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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 Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD).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.
( Jongsun Park ),( Woochan Kwon ),( Seung-beom Hong ),( Kap-hoon Han ) 한국균학회 2020 Mycobiology Vol.48 No.6
Scopulariopsis brevicaulis is a widely distributed soil fungus known as a common saprotroph of biodegradation. It is also an opportunistic human pathogen that can produce various secondary metabolites. Here, we report the first complete mitochondrial genome sequence of S. brevicaulis isolated from air in South Korea. Total length of the mitochondrial genome is 28,829 bp and encoded 42 genes (15 protein-coding genes, 2 rRNAs, and 25 tRNAs). Nucleotide sequence of coding region takes over 26.2%, and overall GC content is 27.6%. Phylogenetic trees present that S. brevicaulis is clustered with Lomentospora prolificans with presenting various mitochondrial genome length.
Park, Minkyu,Park, Jongsun,Kim, Seungill,Kwon, Jin‐,Kyung,Park, Hye Mi,Bae, Ik Hyun,Yang, Tae‐,Jin,Lee, Yong‐,Hwan,Kang, Byoung‐,Cheorl,Choi, Doil Blackwell Publishing Ltd 2012 The Plant journal Vol.69 No.6
<P><B>Summary</B></P><P>Although plant genome sizes are extremely diverse, the mechanism underlying the expansion of huge genomes that did not experience whole‐genome duplication has not been elucidated. The pepper, <I>Capsicum annuum</I>, is an excellent model for studies of genome expansion due to its large genome size (2700 Mb) and the absence of whole genome duplication. As most of the pepper genome structure has been identified as constitutive heterochromatin, we investigated the evolution of this region in detail. Our findings show that the constitutive heterochromatin in pepper was actively expanded 20.0–7.5 million years ago through a massive accumulation of single‐type <I>Ty3/Gypsy</I>‐like elements that belong to the Del subgroup. Interestingly, derivatives of the Del elements, such as non‐autonomous long terminal repeat retrotransposons and long‐unit tandem repeats, played important roles in the expansion of constitutive heterochromatic regions. This expansion occurred not only in the existing heterochromatic regions but also into the euchromatic regions. Furthermore, our results revealed a repeat of unit length 18–24 kb. This repeat was found not only in the pepper genome but also in the other solanaceous species, such as potato and tomato. These results represent a characteristic mechanism for large genome evolution in plants.</P>
GOLGA2 loss causes fibrosis with autophagy in the mouse lung and liver
Park, Sungjin,Kim, Sanghwa,Kim, Min Jung,Hong, Youngeun,Lee, Ah Young,Lee, Hyunji,Tran, Quangdon,Kim, Minhee,Cho, Hyeonjeong,Park, Jisoo,Kim, Kwang Pyo,Park, Jongsun,Cho, Myung-Haing Elsevier 2018 Biochemical and biophysical research communication Vol.495 No.1
<P><B>Abstract</B></P> <P>Autophagy is a biological recycling process via the self-digestion of organelles, proteins, and lipids for energy-consuming differentiation and homeostasis. The Golgi serves as a donor of the double-membraned phagophore for autophagosome assembly. In addition, recent studies have demonstrated that pulmonary and hepatic fibrosis is accompanied by autophagy. However, the relationships among Golgi function, autophagy, and fibrosis are unclear. Here, we show that the deletion of <I>GOLGA2</I>, encoding a cis-Golgi protein, induces autophagy with Golgi disruption. The induction of autophagy leads to fibrosis along with the reduction of subcellular lipid storage (lipid droplets and lamellar bodies) by autophagy in the lung and liver. <I>GOLGA2</I> knockout mice clearly demonstrated fibrosis features such as autophagy-activated cells, densely packed hepatocytes, increase of alveolar macrophages, and decrease of alveolar surfactant lipids (dipalmitoylphosphatidylcholine). Therefore, we confirmed the associations among Golgi function, fibrosis, and autophagy. Moreover, <I>GOLGA2</I> knockout mice may be a potentially valuable animal model for studying autophagy-induced fibrosis.</P> <P><B>Highlights</B></P> <P> <UL> <LI> GOLGA2/GM130 loss induces autophagy with Golgi disruption in liver cells and transgenic mice. </LI> <LI> GOLGA2/GM130 loss leads to degradation of lipid structures (LBs and LDs) by autophagy. </LI> <LI> GOLGA2/GM130 loss causes liver and lung fibrosis. </LI> </UL> </P>
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>