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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 Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD).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.
PlantGPS: 식물 생물지리 정보 확보와 모니터링을 위한 모바일 어플리케이션
Jongsun Park,Yongsung Kim,Suhwan Nam,Kyeong-In Heo,Hong Xi,Suwang Jang,Suhyeon Park,Sangtae Kim 한국자연보호학회 2016 한국자연보호학회지 Vol.10 No.1
Cost for plant survey has been dramatically reduced due to the development of mobile technology to obtain pictures with their GPS coordination. We developed a PlantGPS system consisting of an Android application specialized for collecting plant pictures and their locations using mobile devices, a server-side component for uploading data, and a web-based interface for managing and analyzing data. As examples of application of our PlantGPS system, surveys of “plants in Nangsae (Daksum) Island” and “ferns in Chollipo arboretum” were conducted. Results showed that our PlantGPS system could be used to quickly survey plant distribution in restricted area with reasonable time and effort.
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,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>
Park, Ji-Young,Kim, Kwang Soo,Lee, Saet-Byul,Ryu, Jae-Sung,Chung, Kwang Chul,Choo, Young-Kug,Jou, Ilo,Kim, Jongsun,Park, Sang Myun Blackwell Publishing Ltd 2009 Journal of Neurochemistry Vol.110 No.1
<P>Abstract</P><P>&agr;-Synuclein (&agr;-syn) has been known to be a key player of the pathogenesis of Parkinson’s disease and has recently been detected in extracellular biological fluids and shown to be rapidly secreted from cells. The penetration of &agr;-syn into cells has also been observed. In this study, we observed that <SMALL>DL</SMALL>-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol, a glucosyltransferase inhibitor, and proteinase K inhibited the internalization of extracellular monomeric &agr;-syn into BV-2 cells, and the addition of monosialoganglioside GM1 ameliorated the inhibition of &agr;-syn internalization in <SMALL>DL</SMALL>-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol-treated BV-2 cells. Furthermore, inhibition of clathrin-, caveolae-, and dynamin-dependent endocytosis did not prevent the internalization of &agr;-syn, but disruption of lipid raft inhibited it. Inhibition of macropinocytosis and disruption of actin and microtubule structures also did not inhibit the internalization of &agr;-syn. In addition, we further confirmed these observations by co-culture system of BV-2 cells and &agr;-syn-over-expressing SH-SY5Y cells. These findings suggest that extracellular &agr;-syn is internalized into microglia via GM1 as well as hitherto-unknown protein receptors in clathrin-, caveolae-, and dynamin-independent, but lipid raft-dependent manner. Elucidation of the mechanism involved in internalization of &agr;-syn should be greatly helpful in the development of new treatments of &agr;-syn-related neurodegenerative diseases.</P>
Park, Jongsun,Feng, Jianhua,Li, Yuwen,Hammarsten, Ola,Brazil, Derek P,Hemmings, Brian A American Society for Biochemistry and Molecular Bi 2009 The Journal of biological chemistry Vol.284 No.10
<P>DNA-dependent protein kinase (DNA-PK) has been implicated in a variety of nuclear processes including DNA double strand break repair, V(D)J recombination, and transcription. A recent study showed that DNA-PK is responsible for Ser-473 phosphorylation in the hydrophobic motif of protein kinase B (PKB/Akt) in genotoxic-stressed cells, suggesting a novel role for DNA-PK in cell signaling. Here, we report that DNA-PK activity toward PKB peptides is impaired in DNA-PK knock-out mouse embryonic fibroblast cells when compared with wild type. In addition, human glioblastoma cells expressing a mutant form of DNA-PK (M059J) displayed a lower DNA-PK activity when compared with glioblastoma cells expressing wild-type DNA-PK (M059K) when PKB peptide substrates were tested. DNA-PK preferentially phosphorylated PKB on Ser-473 when compared with its known in vitro substrate, p53. A consensus hydrophobic amino acid surrounding the Ser-473 phospho-acceptor site in PKB containing amino acids Phe at position +1 and +4 and Tyr at position -1 are critical for DNA-PK activity. Thus, these data define the specificity of DNA-PK action as a Ser-473 kinase for PKB in DNA repair signaling.</P>