022

Survivin is a mechanosensitive cell cycle regulator in vascular smooth muscle cells

Stiffened arteries are a pathology of atherosclerosis, hypertension, and coronary artery disease and a key risk factor for cardiovascular disease events. The increased stiffness of arteries triggers the hypermigration and hyperproliferation of vascular smooth muscle cells (VSMCs), leading to neointimal hyperplasia and accelerated neointima formation, but the mechanism of this trigger is not known. Our analyses of whole-transcriptome microarray data sets from mouse VSMCs cultured on stiff hydrogels simulating arterial pathology and from injured mouse femoral arteries revealed 80 genes that were differentially regulated (74 upregulated and 6 downregulated) relative to expression in control VSMCs cultured on soft hydrogels and in uninjured femoral arteries. A functional enrichment analysis revealed that these stiffness-sensitive genes are linked to cell cycle progression and proliferation. Furthermore, we found that survivin, a member of the inhibitor of apoptosis protein family, mediates stiffness-sensitive cell cycling and proliferation in vivo and in vitro as determined by gene network and pathway analyses, RT-qPCR, and immunoblotting. The stiffness signal is mechanotransduced via FAK and Rac signaling to regulate survivin expression, establishing a regulatory pathway for how the stiffness of the cellular microenvironment affects VSMC behaviors. Our findings indicate that survivin is necessary for VSMC cycling and proliferation and regulates stiffness-responsive phenotypes.

cell biology↗

bioRxiv2022

Survivin Regulates Intracellular Stiffness and Extracellular Matrix Production in Vascular Smooth Muscle Cells

Vascular dysfunction is a common cause of cardiovascular diseases characterized by the narrowing and stiffening of arteries, such as atherosclerosis, restenosis, and hypertension. Arterial narrowing results from the aberrant proliferation of vascular smooth muscle cells (VSMCs) and their increased synthesis and deposition of extracellular matrix (ECM) proteins. These, in turn, are modulated by arterial stiffness, but the mechanism for this is not fully understood. We found that survivin (an inhibitor of apoptosis) is an important regulator of stiffness-mediated ECM synthesis and intracellular stiffness in VSMCs. Whole-transcriptome analysis and cell culture experiments showed that survivin expression is upregulated in injured femoral arteries in mice and in human VSMCs cultured on stiff fibronectin-coated hydrogels. Suppressed expression of survivin in human VSMCs and mouse embryonic fibroblasts decreased the stiffness-mediated expression of ECM components implicated in arterial stiffness, namely, collagen-I, fibronectin, and lysyl oxidase. By contrast, expression of these proteins was upregulated by the overexpression of survivin in human VSMCs cultured on soft hydrogels. Atomic force microscopy analysis showed that suppressed or enhanced expression of survivin decreases or increases intracellular stiffness, respectively. These findings suggest a novel mechanism by which survivin modulates arterial stiffness.

cell biology↗

bioRxiv2022

Rac rather than Rho drives the early transcriptional response to extracellular matrix stiffness and mediates repression of ATF3

The Rho family GTPases, Rac and Rho, play critical roles in transmitting mechanical information contained within the extracellular matrix (ECM) to the cell. Rac and Rho have well described roles in regulating stiffness-dependent actin remodeling, proliferation and motility. However, much less is known about the relative roles of these GTPases in stiffness-dependent transcription, particularly at the genome-wide level. Here, we selectively inhibited Rac and Rho in mouse embryonic fibroblasts cultured on deformable substrata and used RNA sequencing to elucidate and compare the contribution of these GTPases to the early transcriptional response to ECM stiffness. Surprisingly, we found that Rac activation is almost exclusively responsible for the initial transcriptional response to ECM stiffness. We also identified Activating Transcription Factor 3 (ATF3) as a major target of stiffness/Rac signaling and show that ATF3 repression by ECM stiffness connects the stiffness-dependent activation of Rac to the induction of cyclin D1.

cell biology↗

bioRxiv2022

Korean endemic species no more: on the occurrence of Pelophylax chosenicus in China

Understanding species distribution is the first requirement to work on their behaviour, conservation, and phylogeography. Over the last decades, the number of species described on the Korean peninsula has significantly increased, but areas around the boundaries of the Korean peninsula still have to be surveyed for the presence of these species, especially where the environment is similar and connected. Here, we conducted surveys in the continuous landscapes of the Republic of Korea, the Democratic Peoples Republic of Korea and the Peoples Republic of China to determine the range of the Gold-spotted pond frog, Pelophylax chosenicus. The surveys were conducted between 2016 and 2020 through visual and call encounters. We also used molecular tools to confirm the species identity of the northernmost population, in China, sequencing the mitochondrial DNA 16S gene fragment. We then determined the importance of landscape types for the species, and especially rice paddies, and used landscape models to define suitable habitats across the region. We found the species to be widespread in low elevation wetlands along the coast of the Yellow Sea, with two isolated populations on the south-east of the Korean Peninsula, and the northernmost population in the vicinity of Dandong in PR China. As this species is listed as threatened in the Republic of Korea, knowing its exact distribution will be important for conservation practices, and this first record for PR China provides a baseline for further surveys.

ecology↗

bioRxiv2021

Extracellular Vesicles Deliver Mitochondria and HSP27 Protein to Protect the Blood-Brain Barrier

Ischemic stroke causes brain endothelial cell (BEC) death and damages tight junction integrity of the blood-brain barrier (BBB). We harnessed the innate mitochondrial load of endothelial cell-derived extracellular vesicles (EVs) and utilized mixtures of EV/exogenous heat shock protein 27 (HSP27) as a one-two punch strategy to increase BEC survival (via EV mitochondria) and preserve their tight junction integrity (via HSP27 effects). We demonstrated that the medium-to-large (m/lEV) but not small EVs (sEV) transferred their mitochondrial load, which subsequently colocalized with the mitochondrial network of the recipient primary human BECs. BECs treated with m/lEVs increased relative ATP levels and displayed superior mitochondrial function. Importantly, m/lEVs isolated from oligomycin (mitochondrial complex V inhibitor) or rotenone (mitochondrial complex I inhibitor)-exposed BECs (RTN-m/lEVs or OGM-m/lEVs) did not increase BECs ATP levels compared to naive m/lEVs. In contrast, RTN-sEV and OGM-sEV functionality in increasing cellular ATP levels was minimally impacted in comparison to naive sEVs. Intravenously administered m/lEVs showed a reduction in brain infarct sizes compared to vehicle-injected mice in a mouse middle cerebral artery occlusion model of ischemic stroke. We formulated binary mixtures of human recombinant HSP27 protein with EVs: EV/HSP27 and ternary mixtures of HSP27 and EV with cationic polymer poly (ethylene glycol)-b-poly (diethyltriamine): (PEG-DET/HSP27)/EV. (PEG-DET/HSP27)/EV and EV/HSP27 mixtures decreased the paracellular permeability of small and large molecular mass fluorescent tracers in oxygen glucose-deprived primary human BECs. This one-two-punch approach to increase BEC metabolic function and tight junction integrity is a promising strategy for BBB protection and prevention of long-term neurological dysfunction post-ischemic stroke. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/466491v5_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@dc5493org.highwire.dtl.DTLVardef@134ad7forg.highwire.dtl.DTLVardef@16a8929org.highwire.dtl.DTLVardef@15315bc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMedium-to-large extracellular vesicles (m/lEVs), not small EVs contain mitochondria C_LIO_LIm/lEVs increased ATP and mitochondrial function in brain endothelial cells (BECs) C_LIO_LIm/lEVs from oligomycin-exposed BECs did not increase recipient BEC ATP levels C_LIO_LIIntravenously injected m/lEVs reduced brain infarct sizes in a mouse stroke model C_LIO_LIEV/HSP27 mixtures reduced small and large dextran molecule permeability across BECs C_LI

bioengineering↗

bioRxiv2021

miRNA-34c suppresses osteosarcoma progression in vivo by targeting Notch and E2F

The expression of microRNAs (miRNAs) is dysregulated in many types of cancers including osteosarcoma (OS) due to genetic and epigenetic alterations. Among these, miR-34c, an effector of tumor suppressor P53 and an upstream negative regulator of Notch signaling in osteoblast differentiation, is dysregulated in OS. Here, we demonstrated a tumor suppressive role of miR-34c in OS progression using in vitro assays and in vivo genetic mouse models. We found that miR-34c inhibits the proliferation and the invasion of metastatic OS cells, which resulted in reduction of the tumor burden and increased overall survival in an orthotopic xenograft model. Moreover, the osteoblast specific over expression of miR-34c increased survival in the osteoblast specific p53 mutant OS mouse model. We found that miR-34c regulates the transcription of several genes in Notch signaling (NOTCH1, JAG1 and HEY2) and in p53 mediated cell cycle and apoptosis (CCNE2, E2F5, E2F2 and HDAC1). More interestingly, we found that the metastatic free survival probability was increased among a patient cohort from TARGET OS which has lower expression of direct targets of miR-34c that was identified in our transcriptome analysis such as E2F5 and NOTCH1. In conclusion, we demonstrate that miR-34c is a tumor suppressive miRNA in OS progression in vivo. In addition, we highlight the therapeutic potential of targeting miR-34c in OS.

cancer biology↗

bioRxiv2020

Development of A Decellularized Meniscus Matrix-Based Nanofibrous Scaffold for Meniscus Tissue Engineering

The meniscus plays a critical role in knee mechanical function but is commonly injured given its central load bearing role. In the adult, meniscus repair is limited, given the low number of endogenous cells, the density of the matrix, and the limited vascularity. Menisci are fibrocartilaginous tissues composed of a micro-/nano-fibrous extracellular matrix (ECM) and a mixture of chondrocyte-like and fibroblast-like cells. Here, we developed a fibrous scaffold system that consists of bioactive components (decellularized meniscus ECM (dME) within a poly(e-caprolactone) material) fashioned into a biomimetic morphology (via electrospinning) to support and enhance meniscus cell function and matrix production. This work supports that the incorporation of dME into synthetic nanofibers increased hydrophilicity of the scaffold, leading to enhanced meniscus cell spreading, proliferation, and fibrochondrogenic gene expression. This work identifies a new biomimetic scaffold for therapeutic strategies to substitute or replace injured meniscus tissue. STATEMENT OF SIGNIFICANCEIn this study, we show that a scaffold electrospun from a combination of synthetic materials and bovine decellularized meniscus ECM provides appropriate signals and a suitable template for meniscus fibrochondrocyte spreading, proliferation, and secretion of collagen and proteoglycans. Material characterization and in vitro cell studies support that this new bioactive material is susceptible to enzymatic digestion and supports meniscus-like tissue formation.

bioengineering↗

bioRxiv2020

Mechanosensitive Expression of Lamellipodin Governs Cell Cycle Progression and Intracellular Stiffness

Cells exhibit pathological behaviors in response to increased extracellular matrix (ECM) stiffness, including accelerated cell proliferation and migration [1-9], which are correlated with increased intracellular stiffness and tension [2, 3, 10-12]. The biomechanical signal transduction of ECM stiffness into relevant molecular signals and resultant cellular processes is mediated through multiple proteins associated with the actin cytoskeleton in lamellipodia [2, 3, 10, 11, 13]. However, the molecular mechanisms by which lamellipodial dynamics regulate cellular responses to ECM stiffening remain unclear. Previous work described that lamellipodin, a phosphoinositide- and actin filament-binding protein that is known mostly for controlling cell migration [14-21], promotes ECM stiffness-mediated early cell cycle progression [2], revealing a potential commonality between the mechanisms controlling stiffness-dependent cell migration and those controlling cell proliferation. However, i) whether and how ECM stiffness affects the levels of lamellipodin expression and ii) whether stiffness-mediated lamellipodin expression is required throughout cell cycle progression and for intracellular stiffness have not been explored. Here, we show that the levels of lamellipodin expression in cells are significantly increased by a stiff ECM and that this stiffness-mediated lamellipodin upregulation persistently stimulates cell cycle progression and intracellular stiffness throughout the cell cycle, from the early G1 phase to M phase. Finally, we show that both Rac activation and intracellular stiffening are required for the mechanosensitive induction of lamellipodin. More specifically, inhibiting Rac1 activation in cells on stiff ECM reduces the levels of lamellipodin expression, and this effect is reversed by the overexpression of activated Rac1 in cells on soft ECM. We thus propose that lamellipodin is a critical molecular lynchpin in the control of mechanosensitive cell cycle progression and intracellular stiffness.

cell biology↗

bioRxiv2020

Machine learning approach reveals heterogeneous responses to FAK and Rho GTPases inhibition on smooth muscle spheroid formation

Atherosclerosis and vascular injury are characterized by neointima formation caused by the aberrant accumulation and proliferation of vascular smooth muscle cells (VSMCs) within the vessel wall. Understanding how to control VSMCs would advance the effort to treat vascular disease. However, the response to treatments aimed at VSMCs is often different among patients with the same disease condition, suggesting patient-specific heterogeneity in VSMCs. Here, we present an experimental and computational method called HETEROID (Heterogeneous Spheroid), which examines the heterogeneity of the responses to drug treatments at the single-spheroid level by combining a VSMC spheroid model and machine learning (ML) analysis. First, we established a VSMC spheroid model that mimics neointima formation induced by atherosclerosis and vascular injury. We found that FAK-Rac/Rho, but not Cdc42, pathways regulate the VSMC spheroid formation through N-cadherin. Then, to identify the morphological subpopulations of drug-perturbed spheroids, we used an ML framework that combines deep learning-based spheroid segmentation and morphological clustering analysis. Our ML approach reveals that FAK, Rac, Rho, and Cdc42 inhibitors differentially affect the spheroid morphology, suggesting there exist multiple distinct pathways governing VSMC spheroid formation. Overall, our HETEROID pipeline enables detailed quantitative characterization of morphological changes in neointima formation, that occurs in vivo, by single-spheroid analysis of various drug treatments.

cell biology↗

bioRxiv2018

ATRAID, a genetic factor that regulates the clinical action of nitrogen-containing bisphosphonates on bone.

Nitrogen-containing bisphosphonates (N-BPs), such as alendronate, are the most widely prescribed medications for diseases involving bone, with nearly 200 million prescriptions written annually. Recently, widespread use of N-BPs has been challenged due to the risk of rare but traumatic side effects such as atypical femoral fracture (AFFs) and osteonecrosis of the jaw (ONJ). N-BPs bind to and inhibit farnesyl diphosphate synthase (FDPS), resulting in defects in protein prenylation. Yet it remains poorly understood what other cellular factors might allow N-BPs to exert their pharmacological effects. Here, we performed genome-wide studies in cells and patients to identify the poorly characterized gene, ATRAID. Loss of ATRAID function results in selective resistance to N-BP-mediated loss of cell viability and the prevention of alendronate-mediated inhibition of prenylation. ATRAID is required for alendronate inhibition of osteoclast function, and ATRAID-deficient mice have impaired therapeutic responses to alendronate in both postmenopausal and senile (old age) osteoporosis models. Lastly, we performed exome sequencing on patients taking N-BPs that suffered ONJ or an AFF. ATRAID is one of three genes that contain rare non-synonymous coding variants in patients with ONJ or AFF that is also differentially expressed in poor outcome groups of patients treated with N-BPs. We functionally validated this patient variation in ATRAID as conferring cellular hypersensitivity to N-BPs. Our work adds key insight into the mechanistic action of N-BPs and the processes that might underlie differential responsiveness to N-BPs in people. One Sentence SummaryATRAID is essential for responses to the commonly prescribed osteoporosis drugs nitrogen-containing bisphosphonates. OverlineBONE

genomics↗

bioRxiv2018

Loop-mediated isothermal amplification assay for Enterococcus sp., E. coli and S. aureus in chicken

Bacterial chondronecrosis with osteomyelitis (BCO) is a major cause of lameness in broiler chicken, and results in serious economic losses worldwide. Although the pathogenesis mechanism leading to lameness is not entirely understood, some strains of Enterococcus sp., avian pathogenic Escherichia coli, or Staphylococcus aureus have been long recognized as important causative pathogens. To prevent the progression of Enterococcus sp., avian pathogenic E. coli, or S. aureus infections, we developed rapid, sensitive, and convenient diagnostic assays using loop-mediated isothermal amplification (LAMP). Entero-Common-LAMP assays were developed for a simultaneous detection of eight Enterococcus species. To target specific microorganisms, seven Entero-Specific-LAMP assays for E. faecalis, E. faecium, E. hirae, E. gallinarum, E. avium, E. durans and E. cecorum, and E. coli-LAMP and S. aureus-LAMP assays, were developed. Considering the prevalence and economic impact of Enterococcus sp., E. coli, and S. aureus, the developed ten different LAMP assays have a considerable potential as routine diagnostic methods in the field or in resource-limited environments.

microbiology↗

bioRxiv2017

Deconvolution Of Subcellular Protrusion Heterogeneity And The Underlying Actin Regulator Dynamics From Live Cell Imaging

Cell protrusion is morphodynamically heterogeneous at the subcellular level. However, the mechanistic understanding of protrusion activities is usually based on the ensemble average of actin regulator dynamics at the cellular or population levels. Here, we establish a machine learning-based computational framework called HACKS (deconvolution of Heterogeneous Activity Coordination in cytosKeleton at a Subcellular level) to deconvolve the subcellular heterogeneity of lamellipodial protrusion in migrating cells. HACKS quantitatively identifies distinct subcellular protrusion phenotypes from highly heterogeneous protrusion activities and reveals their underlying actin regulator dynamics at the leading edge. Furthermore, it can identify specific subcellular protrusion phenotypes susceptible to pharmacological perturbation and reveal how actin regulator dynamics are changed by the perturbation. Using our method, we discovered accelerating protrusion phenotype in addition to fluctuating and periodic protrusions. Intriguingly, the accelerating protrusion was driven by the temporally coordinated actions between Arp2/3 and VASP: initiated by Arp2/3-mediated actin nucleation, and then accelerated by VASP-mediated actin elongation. We were able to confirm it by pharmacological perturbations using CK666 and Cytochalasin D, which specifically reduced strong accelerating protrusion activities. Taken together, we have demonstrated that HACKS allows us to discover the fine differential coordination of molecular dynamics underlying subcellular protrusion heterogeneity via a machine learning analysis of live cell imaging data.

cell biology↗