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Yong-Jin Park

Publications and source records attributed to Yong-Jin Park.

10 recordsLinked to original sources
PubMed2026

CRISPR/Cas9-Mediated Mutagenesis of OsERF94 Enhances Pre-Harvest Sprouting in Rice.

Pre-harvest sprouting (PHS), where seeds germinate on panicles before harvest under humid conditions, is a serious global issue in cereal crop production, including rice. Fine-mapping of the previously reported chromosome 4 locus identified OsERF94 as a strong candidate gene for functional validation. In this study, we investigated the role of OsERF94 in PHS using CRISPR/Cas9 gene editing. The CRISPR/Cas9-mediated mutagenesis of OsERF94 induced frameshift mutations, resulting in a loss-of-function of OsERF94 in the 1-I-ET and 2-D-ET lines. The 1-I-ET and 2-D-ET lines exhibited significantly higher germination rates under PHS conditions compared to the wild type, indicating increased susceptibility to PHS. Whole-genome re-sequencing confirmed that few or no mutations could be detected at off-target candidate sites in both edited lines, ensuring the precision of the CRISPR/Cas9 gene editing. A transcriptome analysis revealed altered expression patterns of several GA-related genes, including OsLOL1, OsKO3, OsGA3ox2, and OsGA2ox5 in the OsERF94 mutant lines. The up-regulation of GA biosynthetic genes and the down-regulation of GA deactivation genes observed in both the OsERF94 mutant lines suggest possible alterations in GA metabolism during the early stages of PHS. Transient luciferase reporter assays using a single-luciferase system suggested that OsERF94 may be associated with changes in the promoter activities of several GA- and ethylene-related genes. These findings suggest that OsERF94 may contribute to the regulation of PHS, potentially through moderation of GA- and ethylene-related pathways. Overall, this study improves our understanding of the molecular role of OsERF94 in PHS and highlights its potential as a target for the genetic improvement of PHS resistance in rice-breeding programs.

OsERF94↗
PubMed2006

Reverse transcriptase domain sequences from Mungbean (Vigna radiata) LTR retrotransposons: sequence characterization and phylogenetic analysis.

The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were amplified from mungbean (Vigna radiata) genome using degenerate primers, cloned and sequenced. Among these 34% and 65% of respective clones of copia and gypsy RT sequences possessed stop codons or frame-shifts or both. The RT sequences corresponding to both the groups exhibit significant levels of heterogeneity. Presence of mungbean copia and gypsy RT sequences in other papilionoid legumes of the same (Phaseoleae) and different lineages (Loteae, Trifoleae, Cicereae) indicates existence of these elements prior to the radiation of papilionoid legumes and also supports the recent interpretations of close relationship between Phaseoleae and Loteae tribes of Papilionoideae subfamily. On the other hand significant homologies of some mungbean copia as well as gypsy RT sequences with those of unrelated plant species suggest their origin from different plant lineages and also that heterogeneous population of related elements were already existed throughout (even before the divergence of monocot and dicot) the evolution of these genera from their common ancestor.

Amino Acid Sequence↗
PubMed2006

Genetic diversity and phylogenetic relationship in AA Oryza species as revealed by Rim2/Hipa CACTA transposon display.

CACTA is a class 2 transposon, that is very abundantly present in plant genomes. Using Rim2/Hipa CACTA transposon display (hereafter Rim2/Hipa-TD), we analyzed several A-genome diploid Oryza species that have a high distribution of the CACTA motifs. High levels of polymorphism were detected within and between the Oryza species. The African taxa, O. glaberrima and O. barthii, both showed lower levels of polymorphism than the Asian taxa, O. sativa, O. rufipogon, and O. nivara. However, O. longistaminata, another African taxon, showed levels of polymorphism that were similar to the Asian taxa. The Latin American taxon, O. glumaepatula, and the Australian taxon, O. meridionalis, exhibited intermediate levels of polymorphism between those of the Asian and African taxa. The lowest level of polymorphism was observed in O. glaberrima (32.1%) and the highest level of polymorphism was observed in O. rufipogon (95.7%). The phylogenetic tree revealed three major groups at the genetic similarity level of 0.409. The first group consisted of three Asian taxa, O. sativa, O. rufipogon and O. nivara. The second group consisted of three African taxa, O. glaberrima, O. barthii, O. longistaminata, and an American taxon, O. glumaepatula. The third group contained an Australian taxon, O. meridionalis. The clustering patterns of these species matched well with their geographical origins. Rim2/Hipa-TD appears to be a useful marker system for studying the genetic diversity and species relationships among the AA diploid Oryza species.

Chromosome Mapping↗
PubMed2004

Neuropathology in rhinosinusitis.

Pathophysiologic differences in neural responses to hypertonic saline (HTS) were investigated in subjects with acute sinusitis (n = 25), subjects with chronic fatigue syndrome (CFS) with nonallergic rhinitis (n = 14), subjects with active allergic rhinitis (AR; n = 17), and normal (n = 20) subjects. Increasing strengths of HTS were sprayed into their nostrils at 5-minute intervals. Sensations of nasal pain, blockage, and drip increased with concentration and were significantly elevated above normal. These parallels suggested activation of similar subsets of afferent neurons. Urea and lysozyme secretion were dose dependent in all groups, suggesting that serous cell exocytosis was one source of urea after neural stimulation. Only AR and normal groups had mucin dose responses and correlations between symptoms and lysozyme secretion (R(2) = 0.12-0.23). The lysozyme dose responses may represent axon responses in these groups. The neurogenic stimulus did not alter albumin (vascular) exudation in any group. Albumin and mucin concentrations were correlated in sinusitis, suggesting that nonneurogenic factors predominated in sinusitis mucous hypersecretion. CFS had neural hypersensitivity (pain) but reduced serous cell secretion. HTS nasal provocations identified significant, unique patterns of neural and mucosal dysregulation in each rhinosinusitis syndrome.

Acute Disease↗
PubMed2004

Further evidence of microcolinearity between barley and rice genomes at two orthologous regions.

Two genetic markers, BCD135 and RZ567 were used to select clones from genomic BAC libraries of barley and rice for sequencing and subsequent sequence comparisons. A set of two orthologous BACs each from barley and rice was selected by hybridization with BCD135 and RZ567 cDNA probes. A total of 556-kb stretch including two barley BACs (773K135 and 745C13) and two orthologous rice BACs (24K23 and 49D11) was completely sequenced. Comparative sequence analysis between orthologous BACs from the two species revealed presence of two conserved genes at BCD135 region and only one gene at the RZ567 regions. The two conserved genes were in the same order and orientation in both the species however, separated by significantly larger distance in barley. The larger distance between two barley genes was mainly due to presence of different retrotransposable elements and their derivatives (78.9% of the intergenic region) that expanded the barley BCD135 region at the rate of 9.1X. An additional gene of unknown function was also inserted along with several retrotransposable elements between two conserved genes at barley BCD135 region. More genome expansion rate (10X) around barley RZ567 locus was estimated by extremely high proportion (> 70%) of retrotransposons. Among different retrotransposons, the Sabrina elements rather than BARE were more prevalent in both the regions. Contrary to it, the BCD135 region of rice was composed of only 17.1% retrotransposable elements and no significant retrotransposons except 14 miniature inverted transposable elements (MITEs) were observed in its RZ567 region. The sequence comparison between orthologous regions of rice and barley genomes was useful for gene identification and determination of individual gene structure indicating the possibility of effective utilization of rice genome sequences in understanding the large genome of barley. (The sequence data described in this paper have been submitted to the GenBank data library under the accession no. AF474072 (773K14), AF474071 (745C13), AF480497 (24K23) and AF480496 (49D11)).

Chromosomes, Artificial, Bacterial↗
PubMed2004

Gene loss and movement in the maize genome.

Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridization of two closely related progenitors. To investigate the fate of its genes after tetraploidization, we analyzed the sequence of five duplicated regions from different chromosomal locations. We also compared corresponding regions from sorghum and rice, two important crops that have largely collinear maps with maize. The split of sorghum and maize progenitors was recently estimated to be 11.9 Mya, whereas rice diverged from the common ancestor of maize and sorghum approximately 50 Mya. A data set of roughly 4 Mb yielded 206 predicted genes from the three species, excluding any transposon-related genes, but including eight gene remnants. On average, 14% of the genes within the aligned regions are noncollinear between any two species. However, scoring each maize region separately, the set of noncollinear genes between all four regions jumps to 68%. This is largely because at least 50% of the duplicated genes from the two progenitors of maize have been lost over a very short period of time, possibly as short as 5 million years. Using the nearly completed rice sequence, we found noncollinear genes in other chromosomal positions, frequently in more than one. This demonstrates that many genes in these species have moved to new chromosomal locations in the last 50 million years or less, most as single gene events that did not dramatically alter gene structure.

Chromosomes, Artificial, Bacterial↗
PubMed2002

Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley.

Barley (Hordeum vulgare L.) is one of the most important large-genome cereals with extensive genetic resources available in the public sector. Studies of genome organization in barley have been limited primarily to genetic markers and sparse sequence data. Here we report sequence analysis of 417.5 kb DNA from four BAC clones from different genomic locations. Sequences were analyzed with respect to gene content, the arrangement of repetitive sequences and the relationship of gene density to recombination frequencies. Gene densities ranged from 1 gene per 12 kb to 1 gene per 103 kb with an average of 1 gene per 21 kb. In general, genes were organized into islands separated by large blocks of nested retrotransposons. Single genes in apparent isolation were also found. Genes occupied 11% of the total sequence, LTR retrotransposons and other repeated elements accounted for 51.9% and the remaining 37.1% could not be annotated.

Chromosomes, Artificial, Bacterial↗
PubMed2002

Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes.

Orthologous regions in barley, rice, sorghum, and wheat were studied by bacterial artificial chromosome sequence analysis. General microcolinearity was observed for the four shared genes in this region. However, three genic rearrangements were observed. First, the rice region contains a cluster of 48 predicted small nucleolar RNA genes, but the comparable region from sorghum contains no homologous loci. Second, gene 2 was inverted in the barley lineage by an apparent unequal recombination after the ancestors of barley and wheat diverged, 11-15 million years ago (mya). Third, gene 4 underwent direct tandem duplication in a common ancestor of barley and wheat 29-41 mya. All four of the shared genes show the same synonymous substitution rate, but nonsynonymous substitution rates show significant variations between genes 4a and 4b, suggesting that gene 4b was largely released from the strong purifying selection that acts on gene 4a in both barley and wheat. Intergenic retrotransposon blocks, many of them organized as nested insertions, mostly account for the lower gene density of the barley and wheat regions. All but two of the retrotransposons were found in the regions between genes, while all but 2 of the 51 inverted repeat transposable elements were found as insertions in genic regions and outside the retrotransposon blocks.

Biological Evolution↗
PubMedDate not supplied

Cytokines in nasal lavage fluids from acute sinusitis, allergic rhinitis, and chronic fatigue syndrome subjects.

The aim of this study was to compare the degree of inflammation present in acute sinusitis, allergic rhinitis, chronic Fatigue Syndrome (CFS), and non-CFS control subjects by measuring cytokine concentrations in nasal lavage fluids. The concentrations of total protein (TP; Lowry assay), nerve growth factor (NGF), tumor necrosis factor (TNF) alpha, and interleukin (IL)-8 were measured by ELISA in nasal lavage fluids from acute sinusitis (n = 13), active allergic rhinitis (n = 16), CFS (n = 95), and non-CFS (n = 89) subjects. CFS and non-CFS groups were subdivided further using allergy skin test and rhinitis score results. Acute sinusitis subjects had significantly higher TP (p = 0.011, ANOVA), TNF-alpha (p = 0.00071), and IL-8 (p = 0.0000027) concentrations and IL-8/TP ratios (p = 0.0030) than the other three patient groups. There were no differences based on skin test or rhinitis score severity within either the CFS or non-CFS groups. The mucopurulent discharge of acute sinusitis contained significantly higher TNF-alpha and IL-8. Neutrophils were a likely source for these cytokines. There were no differences between CFS and non-CFS subjects, making it unlikely that the rhinitis of CFS has an inflammatory component.

Adult↗