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65 result(s) for "Lee, Ha-Rim"
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Genetic diversity and population structure analysis of Forsythia ovata, a Korean endemic, based on genotyping-by-sequencing
The perennial shrub Forsythia ovata Nakai, native to the Korean Peninsula, has a highly restricted natural habitat, occurring only in a small area within the Baekdudaegan Mountain Range located in Gangwon-do Province. These characteristics give this species high conservation value, but there is a significant lack of genetic concerning about its populations for conservation purposes. In this study, we utilized genotyping-by-sequencing (GBS) to examine the genetic diversity and population structure of F. ovata . Our analysis including 5,017 single nucleotide polymorphisms (SNPs) from 72 individuals, representing nine distinct populations. The results revealed a mean expected heterozygosity ( He ) of 0.212, indicating a moderate level of genetic diversity within the species. Additionally, a relatively low levels of genetic differentiation ( F ST ) and high gene flow ( N m ) between populations were detected. The analysis of molecular variance (AMOVA) results indicated that most genetic variation occurred within individuals, accounting for 86.66% of the total variance. In contrast, only 6.90% and 6.44% of the molecular variance was attributed to differences among individuals and between populations, respectively. Considering the results of Bayesian structure analysis on the basis of ∆ K , principal coordinate analysis and phylogenetic analysis, we propose two management units for conservation. In addition, given the current conditions faced by F. ovata , both in situ and ex situ conservation should be considered for some populations (SG and BD).
The complete chloroplast genome sequences of eight Orostachys species: Comparative analysis and assessment of phylogenetic relationships
We analyzed the complete chloroplast genomes of eight Orostachys species and compared the sequences to those of published chloroplast genomes of the congeneric and closely related genera, Meterostachys and Hylotelephium . The total chloroplast genome length of thirteen species, including the eight species analyzed in this study and the five species analyzed in previous studies, ranged from 149,860 ( M . sikokianus ) to 151,707 bp ( H . verticillatum ). The overall GC contents of the genomes were almost identical (37.6 to 37.8%). The thirteen chloroplast genomes each contained 113 unique genes comprising 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Among the annotated genes, sixteen genes contained one or two introns. Although the genome structures of all Orostachys and Hylotelephium species were identical, Meterostachys differed in structure due to a relatively large gene block ( trnS-GCU-trnS-GGA ) inversion. The nucleotide diversity among the subsect. Orostachys chloroplast genomes was extremely low in all regions, and among the subsect. Appendiculatae , genus Orostachys , and all thirteen chloroplast genomes showed high values of Pi (>0.03) in one, five, or three regions. The phylogenetic analysis showed that Orostachys formed polyphyly, and subsect. Orostachys and Appendiculatae were clustered with Hylotelephium and Meterostachys , respectively, supporting the conclusion that each subsection should be considered as an independent genus. Furthermore, the data supported the taxonomic position of O . margaritifolia and O . iwarenge f. magnus , which were treated as synonyms for O . iwarenge in a previous study, as independent taxa. Our results suggested that O . ramosa and O . japonica f. polycephala were individual variations of O . malacophylla and O . japonica , respectively. The exact taxonomic position of O . latielliptica and the phylogenetic relationship among the three species, O . chongsunensis , O . malacophylla and O . ramosa , should be a topic of future study.
The complete chloroplast genome sequences of six Hylotelephium species: Comparative genomic analysis and phylogenetic relationships
To evaluate the phylogenetic relationships between Hylotelephium and Orostachys , and to provide important information for further studies, we analyzed the complete chloroplast genomes of six Hylotelephium species and compared the sequences to those of published chloroplast genomes of congeneric species and species of the closely related genus , Orostachys . The total chloroplast genome length of nineteen species, including the six Hylotelephium species analyzed in this study and the thirteen Hylotelephium and Orostachys species analyzed in previous studies, ranged from 150,369 bp ( O . minuta ) to 151,739 bp ( H . spectabile ). Their overall GC contents were almost identical (37.7–37.8%). The chloroplast genomes of the nineteen species contained 113 unique genes comprising 79 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Among the annotated genes, fourteen genes contained one intron, and two genes contained two introns. The chloroplast genomes of the nineteen Hylotelephium and Orostachys species had identical structures. Additionally, the large single copy (LSC), inverted repeat (IR), and small single copy (SSC) junction regions were conserved in the Hylotelephium and Orostachys species. The nucleotide diversity between the Hylotelephium chloroplast genomes was extremely low in all regions, and only one region showed a high Pi value (>0.03). In all nineteen chloroplast genomes, six regions had a high Pi value (>0.03). The phylogenetic analysis showed that the genus delimitation could not be clearly observed even in this study because Hylotelephium formed a paraphyly with subsect. Orostachys of the genus Orostachys . Additionally, the data supported the taxonomic position of Sedum taqeutii , which was treated as a synonym for H . viridescens in previous studies, as an independent taxon.
Phylogenomic study of Orostachys using Angiosperms353: polyphyly of subsections with taxonomic consequences
The genus (Crassulaceae) has been subject to considerable disagreement regarding its taxonomic boundaries because of extensive morphological similarities among taxa and widespread intraspecific variation. Additionally, previous phylogenetic studies based on molecular markers have consistently demonstrated that the two subsections of (subsect. and subsect. ) do not constitute a monophyletic group, leaving the generic boundaries unresolved to date. Therefore, we aimed to evaluate the generic boundaries and accurate taxonomic positions of individual taxa via the Angiosperms353 target enrichment approach. We analyzed a total of 43 individuals representing 25 taxa from 5 genera, including 14 taxa and closely related genera such as and . High-quality genomic data were obtained, with an average gene recovery rate of 99.1% (349.5/353 genes) and substantial sequence length recovery (average 1,223 bp per locus), resulting in concatenated datasets of 397-400 kbp sequences. Phylogenetic analyses using concatenation and coalescent-based approaches with datasets based on different threshold values were conducted. Phylogenetic analyses revealed exceptionally high concordance across all phylogenetic trees, with most nodes having UFBoot values ≥95% and LPP values ≥0.95. Our findings showed the polyphyletic nature of , with O. subsect. forming a monophylum distinct from O. subsect. Appendiculatae and related genera. O. subsect. constituted a monophyletic group rather than exhibiting a paraphyletic relationship with Hylotelephium. and clustered with and , respectively. , , , and formed independent clades. Unlike previous studies, our Angiosperms353 data demonstrate that O. subsect. forms a completely independent lineage, representing the most important finding of this study. The high support values confirm the reliability of our results and demonstrate the effectiveness of the Angiosperms353 approach in resolving complex evolutionary relationships within morphologically challenging plant groups. Our findings support treating and as synonyms of and , respectively, while recognizing the endemic Korean species , , , and as independent taxa.
Kuwanon V Inhibits Proliferation, Promotes Cell Survival and Increases Neurogenesis of Neural Stem Cells
Neural stem cells (NSCs) have the ability to proliferate and differentiate into neurons and glia. Regulation of NSC fate by small molecules is important for the generation of a certain type of cell. The identification of small molecules that can induce new neurons from NSCs could facilitate regenerative medicine and drug development for neurodegenerative diseases. In this study, we screened natural compounds to identify molecules that are effective on NSC cell fate determination. We found that Kuwanon V (KWV), which was isolated from the mulberry tree (Morus bombycis) root, increased neurogenesis in rat NSCs. In addition, during NSC differentiation, KWV increased cell survival and inhibited cell proliferation as shown by 5-bromo-2-deoxyuridine pulse experiments, Ki67 immunostaining and neurosphere forming assays. Interestingly, KWV enhanced neuronal differentiation and decreased NSC proliferation even in the presence of mitogens such as epidermal growth factor and fibroblast growth factor 2. KWV treatment of NSCs reduced the phosphorylation of extracellular signal-regulated kinase 1/2, increased mRNA expression levels of the cyclin-dependent kinase inhibitor p21, down-regulated Notch/Hairy expression levels and up-regulated microRNA miR-9, miR-29a and miR-181a. Taken together, our data suggest that KWV modulates NSC fate to induce neurogenesis, and it may be considered as a new drug candidate that can regenerate or protect neurons in neurodegenerative diseases.
Characterization and classification of rat neural stem cells and differentiated cells by comparative metabolic and lipidomic profiling
It is necessary to characterize and classify neural stem cells (NSCs) and differentiated cells (DCs) for potential use of NSC to treat neurodegenerative diseases. We therefore performed an analysis of NSCs and DCs using gas chromatography mass spectrometry (GC-MS) and direct infusion mass spectrometry (DI-MS) with elaborate multivariate statistical analysis for the characterization and classification of rat NSCs and DCs. GC-MS and DI-MS detected a total of 92 metabolites and lipids in NSCs and DCs, and the levels of 72 of them differed significantly between NSCs and DCs. The optimal model for partial least squares (PLS) discriminant analysis was constructed by applying 3 and 2 PLS components with a unit-variance scaling method for classifying NSCs and DCs based on the data obtained in the GC-MS and DI-MS analyses, respectively. The obtained results from PCA and PLS-DA suggest that creatinine, lactic acid, lysine, glutamine, glycine, pyroglutamic acid, PG 18:1/20:2, PS 18:0/20:2, PI 18:0/20:3, PC 16:0/20:4, PI 16:0/20:4, and PI 18:1/20:4 were the main contributors that provided distinct characteristics of NSCs and DCs. The results of this study suggest objective and complementary criteria for the characterization and classification of NSCs and DCs for potential clinical applications.
The complete chloroplast genome sequence of Orostachys minuta (Crassulaceae)
The chloroplast (cp) genome sequence is determined and analyzed for Orostachys minuta for the first time. The cp genome was 150,369 bp in length, containing a large single-copy (LSC) of 82,795 bp and a small single-copy (SSC) of 16,854 bp, which were separated by a pair of 25,360 bp inverted repeats (IRs). The overall G + C content of the O. minuta cp genome amounted to 37.7%. In total, 113 unique genes were annotated, consisting of 79 protein-coding genes (PCGs), 30 transfer RNAs (tRNAs), and four ribosomal RNAs (rRNAs). Among these genes, 18 contained one or two introns. A maximum-likelihood (ML) phylogenetic analysis based on 33 taxa showed that O. minuta formed a clade with O. japonica. This study will provide a baseline as well as valuable molecular phylogenomic information for various future studies to determine the taxonomic position and phylogenetic relationships of the genus Orostachys.
Characterization of the chloroplast genome of Meterostachys sikokianus (Makino) Nakai (Crassulaceae) and its phylogenetic analysis
is a monotypic genus of Crassulaceae, though its phylogenetic position remains unclear. Here, we report the complete chloroplast (cp) genome sequence of using the Illumina high-throughput sequencing approach. The cp genome was 149,860 bp in length, containing a large single copy (LSC) of 82,293 bp and a small single copy (SSC) of 16,879 bp, which were separated by a pair of 25,344 bp inverted repeats (IRs). The overall GC content of the cp genome was 37.6%. A total of 113 unique genes were annotated, consisting of 79 protein coding genes (PCGs), 30 transfer RNAs (tRNAs), and four ribosomal RNAs (rRNAs). Among these genes, eighteen contained one or two introns. A maximum-likelihood (ML) phylogenetic analysis based on 30 accessions of Crassulaceae showed that was most closely related to and .
Potential of a cerium hexaboride electron gun as a monochromatic and high current beam via a virtual source mode
Advancements in surface science hinge critically on the evolution of high-performance electron sources, which are essential for achieving the precision level and resolutions required for nanoscale characterization, modification, and fabrication. Cerium hexaboride (CeB 6 ) electron guns, despite being underutilized, stand out for their advantages such as high brightness and operability under high-vacuum environment. This study explores the intrinsic properties and emission conditions of CeB 6 electron guns, demonstrating their remarkable performance potential. By carefully controlling the heating temperature and local electric field in a novel virtual source mode, we significantly enhance the electron emission characteristics of CeB 6 as a thermal electron source. Operating in the proposed virtual source mode, CeB 6 electron guns can reduce chromatic aberrations, offering significant opportunities for high-resolution patterning, spectroscopy, and applications requiring high emission currents. The micrometer-sized electron source exhibits a high angular current density of 48 mA/sr and an energy distribution of 0.32 eV. Additionally, the stability of the virtual source mode was determined to be ± 0.071% at a beam current of 370 nA, a substantial improvement over the ± 0.36% stability value in the crossover mode. With the development of the proposed electron source, new avenues for advanced material characterization, nanoscale fabrication, and precise modifications of material properties will be explored.
High-Performance Compact Pre-Lens Retarding Field Energy Analyzer for Energy Distribution Measurements of an Electron Gun
The energy distribution of an electron gun is one of the most important characteristics determining the performance of electron beam-based instruments, such as electron microscopes and electron energy loss spectroscopes. For accurate measurements of the energy distribution, this study presents a novel retarding field energy analyzer (RFEA) with the feature of an additional integrated pre-lens, which enables an adjustment of beam trajectory into the analyzer. The advantages of this analyzer are its compact size and simple electrode configuration. According to trajectory simulation theories, the optimum condition arises when the incident electron beam inside the RFEA is focused on the center of a retarding electrode. Comparing I–V curves depending on whether the pre-lens working or not, it is confirmed that the use of the pre-lens dramatically improves the energy resolution and efficiency of the signal acquisition process. The pre-lens RFEA was applied to characterize a Schottky electron gun under various temperatures and extraction voltages as operational conditions. When the tip temperature was increased by 50 K, we were able to measure an energy distribution broadening of 13.8 meV with the proposed pre-lens RFEA. The relative standard deviation of energy distribution was 0.7% for each working condition.