A5075058925- Genomics and Phylogenetic Studies
- Genetic and Kidney Cyst Diseases
- Chromosomal and Genetic Variations
- Epigenetics and DNA Methylation
- Microbial Community Ecology and Physiology
- Advanced Proteomics Techniques and Applications
- Evolution and Genetic Dynamics
- Genetics, Aging, and Longevity in Model Organisms
- Developmental Biology and Gene Regulation
- Bacterial Identification and Susceptibility Testing
- Bacterial biofilms and quorum sensing
- CRISPR and Genetic Engineering
- Neuroinflammation and Neurodegeneration Mechanisms
- Neonatal Respiratory Health Research
- Bacteriophages and microbial interactions
- Renal and related cancers
- Protist diversity and phylogeny
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Ubiquitin and proteasome pathways
- Stress Responses and Cortisol
- Congenital heart defects research
- Single-cell and spatial transcriptomics
- Connexins and lens biology
- Birth, Development, and Health
Ulsan National Institute of Science and Technology
2016-2025
Institute for Basic Science
2019-2025
Center for Genomic Science
2020
The University of Texas at Austin
2009-2016
Karger Publishers (Switzerland)
2015
The Gurdon Institute
2013
University of Cambridge
2013
The University of Texas Health Science Center at San Antonio
2009
To explore the origins and consequences of tetraploidy in African clawed frog, we sequenced Xenopus laevis genome compared it to related diploid X. tropicalis genome. We characterize allotetraploid origin by partitioning its into two homoeologous subgenomes, marked distinct families 'fossil' transposable elements. On basis activity these elements age hundreds unitary pseudogenes, estimate that progenitor species diverged around 34 million years ago (Ma) combined form an 17–18 Ma. More than...
Abstract Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell developmental model systems, notably the genus Xenopus . Here we report a high-quality reference genome sequence for western clawed frog, tropicalis , along with draft chromosome-scale sequences three distantly related emerging frog species, Eleutherodactylus coqui Engystomops pustulosus Hymenochirus boettgeri Frog chromosomes have remained remarkably...
Abstract Proteins play major roles in most biological processes; as a consequence, protein expression levels are highly regulated. While extensive post‐transcriptional, translational and degradation control clearly influence concentration functionality, it is often thought that abundances primarily determined by the of corresponding mRNAs. Hence surprisingly, recent study showed orthologous nematode fly proteins correlate better than their mRNA abundances. We tested if this phenomenon...
The mechanisms linking systems-level programs of gene expression to discrete cell biological processes in vivo remain poorly understood. In this study, we have defined such a program for multi-ciliated epithelial cells (MCCs), type critical proper development and homeostasis the airway, brain reproductive tracts. Starting from genomic analysis cilia-associated transcription factor Rfx2, used bioinformatics approaches gain insights into molecular basis cilia assembly function. Moreover,...
For a long time, it has been assumed that the only role of sperm at fertilization is to introduce male genome into egg. Recently, ideas have emerged epigenetic state nucleus could influence transcription in embryo. However, conflicting reports challenged existence marks on genes, and there are no functional tests supporting marking embryonic gene expression. Here, we show epigenetically programmed regulate By comparing development sperm- spermatid-derived frog embryos, programming for...
Gram-negative bacteria produce outer membrane vesicles (OMVs) that package and deliver proteins, small molecules, DNA to prokaryotic eukaryotic cells. The molecular details of OMV biogenesis have not been fully elucidated, but peptidoglycan-associated proteins tether the underlying peptidoglycan shown be critical for formation in multiple Enterobacteriaceae. In this study, we demonstrate OprF OprI, OprL, impact production OMVs by opportunistic pathogen Pseudomonas aeruginosa. Interestingly,...
ABSTRACT Antimicrobial-resistant bacteria pose a serious threat in the clinic. This is particularly true for opportunistic pathogens that possess high intrinsic resistance. Though many studies have focused on understanding acquisition of bacterial resistance upon exposure to antimicrobials, mechanisms controlling are not well understood. In this study, we subjected model superbug Pseudomonas aeruginosa 14 antimicrobials under highly controlled conditions and assessed its response using...
The inner mitochondrial membrane (IMM) proteome plays a central role in maintaining physiology and cellular metabolism. Various important biochemical reactions such as oxidative phosphorylation, metabolite production, biogenesis are conducted by the IMM proteome, mitochondria-targeted therapeutics have been developed for proteins, which is deeply related various human metabolic diseases including cancer neurodegenerative diseases. However, topology of remains largely unclear because lack...
Organ-on-a-chip, which recapitulates the dynamics of in vivo vasculature, has emerged as a promising platform for studying organ-specific vascular beds. However, its practical advantages identifying vascular-targeted drug delivery systems (DDS) over traditional vitro models remain underexplored. This study demonstrates reliability and efficacy organ-on-a-chip screening efficient DDS by comparing performance with that conventional transwell, both designed to simulate blood–brain barrier...
The Gram-negative bacterium Pseudomonas aeruginosa is a common cause of chronic airway infections in individuals with the heritable disease cystic fibrosis (CF). After prolonged colonization CF lung, P. becomes highly resistant to host clearance and antibiotic treatment; therefore, understanding how this evolves during infection important for identifying beneficial adaptations that could be targeted therapeutically. To identify potential adaptive traits infection, we carried out global...
Shotgun proteomics using mass spectrometry is a powerful method for protein identification but suffers limited sensitivity in complex samples. Integrating peptide identifications from multiple database search engines promising strategy to increase the number of and reduce volume unassigned tandem spectra. Existing methods pool statistical significance scores such as p-values or posterior probabilities peptide-spectrum matches (PSMs) after high scoring peptides have been assigned spectra,...
The dopamine system in the midbrain is essential for volitional movement, action selection, and reward-related learning. Despite its versatile roles, it contains only a small set of neurons brainstem. These are especially susceptible to Parkinson's disease prematurely degenerate course progression, while discovery new therapeutic interventions has been disappointingly unsuccessful. Here, we show that O-GlcNAcylation, an post-translational modification various types cells, critical...
The Western clawed frog Xenopus tropicalis is a diploid model system for both genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report chromosome-scale assembly of genome, improving previously published draft genome through use new algorithms, additional sequence data, addition dense genetic map. improved enables mapping specific traits (e.g., sex locus or Mendelian mutants) characterization synteny with other tetrapods. We also an annotation that...
ITGBL1 promotes chondrogenesis and protects joint cartilage from osteoarthritis by inhibiting integrin-extracellular matrix interaction.
While comparatively few amphibian species have been described on the North East Asian mainland in last decades, several subject of taxonomical debates relation to Yellow sea. Here, we sampled Dryophytes sp. treefrogs from Republic Korea, Democratic People's Korea and China clarify status this clade around sea determine impact level change treefrogs' phylogenetic relationships. Based genetics, call properties, adult morphology, tadpole morphology niche modelling, determined segregated D....
An ideal cancer therapeutic strategy involves the selective killing of cells without affecting surrounding normal cells. However, researchers have failed to develop such methods for achieving cell death because shared features between cancerous and In this study, we developed a called cancer-specific insertions-deletions (InDels) attacker (CINDELA) selectively induce using CRISPR-Cas system. CINDELA utilizes previously unexplored idea introducing CRISPR-mediated DNA double-strand breaks...
The specialized cell types of the mucociliary epithelium (MCE) lining respiratory tract enable continuous airway clearing, with its defects leading to chronic diseases. molecular mechanisms driving fate acquisition and temporal specialization during epithelial development remain largely unknown. Here, we profile developing Xenopus MCE from pluripotent mature stages by single-cell transcriptomics, identifying multipotent early progenitors that execute multilineage cues before specializing...
When a duplicate gene has no apparent loss-of-function phenotype, it is commonly considered that the phenotype been masked as result of functional redundancy with remaining paralog. This supported by indirect evidence showing multi-copy genes show phenotypes less often than single-copy and direct tests masking using select sets. Here we take systematic genome-wide RNA interference approach to assess in paralog pairs Caenorhabditis elegans genome. Remarkably, contrast expectations, find makes...
Mammalian target of rapamycin (mTOR) signaling is a core pathway in cellular metabolism, and control the mTOR by shows potential for treatment metabolic diseases. In this study, we employed new proximity biotin-labeling method using promiscuous biotin ligase (pBirA) to identify unknown elements rapamycin-induced interactome on FK506-rapamycin binding (FRB) domain living cells. FKBP25 showed strongest labeling FRB–pBirA presence rapamycin. Immunoprecipitation immunofluorescence experiments...
Chondrocytes secrete massive extracellular matrix (ECM) molecules that are produced, folded, and modified in the endoplasmic reticulum (ER). Thus, ER-associated degradation (ERAD) complex-which removes misfolded unfolded proteins to maintain proteostasis ER- plays an indispensable role building maintaining cartilage. Here, we examined necessity of ERAD complex chondrocytes for cartilage formation maintenance. We show gene expression is exponentially increased during chondrogenesis,...