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FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors.
Park, Jongsun,Park, Jaejin,Jang, Suwang,Kim, Seryun,Kong, Sunghyung,Choi, Jaeyoung,Ahn, Kyohun,Kim, Juhyeon,Lee, Seungmin,Kim, Sunggon,Park, Bongsoo,Jung, Kyongyong,Kim, Soonok,Kang, Seogchan,Lee, Yon Oxford University Press 2008 Bioinformatics Vol.24 No.7
<P>Genomes of more than 60 fungal species have been sequenced to date, yet there has been no systematic approach to analyze fungal transcription factors (TFs) kingdom widely. We developed a standardized pipeline for annotating TFs in fungal genomes. Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31,832 putative fungal TFs, identified from 62 fungal and 3 Oomycete species, were classified into 61 families and phylogenetically analyzed. The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species.</P>
Min-Woo Park,Jaejin Park,Il-Kook Park,Jongsun Kim,Il-Hun Kim,Daesik Park 한국양서ㆍ파충류학회 2022 한국양서·파충류학회 학술대회 Vol.2022 No.07
To date, more than 1,000 species of barnacles have been reported, and some barnacles spend most of their life attached to marine vertebrates. As their distribution patterns are as diverse as their species diversity, they can be important data for understanding the behavior or ecology of host organisms as epibiont. However, in Korea, further research is needed because studies on the relationship between barnacles and marine vertebrates are still insufficient. In this study, we report a barnacle attached to a Chinese sea krait (Laticauda semifasciata) caught in the sea of Korea. On September 7, 2016, in the sea near Udo Island, Jeju (33.56°N, 127.02°E), a total of 22 barnacles were found to attach to one L. semifasciata caught. We identified these barnacles as Conchoderma virgatum based on their morphological characteristics such as distinctive feature of the capitulum and peduncle, the number of capitulum with reduced 5 plates, and the number of 2 scutum in Y-shape. There are a total of two types of barnacles (C. virgatum and Platylepas ophiophilus) that have been reported to attach to L. semifasciata in the world. Attached barnacles, including the C. virgatum, may restrict the behavior of sea kraits, cause dysecdysis, or cause the secondary infection through epithelial tissue damage. Therefore, further study on the relationship between barnacles and marine reptiles might be needed.
Park, Jongsun,Oh, Youngmin Institut Za Lokalno Samoupravo in Javna Narocila M 2017 Lex localis : revija za lokalno samoupravo Vol.15 No.1
<P>Many empirical studies have found that local public contracting reduces the inputs and outcomes of public services. However, few studies have examined what factors are associated with such inputs and outcomes. To address the limitation, this study conceptualizes two competing contracting management models (competitive and cooperative) and empirically tests the associations between these contracting approaches and service inputs and outcomes. The findings report that while local governments using competitive contracting elements have lower service inputs through reduced local operating expenditures and part-time employment; cooperative contracting elements do not necessarily produce enhanced service outcomes.</P>
Recognition of Transmembrane Protein 39A as a Tumor-Specific Marker in Brain Tumor
Park, Jisoo,Lee, Hyunji,Tran, Quangdon,Mun, Kisun,Kim, Dohoon,Hong, Youngeun,Kwon, So Hee,Brazil, Derek,Park, Jongsun,Kim, Seon-Hwan Korean Society of ToxicologyKorea Environmental Mu 2017 Toxicological Research Vol.33 No.1
Transmembrane protein 39A (TMEM39A) belongs to the TMEM39 family. TMEM39A gene is a susceptibility locus for multiple sclerosis. In addition, TMEM39A seems to be implicated in systemic lupus erythematosus. However, any possible involvement of TMEM39A in cancer remains largely unknown. In the present report, we provide evidence that TMEM39A may play a role in brain tumors. Western blotting using an anti-TMEM39A antibody indicated that TMEM39A was overexpressed in glioblastoma cell lines, including U87-MG and U251-MG. Deep-sequencing transcriptomic profiling of U87-MG and U251-MG cells revealed that TMEM39A transcripts were upregulated in such cells compared with those of the cerebral cortex. Confocal microscopic analysis of U251-MG cells stained with anti-TMEM39A antibody showed that TMEM39A was located in dot-like structures lying close to the nucleus. TMEM39A probably located to mitochondria or to endosomes. Immunohistochemical analysis of glioma tissue specimens indicated that TMEM39A was markedly upregulated in such samples. Bioinformatic analysis of the Rembrandt knowledge base also supported upregulation of TMEM39A mRNA levels in glioma patients. Together, the results afford strong evidence that TMEM39A is upregulated in glioma cell lines and glioma tissue specimens. Therefore, TMEM39A may serve as a novel diagnostic marker of, and a therapeutic target for, gliomas and other cancers.
Park, Bongsoo,Park, Jongsun,Cheong, Kyeong-Chae,Choi, Jaeyoung,Jung, Kyongyong,Kim, Donghan,Lee, Yong-Hwan,Ward, Todd J.,O'Donnell, Kerry,Geiser, David M.,Kang, Seogchan Oxford University Press 2011 Nucleic acids research Vol.39 No.1
<P>The fungal genus <I>Fusarium</I> includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify <I>Fusarium</I> morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for <I>Fusarium</I> classification. Genomes of four <I>Fusarium</I> species have been published with more being currently sequenced. The Cyber infrastructure for <I>Fusarium</I> (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education.</P>
Multiple Bit Encodings of Multilayer Porous Silicon
Jongsun Park,Honglae Sohn,Sungdong Cho,고영춘 한국물리학회 2007 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.50 No.3
Photonic crystals containing the rugate structure result in a mirror with high reflectivity in a specific narrow spectral region and are prepared by applying a computer-generated pseudo-sinusoidal current waveform. Strategies to encode multiple rugate structures have been investigated. Multiple rugate structures can be etched on a silicon wafer and placed in the same physical location, showing that many sharp spectral lines can be obtained in the optical reflectivity spectrum. The method used to generate multiple rugate structures containing all the encoding information displays five rugate peaks corresponding to each of the sine components from 0.16 to 0.24 Hz, with a spacing of 0.02 Hz between each sine component. The complete deletion of a peak has been achieved and demonstrates the capacity of this method to create binary codes. The free-standing rugate porous silicon has been treated with the solution PMMA to produce composite materials which are highly flexible at room temperature. They display significantly improved mechanical stability and no apparent degradation in their optical reflectivity properties upon flexing. The spectral feature is shifted to longer wavelengths, indicating that the polymer has infiltrated the pores of the porous silicon matrix. The composites are stable in aqueous HF or alkaline (3 M KOH) solutions for several days without apparent degradation.
Park, Sook-Young,Choi, Jaeyoung,Lim, Se-Eun,Lee, Gir-Won,Park, Jongsun,Kim, Yang,Kong, Sunghyung,Kim, Se Ryun,Rho, Hee-Sool,Jeon, Junhyun,Chi, Myung-Hwan,Kim, Soonok,Khang, Chang Hyun,Kang, Seogchan,L Public Library of Science 2013 PLoS pathogens Vol.9 No.6
<▼1><P>Because most efforts to understand the molecular mechanisms underpinning fungal pathogenicity have focused on studying the function and role of individual genes, relatively little is known about how transcriptional machineries globally regulate and coordinate the expression of a large group of genes involved in pathogenesis. Using quantitative real-time PCR, we analyzed the expression patterns of 206 transcription factor (TF) genes in the rice blast fungus <I>Magnaporthe oryzae</I> under 32 conditions, including multiple infection-related developmental stages and various abiotic stresses. The resulting data, which are publicly available via an online platform, provided new insights into how these TFs are regulated and potentially work together to control cellular responses to a diverse array of stimuli. High degrees of differential TF expression were observed under the conditions tested. More than 50% of the 206 TF genes were up-regulated during conidiation and/or in conidia. Mutations in ten conidiation-specific TF genes caused defects in conidiation. Expression patterns <I>in planta</I> were similar to those under oxidative stress conditions. Mutants of <I>in planta</I> inducible genes not only exhibited sensitive to oxidative stress but also failed to infect rice. These experimental validations clearly demonstrated the value of TF expression patterns in predicting the function of individual TF genes. The regulatory network of TF genes revealed by this study provides a solid foundation for elucidating how <I>M. oryzae</I> regulates its pathogenesis, development, and stress responses.</P></▼1><▼2><P><B>Author Summary</B></P><P>Rice blast disease, caused by <I>Magnaporthe oryzae</I>, destroys rice crop enough to feed 60 million people every year and has served as a model pathosystem for understanding host-parasite interactions. However, little is known about how <I>M. oryzae</I> globally regulates and coordinates its gene expression at the whole-genome scale. We analyzed the expression patterns of 206 <I>M. oryzae</I> genes encoding transcription factors (TFs) under 32 conditions, including infection-related developmental stages and various abiotic stresses, using quantitative real-time PCR. We focused on identifying the TF genes that are induced during the two most important infection-related morphogenetic changes; conidiation and infectious growth in rice. We identified 57 conidiation-specific TF genes and functionally characterized ten of them. Our data also showed that infectious growth <I>in planta</I> and oxidative stress responses <I>in vitro</I> involve largely overlapping groups of TFs. Comprehensive TF expression data and functional validation provided new insights into the regulatory mechanism underpinning pathogenicity and stress responses in <I>M. oryzae</I>. These data will also serve as a guide in studying the role of individual TF genes and the coordination of their expression in controlling development, pathogenicity, and abiotic stress responses in <I>M. oryzae</I>.</P></▼2>
Park Jongsun,서화정,XIHONG 한국식물분류학회 2024 식물 분류학회지 Vol.54 No.1
The genus <i>Agrimonia</i> L. (1753) is a small group consisting of 19 species and three varieties. We completed two <i>Agrimonia</i> chloroplast genomes, <i>Agrimonia coreana</i> Nakai and <i>Agrimonia nipponica</i> Koidz, collected in Korea and conducted comprehensive analyses of six <i>Agrimonia</i> chloroplast genomes. Two of the <i>Agrimonia</i> chloroplasts genomes have a typical quadripartite structure with lengths ranging from 155,161 bp to 151,362 bp, similar to the remaining A<i>Agrimonia</i> chloroplast genomes. High nucleotide diversity was detected in the <i>ycf1</i> gene, which can serve as a molecular marker. Intraspecific variations of four <i>A. pilosa</i> chloroplast genomes and interspecific variations of three <i>Agrimonia</i> species revealed that KY419942 is distinct to the other three <i>A. pilosa</i> chloroplast genomes. A phylogenetic analysis demonstrated that KY419942 was clustered with <i>A. nipponica</i>, requiring further analyses to understand <i>Agrimonia</i> species in East Asia. A comparison of simple sequence repeats identified from the six <i>Agrimonia</i> chloroplast genomes suggests potential molecular markers to distinguish species or populations of the same species. Our results define the phylogenetic relationship of three <i>Agrimonia</i> species and provide insight into the intraspecific features of <i>Agrimonia</i> chloroplast genomes with which to gain a better understanding of the genetic structure of <i>Agrimonia</i> species.