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Babiarz J, Ryu H, Williams C, Ham Y, Rivera Sarti J, Levander XA. Slicing through silos: Development and evaluation of a hospital-based telehealth hepatitis C virus treatment program. Int J Drug Policy 2024; 127:104396. [PMID: 38593518 DOI: 10.1016/j.drugpo.2024.104396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND There exist many barriers to hepatitis C virus (HCV) treatment for those with substance use disorder (SUD) or who lack access to routine medical care. A hospital-based telehealth program was developed to provide treatment opportunities for hospitalized patients living with HCV. METHODS This single site prospective cohort study conducted from July 2022 to March 2023 aimed to measure linkage to care with an HCV clinician and initiation of HCV treatment in hospitalized patients. Patients were assessed in-person by a social worker then seen via telehealth by a clinician who prescribed either glecaprevir/pibrentasvir or sofosbuvir/velpatasvir. Treatment was initiated with pharmacist assistance. The team conducted in-person and/or telephonic outreach during and after hospitalization. Cure was confirmed by sustained virologic response at 12 weeks (SVR12) post-treatment. RESULTS A total of 25 patients were enrolled and completed telehealth visits. All patients had a history of SUD and 18 (72 %) were unstably housed. Nineteen patients (76 %) initiated treatment, and 14 (56 %) successfully completed treatment. Twelve patients (48 %) completed post-treatment labs, including two who prematurely discontinued treatment. Eleven patients (44 %) achieved confirmed cure with SVR12. CONCLUSION A hospital-based, multidisciplinary telehealth program can be an innovative care model to successfully treat HCV in a difficult-to-treat patient populations.
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Affiliation(s)
- J Babiarz
- Department of Medicine, Division of Internal Medicine and Geriatrics, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239 United States
| | - H Ryu
- Department of Pharmacy, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239 United States
| | - C Williams
- Department of Care Management, Division of General Internal Medicine and Geriatrics, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239 United States
| | - Y Ham
- Department of Pharmacy, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239 United States
| | - J Rivera Sarti
- Department of Medicine, Division of Infectious Disease, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239 United States
| | - X A Levander
- Department of Medicine, Division of General Internal Medicine and Geriatrics, Section of Addiction Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239 United States
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Geem KR, Lim Y, Hong J, Bae W, Lee J, Han S, Gil J, Cho H, Ryu H. Cytokinin signaling promotes root secondary growth and bud formation in Panax ginseng. J Ginseng Res 2024; 48:220-228. [PMID: 38465220 PMCID: PMC10919999 DOI: 10.1016/j.jgr.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/24/2023] [Accepted: 11/06/2023] [Indexed: 03/12/2024] Open
Abstract
Background Panax ginseng, one of the valuable perennial medicinal plants, stores numerous pharmacological substrates in its storage roots. Given its perennial growth habit, organ regeneration occurs each year, and cambium stem cell activity is necessary for secondary growth and storage root formation. Cytokinin (CK) is a phytohormone involved in the maintenance of meristematic cells for the development of storage organs; however, its physiological role in storage-root secondary growth remains unknown. Methods Exogenous CK was repeatedly applied to P. ginseng, and morphological and histological changes were observed. RNA-seq analysis was used to elucidate the transcriptional network of CK that regulates P. ginseng growth and development. The HISTIDINE KINASE 3 (PgHK3) and RESPONSE REGULATOR 2 (PgRR2) genes were cloned in P. ginseng and functionally analyzed in Arabidopsis as a two-component system involved in CK signaling. Results Phenotypic and histological analyses showed that CK increased cambium activity and dormant axillary bud formation in P. ginseng, thus promoting storage-root secondary growth and bud formation. The evolutionarily conserved two-component signaling pathways in P. ginseng were sufficient to restore CK signaling in the Arabidopsis ahk2/3 double mutant and rescue its growth defects. Finally, RNA-seq analysis of CK-treated P. ginseng roots revealed that plant-type cell wall biogenesis-related genes are tightly connected with mitotic cell division, cytokinesis, and auxin signaling to regulate CK-mediated P. ginseng development. Conclusion Overall, we identified the CK signaling-related two-component systems and their physiological role in P. ginseng. This scientific information has the potential to significantly improve the field-cultivation and biotechnology-based breeding of ginseng.
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Affiliation(s)
- Kyoung Rok Geem
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Yookyung Lim
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jeongeui Hong
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Republic of Korea
| | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jinsu Lee
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Soeun Han
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jinsu Gil
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyunwoo Cho
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Republic of Korea
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Kim BK, Choi WS, Jeong JH, Oh S, Park JH, Yun YS, Min SC, Kang DH, Kim EG, Ryu H, Kim HK, Baek YH, Choi YK, Song MS. A Rapid Method for Generating Infectious SARS-CoV-2 and Variants Using Mutagenesis and Circular Polymerase Extension Cloning. Microbiol Spectr 2023; 11:e0338522. [PMID: 36877070 PMCID: PMC10100849 DOI: 10.1128/spectrum.03385-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 02/12/2023] [Indexed: 03/07/2023] Open
Abstract
The appearance of SARS-CoV-2 variants in late 2020 raised alarming global public health concerns. Despite continued scientific progress, the genetic profiles of these variants bring changes in viral properties that threaten vaccine efficacy. Thus, it is critically important to investigate the biologic profiles and significance of these evolving variants. In this study, we demonstrate the application of circular polymerase extension cloning (CPEC) to the generation of full-length clones of SARS-CoV-2. We report that, combined with a specific primer design scheme, this yields a simpler, uncomplicated, and versatile approach for engineering SARS-CoV-2 variants with high viral recovery efficiency. This new strategy for genomic engineering of SARS-CoV-2 variants was implemented and evaluated for its efficiency in generating point mutations (K417N, L452R, E484K, N501Y, D614G, P681H, P681R, Δ69-70, Δ157-158, E484K+N501Y, and Ins-38F) and multiple mutations (N501Y/D614G and E484K/N501Y/D614G), as well as a large truncation (ΔORF7A) and insertion (GFP). The application of CPEC to mutagenesis also allows the inclusion of a confirmatory step prior to assembly and transfection. This method could be of value in the molecular characterization of emerging SARS-CoV-2 variants as well as the development and testing of vaccines, therapeutic antibodies, and antivirals. IMPORTANCE Since the first emergence of the SARS-CoV-2 variant in late 2020, novel variants have been continuously introduced to the human population, causing severe public health threats. In general, because these variants acquire new genetic mutation/s, it is critical to analyze the biological function of viruses that such mutations can confer. Therefore, we devised a method that can construct SARS-CoV-2 infectious clones and their variants rapidly and efficiently. The method was developed based on a PCR-based circular polymerase extension cloning (CPEC) combined with a specific primer design scheme. The efficiency of the newly designed method was evaluated by generating SARS-CoV-2 variants with single point mutations, multiple point mutations, and a large truncation and insertion. This method could be of value for the molecular characterization of emerging SARS-CoV-2 variants and the development and testing of vaccines and antiviral agents.
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Affiliation(s)
- Beom Kyu Kim
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Won-Suk Choi
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Ju Hwan Jeong
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Sol Oh
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Ji-Hyun Park
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Yu Soo Yun
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Seong Cheol Min
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Da Hyeon Kang
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Eung-Gook Kim
- Department of Biochemistry, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Hojin Ryu
- Department of Biological Sciences and Biotechnology, College of Natural Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Hye Kwon Kim
- Department of Biological Sciences and Biotechnology, College of Natural Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Yun Hee Baek
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Young Ki Choi
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Min-Suk Song
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
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Kim S, Eom H, Nandre R, Choi YJ, Lee H, Ryu H, Ro HS. Comparative structural analysis on the mitochondrial DNAs from various strains of Lentinula edodes. Front Microbiol 2022; 13:1034387. [DOI: 10.3389/fmicb.2022.1034387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/09/2022] [Indexed: 11/30/2022] Open
Abstract
The evolution of mitochondria through variations in mitochondrial DNA (mtDNA) is one of the intriguing questions in eukaryotic cells. In order to assess the causes of the variations in mitochondria, the mtDNAs of the 21 strains of Lentinula edodes were assembled for this study, and analyzed together with four published mtDNA sequences. The mtDNAs were within the sizes of 117 kb ~ 122 kb. The gene number was observed consistent except for two mtDNAs, which carry a duplicated trnG1-trnG2 unit or a putative gene deletion. The size variation was largely attributed to the number of introns, repeated sequences, transposable elements (TEs), and plasmid-related sequences. Intron loss and gain were found from cox1, rnl, and rns of three mtDNAs. Loss of two introns in cox1 of KY217797.1 reduced its size by 2.7 kb, making it the smallest cox1 gene (8.4 kb) among the cox1s of the 25 mtDNAs, whereas gain of a Group II intron (2.65 kb) and loss of a Group I intron (1.7 kb) in cox1 of MF774813.1 resulted in the longest cox1 (12 kb). In rnl of L. edodes, we discovered four intron insertion consensus sequences which were unique to basidiomycetes but not ascomycetes. Differential incorporation of introns was the primary cause of the rnl size polymorphism. Homing endonucleases (HEGs) were suggestively involved in the mobilization of the introns because all of the introns have HEG genes of the LAGRIDADG or GIY-YIG families with the conserved HEG cleavage sites. TEs contributed to 11.04% of the mtDNA size in average, of which 7.08% was LTR-retrotransposon and 3.96% was DNA transposon, whereas the repeated sequences covered 4.6% of the mtDNA. The repeat numbers were variable in a strain-dependent manner. Both the TEs and repeated sequences were mostly found in the intronic and intergenic regions. Lastly, two major deletions were found in the plasmid-related sequence regions (pol2-pol3 and pol1-atp8) in the five mtDNAs. Particularly, the 6.8 kb-long deletion at pol2-pol3 region made MF774813.1 the shortest mtDNA of all. Our results demonstrate that mtDNA is a dynamic molecule that persistently evolves over a short period of time by insertion/deletion and repetition of DNA segments at the strain level.
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Lee HY, Jo JW, Kwak YN, Lee H, Ryu H, Sung J, So YS, Kim CS, Chung JW. The complete mitochondrial genome of the poisonous mushroom Trichoderma cornu-damae (Hypocreaceae). Mitochondrial DNA B Resour 2022; 7:1899-1901. [PMID: 36353061 PMCID: PMC9639550 DOI: 10.1080/23802359.2022.2135393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trichoderma cornu-damae is a poisonous mushroom that contains trichothecene mycotoxins. The complete mitochondrial genome of this mushroom was determined using next-generation sequencing. This mitogenome is a circular molecule 94,608 bp in length with a GC content of 27.94% and contains 15 protein-coding genes, two rRNA genes (rnl and rns), and 25 tRNA genes. Phylogenetic analysis placed T. cornu-damae in the family Hypocreaceae group, which includes the genus Trichoderma. The mitogenome of T. cornu-damae will contribute to our understanding of the phylogeny, taxonomy, and population genetics of this mushroom.
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Affiliation(s)
- Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jong Won Jo
- Forest Biodiversity Research Division, Korea National Arboretum, Pocheon, Republic of Korea
| | - Young-Nam Kwak
- Forest Biodiversity Research Division, Korea National Arboretum, Pocheon, Republic of Korea
| | - Hyun Lee
- Forest Biodiversity Research Division, Korea National Arboretum, Pocheon, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jwakyung Sung
- Department of Crop Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Chang-Sun Kim
- Forest Biodiversity Research Division, Korea National Arboretum, Pocheon, Republic of Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
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Geem KR, Kim H, Ryu H. SCF FBS1 Regulates Root Quiescent Center Cell Division via Protein Degradation of APC/C CCS52A2. Mol Cells 2022; 45:695-701. [PMID: 36116942 PMCID: PMC9589370 DOI: 10.14348/molcells.2022.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 12/05/2022] Open
Abstract
Homeostatic regulation of meristematic stem cells accomplished by maintaining a balance between stem cell self-renewal and differentiation is critical for proper plant growth and development. The quiescent center (QC) regulates root apical meristem homeostasis by maintaining stem cell fate during plant root development. Cell cycle checkpoints, such as anaphase promoting complex/cyclosome/CELL CYCLE SWITCH 52 A2 (APC/CCCS52A2), strictly control the low proliferation rate of QC cells. Although APC/CCCS52A2 plays a critical role in maintaining QC cell division, the molecular mechanism that regulates its activity remains largely unknown. Here, we identified SCFF-BOX STRESS INDUCED 1 (FBS1), a ubiquitin E3 ligase, as a key regulator of QC cell division through the direct proteolysis of CCS52A2. FBS1 activity is positively associated with QC cell division and CCS52A2 proteolysis. FBS1 overexpression or ccs52a2-1 knockout consistently resulted in abnormal root development, characterized by root growth inhibition and low mitotic activity in the meristematic zone. Loss-of-function mutation of FBS1, on the other hand, resulted in low QC cell division, extremely low WOX5 expression, and rapid root growth. The 26S proteasome-mediated degradation of CCS52A2 was facilitated by its direct interaction with F-box stress induced 1 (FBS1). The FBS1 genetically interacted with APC/CCCS52A2-ERF115-PSKR1 signaling module for QC division. Thus, our findings establish SCFFBS1-mediated CCS52A2 proteolysis as the molecular mechanism for controlling QC cell division in plants.
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Affiliation(s)
- Kyoung Rok Geem
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
| | - Hyemin Kim
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Korea
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Hong J, Geem KR, Kim J, Jo IH, Yang TJ, Shim D, Ryu H. Prolonged Exposure to High Temperature Inhibits Shoot Primary and Root Secondary Growth in Panax ginseng. Int J Mol Sci 2022; 23:ijms231911647. [PMID: 36232949 PMCID: PMC9569605 DOI: 10.3390/ijms231911647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
High temperature is one of the most significant abiotic stresses reducing crop yield and quality by inhibiting plant growth and development. Global warming has recently increased the frequency of heat waves, which negatively impacts agricultural fields. Despite numerous studies on heat stress responses and signal transduction in model plant species, the molecular mechanism underlying thermomorphogenesis in Panax ginseng remains largely unknown. Here, we investigated the high temperature response of ginseng at the phenotypic and molecular levels. Both the primary shoot growth and secondary root growth of ginseng plants were significantly reduced at high temperature. Histological analysis revealed that these decreases in shoot and root growth were caused by decreases in cell elongation and cambium stem cell activity, respectively. Analysis of P. ginseng RNA-seq data revealed that heat-stress-repressed stem and root growth is closely related to changes in photosynthesis, cell wall organization, cell wall loosening, and abscisic acid (ABA) and jasmonic acid (JA) signaling. Reduction in both the light and dark reactions of photosynthesis resulted in defects in starch granule development in the storage parenchymal cells of the main tap root. Thus, by combining bioinformatics and histological analyses, we show that high temperature signaling pathways are integrated with crucial biological processes that repress stem and root growth in ginseng, providing novel insight into the heat stress response mechanism of P. ginseng.
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Affiliation(s)
- Jeongeui Hong
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Korea
| | - Kyoung Rok Geem
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Korea
| | - Jaewook Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
- Correspondence: (D.S.); (H.R.); Tel.: +82-42-821-6279 (D.S.); +82-43-261-2293 (H.R.); Fax: +82-42-822-9690 (D.S.); +82-43-260-2298 (H.R.)
| | - Hojin Ryu
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Korea
- Correspondence: (D.S.); (H.R.); Tel.: +82-42-821-6279 (D.S.); +82-43-261-2293 (H.R.); Fax: +82-42-822-9690 (D.S.); +82-43-260-2298 (H.R.)
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Park K, Nam J, Lee H, Kim T, Ryu H, Ki Y, Kim JJ, Oh S, Oh S, Hong Y. 1745P Phase II study of neoadjuvant chemotherapy with 4 cycles of dose dense MVAC followed by radical surgery in Korean patients with MIBC and locally advanced urothelial carcinoma of bladder (NCT04047693). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Yoo C, Kim KP, Kim I, Kang M, Cheon J, Kang B, Ryu H, Jeong J, Lee J, Kim K, Ryoo BY, Abou-Alfa G. 55P Final results from the NIFTY trial, a phase IIb, randomized, open-label study of liposomal Irinotecan (nal-IRI) plus fluorouracil (5-FU)/leucovorin (LV) in patients (pts) with previously treated metastatic biliary tract cancer (BTC). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Kim G, Ryu H, Sung J. Hormonal Crosstalk and Root Suberization for Drought Stress Tolerance in Plants. Biomolecules 2022; 12:biom12060811. [PMID: 35740936 PMCID: PMC9220869 DOI: 10.3390/biom12060811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 12/10/2022] Open
Abstract
Higher plants in terrestrial environments face to numerous unpredictable environmental challenges, which lead to a significant impact on plant growth and development. In particular, the climate change caused by global warming is causing drought stress and rapid desertification in agricultural fields. Many scientific advances have been achieved to solve these problems for agricultural and plant ecosystems. In this review, we handled recent advances in our understanding of the physiological changes and strategies for plants undergoing drought stress. The activation of ABA synthesis and signaling pathways by drought stress regulates root development via the formation of complicated signaling networks with auxin, cytokinin, and ethylene signaling. An abundance of intrinsic soluble sugar, especially trehalose-6-phosphate, promotes the SnRK-mediated stress-resistance mechanism. Suberin deposition in the root endodermis is a physical barrier that regulates the influx/efflux of water and nutrients through complex hormonal and metabolic networks, and suberization is essential for drought-stressed plants to survive. It is highly anticipated that this work will contribute to the reproduction and productivity improvements of drought-resistant crops in the future.
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Affiliation(s)
- Gaeun Kim
- Department of Crop Science, Chungbuk National University, Cheong-ju 28644, Korea;
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheong-ju 28644, Korea
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheong-ju 28644, Korea
- Correspondence: (H.R.); (J.S.); Tel.: +82-043-261-2293 (H.R.); +82-043-261-2512 (J.S.)
| | - Jwakyung Sung
- Department of Crop Science, Chungbuk National University, Cheong-ju 28644, Korea;
- Correspondence: (H.R.); (J.S.); Tel.: +82-043-261-2293 (H.R.); +82-043-261-2512 (J.S.)
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Geem KR, Kim J, Bae W, Jee MG, Yu J, Jang I, Lee DY, Hong CP, Shim D, Ryu H. Nitrate enhances the secondary growth of storage roots in Panax ginseng. J Ginseng Res 2022; 47:469-478. [DOI: 10.1016/j.jgr.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022] Open
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Ryu H, Song C, Kim J, Jeon J, Cho S, Kim K, Jheon S, Kim S, Kim Y, Lee J. PO-1241 Role of Prognostic Nutritional Index in Postoperative Radiotherapy for Non-Small Cell Lung Cancer. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)03205-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hong CP, Kim CK, Lee DJ, Jeong HJ, Lee Y, Park SG, Kim HJ, Kang JN, Ryu H, Kwon SJ, Kang SH. Long-read transcriptome sequencing provides insight into lignan biosynthesis during fruit development in Schisandra chinensis. BMC Genomics 2022; 23:17. [PMID: 34996357 PMCID: PMC8742460 DOI: 10.1186/s12864-021-08253-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/14/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Schisandra chinensis, an ancient member of the most basal angiosperm lineage which is known as the ANITA, is a fruit-bearing vine with the pharmacological effects of a multidrug system, such as antioxidant, anti-inflammatory, cardioprotective, neuroprotective, anti-osteoporosis effects. Its major bioactive compound is represented by lignans such as schisandrin. Molecular characterization of lignan biosynthesis in S. chinensis is of great importance for improving the production of this class of active compound. However, the biosynthetic mechanism of schisandrin remains largely unknown. RESULTS To understand the potential key catalytic steps and their regulation of schisandrin biosynthesis, we generated genome-wide transcriptome data from three different tissues of S. chinensis cultivar Cheongsoon, including leaf, root, and fruit, via long- and short-read sequencing technologies. A total of 132,856 assembled transcripts were generated with an average length of 1.9 kb and high assembly completeness. Overall, our data presented effective, accurate gene annotation in the prediction of functional pathways. In particular, the annotation revealed the abundance of transcripts related to phenylpropanoid biosynthesis. Remarkably, transcriptome profiling during fruit development of S. chinensis cultivar Cheongsoon revealed that the phenylpropanoid biosynthetic pathway, specific to coniferyl alcohol biosynthesis, showed a tendency to be upregulated at the postfruit development stage. Further the analysis also revealed that the pathway forms a transcriptional network with fruit ripening-related genes, especially the ABA signaling-related pathway. Finally, candidate unigenes homologous to isoeugenol synthase 1 (IGS1) and dirigent-like protein (DIR), which are subsequently activated by phenylpropanoid biosynthesis and thus catalyze key upstream steps in schisandrin biosynthesis, were identified. Their expression was increased at the postfruit development stage, suggesting that they may be involved in the regulation of schisandrin biosynthesis in S. chinensis. CONCLUSIONS Our results provide new insights into the production and accumulation of schisandrin in S. chinensis berries and will be utilized as a valuable transcriptomic resource for improving the schisandrin content.
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Affiliation(s)
- Chang Pyo Hong
- Theragen Bio Co., Ltd., Suwon, 16229, Republic of Korea.
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Dong Jin Lee
- Theragen Bio Co., Ltd., Suwon, 16229, Republic of Korea
| | - Hee Jeong Jeong
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Yi Lee
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Sin-Gi Park
- Theragen Bio Co., Ltd., Suwon, 16229, Republic of Korea
| | - Hyo-Jin Kim
- Jeollabukdo ARES Medicinal Resource Research Institute, Jinan, 55440, Republic of Korea
| | - Ji-Nam Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Hojin Ryu
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Soo-Jin Kwon
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea.
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Jo IH, Han S, Shim D, Ryu H, Hyun TK, Lee Y, Kim D, So YS, Chung JW. Complete Chloroplast Genome of the Inverted Repeat-Lacking Species Vicia bungei and Development of Polymorphic Simple Sequence Repeat Markers. Front Plant Sci 2022; 13:891783. [PMID: 35651765 PMCID: PMC9149428 DOI: 10.3389/fpls.2022.891783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/26/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Vicia bungei is an economically important forage crop in South Korea and China. Although detailed genetic and genomic data can improve population genetic studies, conservation efforts, and improved breeding of crops, few such data are available for Vicia species in general and none at all for V. bungei. Therefore, the main objectives of this study were to sequence, assemble, and annotate V. bungei chloroplast genome and to identify simple sequence repeats (SSRs) as polymorphic genetic markers. RESULTS The whole-genome sequence of V. bungei was generated using an Illumina MiSeq platform. De novo assembly of complete chloroplast genome sequences was performed for the low-coverage sequence using CLC Genome Assembler with a 200-600-bp overlap size. Vicia bungei chloroplast genome was 130,796-bp long. The genome lacked an inverted repeat unit and thus resembled those of species in the inverted repeat-lacking clade within Fabaceae. Genome annotation using Dual OrganellarGenoMe Annotator (DOGMA) identified 107 genes, comprising 75 protein-coding, 28 transfer RNA, and 4 ribosomal RNA genes. In total, 432 SSRs were detected in V. bungei chloroplast genome, including 64 mononucleotides, 14 dinucleotides, 5 trinucleotides, 4 tetranucleotides, 233 pentanucleotides, 90 hexanucleotides, and 14 complex repeated motifs. These were used to develop 232 novel chloroplast SSR markers, 39 of which were chosen at random to test amplification and genetic diversity in Vicia species (20 accessions from seven species). The unweighted pair group method with arithmetic mean cluster analysis identified seven clusters at the interspecies level and intraspecific differences within clusters. CONCLUSION The complete chloroplast genome sequence of V. bungei was determined. This reference genome should facilitate chloroplast resequencing and future searches for additional genetic markers using population samples. The novel chloroplast genome resources and SSR markers will greatly contribute to the conservation of the genus Vicia and facilitate genetic and evolutionary studies of this genus and of other higher plants.
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Affiliation(s)
- Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, South Korea
| | - Seahee Han
- Division of Botany, Honam National Institute of Biological Resources, Mokpo, South Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, South Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, South Korea
| | - Tae Kyung Hyun
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
| | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
| | - Daeil Kim
- Department of Horticulture, Chungbuk National University, Cheongju, South Korea
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, South Korea
- *Correspondence: Yoon-Sup So,
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
- Jong-Wook Chung,
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15
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Moon S, An JY, Choi YJ, Oh YL, Ro HS, Ryu H. Construction of a CRISPR/Cas9-Mediated Genome Editing System in Lentinula edodes. Mycobiology 2021; 49:599-603. [PMID: 35035251 PMCID: PMC8725921 DOI: 10.1080/12298093.2021.2006401] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/13/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
CRISPR/Cas9 genome editing systems have been established in a broad range of eukaryotic species. Herein, we report the first method for genetic engineering in pyogo (shiitake) mushrooms (Lentinula edodes) using CRISPR/Cas9. For in vivo expression of guide RNAs (gRNAs) targeting the mating-type gene HD1 (LeA1), we identified an endogenous LeU6 promoter in the L. edodes genome. We constructed a plasmid containing the LeU6 and glyceraldehyde-3-phosphate dehydrogenase (LeGPD) promoters to express the Cas9 protein. Among the eight gRNAs we tested, three successfully disrupted the LeA1 locus. Although the CRISPR-Cas9-induced alleles did not affect mating with compatible monokaryotic strains, disruption of the transcription levels of the downstream genes of LeHD1 and LeHD2 was detected. Based on this result, we present the first report of a simple and powerful genetic manipulation tool using the CRISPR/Cas9 toolbox for the scientifically and industrially important edible mushroom, L. edodes.
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Affiliation(s)
- Suyun Moon
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Korea
| | | | - Yeon-Jae Choi
- Department of Bio & Medical Big Data and Research Institute of Life Sciences, Gyeongsang National University, Jinju, Korea
| | - Youn-Lee Oh
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
| | - Hyeon-Su Ro
- Department of Bio & Medical Big Data and Research Institute of Life Sciences, Gyeongsang National University, Jinju, Korea
| | - Hojin Ryu
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Korea
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16
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Kim J, Yoo C, Seo S, Jeong J, Ryoo BY, Kim KP, Lee J, Lee KW, Kim JW, Kim IH, Kang M, Ryu H, Cheon J, Park S. 1690P A multicenter randomized phase II open label study to compare the safety and efficacy of direct oral anticoagulants versus subcutaneous dalteparin for cancer-associated venous thromboembolism in patients with advanced upper gastrointestinal, hepatobiliary and pancreatic cancer. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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17
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Lee J, Kim H, Park SG, Hwang H, Yoo SI, Bae W, Kim E, Kim J, Lee HY, Heo TY, Kang KK, Lee Y, Hong CP, Cho H, Ryu H. Brassinosteroid-BZR1/2-WAT1 module determines the high level of auxin signalling in vascular cambium during wood formation. New Phytol 2021; 230:1503-1516. [PMID: 33570747 DOI: 10.1111/nph.17265] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
The tight regulation of local auxin homeostasis and signalling maxima in xylem precursor cells specifies the organising activity of the vascular cambium and consequently promotes xylem differentiation and wood formation. However, the molecular mechanisms underlying the local auxin signalling maxima in the vascular cambium are largely unknown. Here, we reveal that brassinosteroid (BR)-activated WALLS ARE THIN1 (WAT1) facilitates wood formation by enhancing local auxin signalling in the vascular cambium in Solanum lycopersicum. Growth defects and low auxin signalling readouts in the BR-deficient tomato cultivar, Micro-Tom, were associated with a novel recessive allele, Slwat1-copi, created by the insertion of a retrotransposon in the last exon of the SlWAT1 locus. Molecular and genetic studies by generating the gain-of-function and loss-of-function tomato mutants revealed that SlWAT1 is a critical regulator for fine tuning local auxin homeostasis and signalling outputs in vascular cambium to facilitate secondary growth. Finally, we discovered that BR-regulated SlBZR1/2 directly activated downstream auxin responses by SlWAT1 upregulation in xylem precursor cells to facilitate xylem differentiation and subsequent wood formation. Our data suggest that the BR-SlBZR1/2-WAT1 signalling network contributes to the high level of auxin signalling in the vascular cambium for secondary growth.
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Affiliation(s)
- Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju, 28644, Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hyemin Kim
- Department of Biology, Chungbuk National University, Cheongju, 28644, Korea
| | | | - Hyeona Hwang
- Department of Biology, Chungbuk National University, Cheongju, 28644, Korea
| | | | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju, 28644, Korea
| | - Eunhui Kim
- Department of Biology, Chungbuk National University, Cheongju, 28644, Korea
| | - Jaehoon Kim
- Department of Information and Statistics, Chungbuk National University, Cheongju, 28644, Korea
| | - Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju, 28644, Korea
| | - Tae-Young Heo
- Department of Information and Statistics, Chungbuk National University, Cheongju, 28644, Korea
| | - Kwon Kyoo Kang
- Department of Horticulture, Hankyong National University, Ansung, 17579, Korea
| | - Yuree Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | | | - Hyunwoo Cho
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 28644, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, 28644, Korea
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18
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Hwang H, Lee HY, Ryu H, Cho H. Functional Characterization of BRASSINAZOLE-RESISTANT 1 in Panax Ginseng ( PgBZR1) and Brassinosteroid Response during Storage Root Formation. Int J Mol Sci 2020; 21:ijms21249666. [PMID: 33352948 PMCID: PMC7766047 DOI: 10.3390/ijms21249666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 11/17/2022] Open
Abstract
Brassinosteroids (BRs) play crucial roles in the physiology and development of plants. In the model plant Arabidopsis, BR signaling is initiated at the level of membrane receptors, BRASSINOSTEROIDS INSENSITIVE 1 (BRI1) and BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1) complex, thus activating the transcription factors (TFs) BRASSINAZOLE RESISTANT 1/BRI1-EMS-SUPPRESSOR 1 (BZR1/BES1) to coordinate BR responsive genes. BRASSINOSTEROIDS INSENSITIVE 2 (BIN2), glycogen synthase kinase 3 (GSK3) like-kinase, negatively regulates BZR1/BES1 transcriptional activity through phosphorylation-dependent cytosolic retention and shuttling. However, it is still unknown whether this mechanism is conserved in Panax ginseng C. A. Mayer, a member of the Araliaceae family, which is a shade-tolerant perennial root crop. Despite its pharmacological and agricultural importance, the role of BR signaling in the development of P. ginseng and characterization of BR signaling components are still elusive. In this study, by utilizing the Arabidopsisbri1 mutant, we found that ectopic expression of the gain of function form of PgBZR1 (Pgbzr1-1D) restores BR deficiency. In detail, ectopic expression of Pgbzr1-1D rescues dwarfism, defects of floral organ development, and hypocotyl elongation of bri1-5, implying the functional conservation of PgBZR1 in P. ginseng. Interestingly, brassinolide (BL) and BRs biosynthesis inhibitor treatment in two-year-old P. ginseng storage root interferes with and promotes, respectively, secondary growth in terms of xylem formation. Altogether, our results provide new insight into the functional conservation and potential diversification of BR signaling and response in P. ginseng.
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Affiliation(s)
- Hyeona Hwang
- Department of Biology, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea;
| | - Hwa-Yong Lee
- Department of Forest Science, College of Agriculture, Life & Environmental Sciences, Chungbuk National University, Cheongju 28644, Korea;
| | - Hojin Ryu
- Department of Biology, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea;
- Correspondence: (H.R.); (H.C.)
| | - Hyunwoo Cho
- Department of Industrial Plant Science & Technology, College of Agriculture, Life & Environmental Sciences, Chungbuk National University, Cheongju 28644, Korea
- Correspondence: (H.R.); (H.C.)
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19
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Hong CP, Moon S, Yoo SI, Noh JH, Ko HG, Kim HA, Ro HS, Cho H, Chung JW, Lee HY, Ryu H. Functional Analysis of a Novel ABL ( Abnormal Browning Related to Light) Gene in Mycelial Brown Film Formation of Lentinula edodes. J Fungi (Basel) 2020; 6:E272. [PMID: 33182449 PMCID: PMC7712820 DOI: 10.3390/jof6040272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/30/2022] Open
Abstract
Lentinula edodes is a globally important edible mushroom species that is appreciated for its medicinal properties as well as its nutritional value. During commercial cultivation, a mycelial brown film forms on the surface of the sawdust growth medium at the late vegetative stage. Mycelial film formation is a critical developmental process that contributes to the quantity and quality of the mushroom yield. However, little is known regarding the genetic underpinnings of brown film formation on the surface of mycelial tissue. A novel causal gene associated with the formation of the mycelial brown film, named ABL (Abnormal browning related to light), was identified in this study. The comparative genetic analysis by dihybrid crosses between normal and abnormal browning film cultivars demonstrated that a single dominant allele was responsible for the abnormal mycelium browning phenotype. Whole-genome sequencing analysis of hybrid isolates revealed five missense single-nucleotide polymorphisms (SNPs) in the ABL locus of individuals forming abnormal partial brown films. Additional whole-genome resequencing of a further 16 cultivars showed that three of the five missense SNPs were strongly associated with the abnormal browning phenotype. Overexpression of the dominant abl-D allele in a wild-type background conferred the abnormal mycelial browning phenotype upon transformants, with slender hyphae observed as a general defective mycelial growth phenotype. Our methodology will aid the future discovery of candidate genes associated with favorable traits in edible mushrooms. The discovery of a novel gene, ABL, associated with mycelial film formation will facilitate marker-associated breeding in L. edodes.
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Affiliation(s)
- Chang Pyo Hong
- Department of R&D Planning & Management, Theragen Bio, Suwon 16229, Korea; (C.P.H.); (S.-i.Y.); (H.A.K.)
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea;
| | - Seung-il Yoo
- Department of R&D Planning & Management, Theragen Bio, Suwon 16229, Korea; (C.P.H.); (S.-i.Y.); (H.A.K.)
| | - Jong-Hyun Noh
- Forest Mushroom Research Center, National Forestry Cooperative Federation, Yeoju 12653, Korea; (J.-H.N.); (H.-G.K.)
| | - Han-Gyu Ko
- Forest Mushroom Research Center, National Forestry Cooperative Federation, Yeoju 12653, Korea; (J.-H.N.); (H.-G.K.)
| | - Hyun A. Kim
- Department of R&D Planning & Management, Theragen Bio, Suwon 16229, Korea; (C.P.H.); (S.-i.Y.); (H.A.K.)
| | - Hyeon-Su Ro
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Korea;
| | - Hyunwoo Cho
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea; (H.C.); (J.-W.C.)
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea; (H.C.); (J.-W.C.)
| | - Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea;
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20
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Kim J, Choo M, Ryu H, Byun S, Lee S. Interpretation of uroflowmetrogram: Application with artificial intelligence. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)33952-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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21
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Lee SH, Lee SH, Won K, Kim MS, Ryu H, Kim YH, Ahn JY. Loop-Mediated Isothermal Amplification (LAMP)-Based Turn on Fluorescent Paper (ToFP) Device for Detecting Rosellinia necatrix. J Biomed Nanotechnol 2020; 16:166-178. [PMID: 32252878 DOI: 10.1166/jbn.2020.2889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
White root rot (WRR) disease caused by Rosellinia necatrix, a fungal pathogen, results in severe damage to various fruit trees, decreasing their marketability. Regular monitoring is a major process because the pathogen can remain in the soil around the host for a long time. Loop-mediated isothermal amplification (LAMP) is a highly sensitive and efficient amplification technology of nucleic acids (DNA or RNA) that can be performed at constant temperatures. Thus, it has been spotlighted as a useful tool for detecting several infectious agents. In the present study, LAMP-based Turn-on Fluorescent Paper (ToFP) devices were designed and applied to detect R. necatrix. LAMP conditions were optimized and found to be optimal at a reaction temperature (62 °C) and a reaction time (30 minutes). These reaction conditions were confirmed by applying them to infectious soil samples collected from the field. The limitation of detection was identified as 10 fg of genomic DNA under optimized LAMP conditions. These LAMP-based ToFP devices were generated with easily available stationery materials and the utility of these devices to analyze the LAMP results were confirmed through several experiments on a total of 14 field samples. The results showed that the developed LAMP-based detection system was very sensitive and had the advantages of rapid detection and high availability in the field.
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Lee HY, Moon S, Ro HS, Chung JW, Ryu H. Analysis of Genetic Diversity and Population Structure of Wild Strains and Cultivars Using Genomic SSR Markers in Lentinula edodes. Mycobiology 2020; 48:115-121. [PMID: 32363039 PMCID: PMC7178855 DOI: 10.1080/12298093.2020.1727401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/24/2019] [Accepted: 01/25/2020] [Indexed: 05/11/2023]
Abstract
In this study, the genetic diversity and the population structure of 77 wild strains and 23 cultivars of Lentinula edodes from Korea were analyzed using 20 genomic SSRs, and their genetic relationship was investigated. The tested strains of L. edodes were divided into three sub-groups consisting of only wild strains, mainly wild strains and several cultivars, and mainly cultivars and several wild strains by distance-based analysis. Using model-based analysis, L. edodes strains were divided into two subpopulations; the first one consisting of only wild strains and the second one with mainly cultivars and several wild strains. Moreover, AMOVA analysis revealed that the genetic variation in the cultivars was higher than that in the wild strains. The expected and observed heterozygosity and values indicating the polymorphic information content of L. edodes cultivars from Korea were also higher than that of the wild strains. Based on these results, we presume that the cultivars in Korea have developed by using numerous strains from other countries. In conclusion, the usage of wild strains for the development of new cultivars could improve the adaptability of L. edodes to biotic and abiotic stress.
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Affiliation(s)
- Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyeon-Su Ro
- Division of Applied Life Science and Research Institute of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
- CONTACT Jong-Wook Chung
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
- Hojin Ryu
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Hidayati N, Poon A, Willowson K, Eslick E, Ryu H, Bailey D. Evaluation of Kidney Dose in Neuroendocrine Tumors Patients after Peptide Receptor Radionuclide Therapy using 177Lu-DOTATATE. Atom Indo 2019. [DOI: 10.17146/aij.2019.910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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24
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Kim H, Shim D, Moon S, Lee J, Bae W, Choi H, Kim K, Ryu H. Transcriptional network regulation of the brassinosteroid signaling pathway by the BES1-TPL-HDA19 co-repressor complex. Planta 2019; 250:1371-1377. [PMID: 31280329 DOI: 10.1007/s00425-019-03233-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/03/2019] [Indexed: 05/26/2023]
Abstract
The brassinosteroid-related BES1 and BZR1 transcription factors dynamically modulate downstream gene networks via the TPL-HDA19 co-repressor complex in BR-signaling pathways in Arabidopsis thaliana. Brassinosteroids (BRs) are plant steroid hormones that are essential for diverse growth and developmental processes across the whole life cycle of plants. In Arabidopsis thaliana, the BR-related transcription factors BRI1-EMS-SUPPRESSOR 1 (BES1) and BRASSINAZOLE-RESISTANT 1 (BZR1) regulate a range of global gene expression in response to BR and several external signaling cues; however, the molecular mechanisms by which they mediate the reprogramming of downstream transcription remain unclear. We here report that formation of a protein complex between BES1 and BZR1 and Histone Deacetylase 19 (HDA19) via the conserved ERF-associated amphiphilic repression (EAR) motif proved essential for regulation of BR-signaling-related gene expression. Defects in BR-related functions of BES1 and BZR1 proteins containing a mutated EAR motif were completely rescued by artificial fusion with EAR-repression domain (SRDX), TOPLESS (TPL), or HDA19 proteins. RNA-sequencing analysis of Arabidopsis plants over-expressing bes1-DmEAR or bes1-DmEAR-HDA19 revealed an essential role for HDA19 activity in regulation of BES1/BZR1-mediated BR signaling. In addition to BR-related gene expression, the BES1-HDA19 transcription factor complex was important for abiotic stress-related drought stress tolerance and organ boundary formation. These results suggested that integrating activation of BR-signaling pathways with the formation of the protein complex containing BES1/BZR1 and TPL-HDA19 via the EAR motif was important in fine-tuning BR-related gene networks in plants.
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Affiliation(s)
- Hyemin Kim
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Donghwan Shim
- Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Hyunmo Choi
- Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Kyunghwan Kim
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Kim M, Hwang JY, Choo KS, Ryu H, Reid SNS, Kim YW, Kim TU, Kim JH. Comparison of image quality of abdominopelvic CT in paediatric patients: low osmolar contrast media versus less iodine-containing iso-osmolar contrast media at different peak kilovoltages. Clin Radiol 2019; 74:896.e9-896.e16. [PMID: 31431254 DOI: 10.1016/j.crad.2019.06.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/21/2019] [Indexed: 10/26/2022]
Abstract
AIM To evaluate the effect of iso-osmolar contrast media (IOCM) at different tube voltages on image quality for abdominal computed tomography (CT) in paediatric patients. MATERIALS AND METHODS The low osmolar contrast media (LOCM) group and IOCM group consisted of 101 and 102 CT examinations, respectively, in patients <18 years old. Images were reviewed retrospectively. Objective measurement of the contrast enhancement and noise were analysed and contrast-to-noise ratios (CNRs) of the abdominal aorta, portal vein, and liver were calculated. Four radiologists participated in subjective analysis using a four-point scale system to evaluate degrees of contrast enhancement, image noise, beam-hardening artefact, and overall image quality. Reader performance for correctly differentiating the two kinds of contrast media was evaluated. RESULTS Regarding the objective measurement, contrast enhancement was significantly higher in the LOCM group (p<0.05). In subjective analysis, only CT using 120 kVp showed significantly stronger enhancement in the LOCM group (p=0.002), and sensitivity to differentiate the IOCM was 80.6%. Overall sensitivity and specificity for correctly differentiating IOCM were 57.1%, and 56.9%, respectively. CONCLUSION The application of IOCM was found to be feasible for performing paediatric abdominopelvic CT with a low tube voltage protocol. Although objective measurements of contrast enhancement were significantly lower in the IOCM group, subjective contrast enhancement and image quality assessments were not statistically different between groups.
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Affiliation(s)
- M Kim
- Department of Radiology, Pusan National University Yangsan Hospital, Geumo-ro 20, Yangsan-si, Gyeongsangnam-do, 50612, Republic of Korea
| | - J Y Hwang
- Department of Radiology, Pusan National University Yangsan Hospital, Geumo-ro 20, Yangsan-si, Gyeongsangnam-do, 50612, Republic of Korea; Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Geumo-ro 20, Yangsan-si, Gyeongsangnam-do, 50612, Republic of Korea.
| | - K S Choo
- Department of Radiology, Pusan National University Yangsan Hospital, Geumo-ro 20, Yangsan-si, Gyeongsangnam-do, 50612, Republic of Korea
| | - H Ryu
- Department of Radiology, Pusan National University Yangsan Hospital, Geumo-ro 20, Yangsan-si, Gyeongsangnam-do, 50612, Republic of Korea
| | - S N S Reid
- College of Creative Human Resource, School of Liberal Arts Education, Kyungsung University, Busan, 48434, Republic of Korea
| | - Y W Kim
- Department of Radiology, Pusan National University Yangsan Hospital, Geumo-ro 20, Yangsan-si, Gyeongsangnam-do, 50612, Republic of Korea
| | - T U Kim
- Department of Radiology, Pusan National University Yangsan Hospital, Geumo-ro 20, Yangsan-si, Gyeongsangnam-do, 50612, Republic of Korea
| | - J H Kim
- Department of Radiology, Pusan National University Yangsan Hospital, Geumo-ro 20, Yangsan-si, Gyeongsangnam-do, 50612, Republic of Korea
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Bang JH, Hong CE, Raveendar S, Bang KH, Ma KH, Kwon SW, Ryu H, Jo IH, Chung JW. Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species. PeerJ 2019; 7:e7479. [PMID: 31410317 PMCID: PMC6689217 DOI: 10.7717/peerj.7479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/15/2019] [Indexed: 01/12/2023] Open
Abstract
Background Licorice (Glycyrrhiza spp. L.) is used as a natural sweetener and medicinal herb in European and Asian countries. Molecular studies have been conducted to find differences between wild and cultivated species because most wild species are highly resistant to abiotic and biotic stresses compared with their cultivated species. However, few molecular markers have been developed for studying the genetic diversity and population structure of licorice species and to identify differences between cultivars. Thus, the present study aimed to develop a set of genomic simple sequence repeat (SSR) markers for molecular studies of these species. Methods In the present study, we developed polymorphic SSR markers based on whole-genomesequence data of Glycyrrhiza lepidota. Then, based on the sequence information, the polymorphic SSR markers were developed. The SSR markers were applied to 23 Glycyrrhiza individual plants. We also evaluated the phylogenetic relationships and interspecies transferability among samples. Results The genetic diversity analysis using these markers identified 2–23 alleles, and the major allele frequency, observed heterozygosity, genetic diversity, and polymorphism information content were 0.11–0.91, 0–0.90, 0.17–0.94, and 0.15–0.93, respectively. Interspecies transferability values were 93.5%, 91.6%, and 91.1% for G. echinata, G. glabra, and G. uralensis, respectively. Phylogenetic analysis clustered cultivated (group 1) and wild (group 2) species into three and two subgroups, respectively. The reported markers represent a valuable resource for the genetic characteri z ation of Glycyrrhiza spp. for theanalysis of its genetic variability, and as a tool for licorice transferability. This is the first intraspecific study in a collection of Glycyrrhiza spp. germplasm using SSR markers.
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Affiliation(s)
- Jun Hyoung Bang
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
| | - Chi Eun Hong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Eumseong, South Korea
| | - Sebastin Raveendar
- National Agrobiodiversity Center, National Institute of Agricultural Science, Jeonju, South Korea
| | - Kyong Hwan Bang
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Eumseong, South Korea
| | - Kyung Ho Ma
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Eumseong, South Korea
| | - Soon Wook Kwon
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, South Korea
| | - Ick Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Eumseong, South Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, South Korea
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You JM, Kim TU, Kim S, Lee NK, Lee JW, Ryu H, Kim JH, Hong SB, Jeon TY, Park DY. Preoperative N stage evaluation in advanced gastric cancer patients using multidetector CT: can the sum of the diameters of metastatic LNs be used for N stage evaluation? Clin Radiol 2019; 74:782-789. [PMID: 31378300 DOI: 10.1016/j.crad.2019.06.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 06/28/2019] [Indexed: 12/23/2022]
Abstract
AIM To compare the diagnostic performance of total counts of metastatic lymph nodes (LN-sum) and conventional multidetector (MD) computed tomography (CT) staging in the nodal evaluation of advanced gastric cancer (AGC) patients. MATERIALS AND METHODS In total, 127 consecutive patients who underwent preoperative MDCT and gastrectomy for AGC were identified. Metastatic LNs on MDCT were defined as LNs with a short axis ≥8 mm, marked or heterogeneous enhancement, and morphological features (central necrosis, round shape, clustering). The sensitivity, specificity, accuracy, positive predictive value (PPV), and negative predictive value (NPV) of the N-stage using LN-sum and conventional MDCT staging were generated and compared. In addition, metastatic LN counts between the MDCT and the histopathological examinations and correlation between LN-sum and histopathological nodal status were analysed. RESULTS The total counts of metastatic LNs on MDCT was significantly smaller than those detected in histopathological assessments (p<0.0001). LN-sum showed significant correlation with the pathological N stage and the number of metastatic LNs (rho=0.69, 0.73, p<0.0001). The areas under the receiver operating characteristic curve were 0.896, and 0.835, for N stage ≥N2 and N3, with cut-off values of 12.5 and 23.5 mm, respectively. LN-sum provided better diagnostic performance than conventional MDCT staging for discriminating N0-2 versus N3; sensitivity, accuracy, PPV and NPV of LN-sum were significantly higher (80.4 versus 52.2%, 81.1 versus 68.5%, 71.2 versus 57.1%, and 88 versus 74.1%). CONCLUSION LN-sum may be sufficiently useful in assessing the N3 stage of AGC and may help to plan appropriate therapy for AGC patients.
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Affiliation(s)
- J M You
- Department of Radiology, Medical Research Institute, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Gyeongsangnam-do, Republic of Korea
| | - T U Kim
- Department of Radiology, Medical Research Institute, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Gyeongsangnam-do, Republic of Korea.
| | - S Kim
- Department of Radiology, Pusan National University Hospital, Pusan National University School of Medicine, Medical Research Institute, Busan, Republic of Korea
| | - N K Lee
- Department of Radiology, Pusan National University Hospital, Pusan National University School of Medicine, Medical Research Institute, Busan, Republic of Korea
| | - J W Lee
- Department of Radiology, Medical Research Institute, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Gyeongsangnam-do, Republic of Korea
| | - H Ryu
- Department of Radiology, Medical Research Institute, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Gyeongsangnam-do, Republic of Korea
| | - J H Kim
- Department of Radiology, Medical Research Institute, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Gyeongsangnam-do, Republic of Korea
| | - S B Hong
- Department of Radiology, Pusan National University Hospital, Pusan National University School of Medicine, Medical Research Institute, Busan, Republic of Korea
| | - T Y Jeon
- Department of Surgery, Pusan National University Hospital, Pusan National University School of Medicine, Medical Research Institute, Busan, Republic of Korea
| | - D Y Park
- Department of Pathology, Pusan National University Hospital, Pusan National University School of Medicine, Medical Research Institute, Busan, Republic of Korea
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Park H, Ryu H, Kim H, Oh K, Oh Y, Lee K, Kim S, Kim Y, Ahn C. SUN-199 URINARY ANGIOTENSINOGEN TO CREATININE RATIO (UAGT/CR) IS NOT A PREDICTIVE BIOMARKER FOR RENAL PROGRESSION IN AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE: KNOW-CKD STUDY. Kidney Int Rep 2019. [DOI: 10.1016/j.ekir.2019.05.602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Hong J, Lee H, Lee J, Kim H, Ryu H. ABSCISIC ACID-INSENSITIVE 3 is involved in brassinosteroid-mediated regulation of flowering in plants. Plant Physiol Biochem 2019; 139:207-214. [PMID: 30908972 DOI: 10.1016/j.plaphy.2019.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 02/28/2019] [Accepted: 03/12/2019] [Indexed: 05/22/2023]
Abstract
ABSCISIC ACID-INSENSITIVE 3 (ABI3) is one of the essential transcription factors of ABSCISIC ACID (ABA) signaling, functioning in seed germination, early seedling development, and abiotic stress tolerance. A recent study showed that epigenetic repression of ABI3 by brassinosteroid (BR)-activated BRI1 EMS SUPPRESSOR1 (BES1)-TOPLESS (TPL)HISTONE DEACETYLASE 19 (HDA19) repressor complex is a critical event for promoting seed germination and early seedling development. However, other physiological roles of the repression of ABI3 and ABA responses by BES1-mediated BR signaling pathways remain elusive. Here, we show that BES1-mediated suppression of ABI3 promotes floral transition and ABI3 acts as a negative regulator for flowering. Ectopic expression of ABI3 specifically compromised the early flowering phenotype of bes1-D and induced severe late-flowering phenotypes in wild-type Arabidopsis and Solanum lycopersicum plants. Both spatiotemporal expression patterns and global transcriptome analysis of ABI3-overexpressing plants supported the biological roles of ABI3 in the negative regulation of floral transition and reproduction. Finally, we confirmed that the loss of function of ABI3 induced early-flowering phenotypes in both long- and short-day conditions. In conclusion, our data suggest that BES1-mediated regulation of ABI3 is important in the reproductive phase transition of plants.
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Affiliation(s)
- Jeongeui Hong
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Horim Lee
- Department of Biotechnology, Duksung Women's University, Seoul, 01369, Republic of Korea.
| | - Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Hyemin Kim
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Lee J, Han S, Lee HY, Jeong B, Heo TY, Hyun TK, Kim K, Je BI, Lee H, Shim D, Park SJ, Ryu H. Brassinosteroids facilitate xylem differentiation and wood formation in tomato. Planta 2019; 249:1391-1403. [PMID: 30673841 DOI: 10.1007/s00425-019-03094-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
BR signaling pathways facilitate xylem differentiation and wood formation by fine tuning SlBZR1/SlBZR2-mediated gene expression networks involved in plant secondary growth. Brassinosteroid (BR) signaling and BR crosstalk with diverse signaling cues are involved in the pleiotropic regulation of plant growth and development. Recent studies reported the critical roles of BR biosynthesis and signaling in vascular bundle development and plant secondary growth; however, the molecular bases of these roles are unclear. Here, we performed comparative physiological and anatomical analyses of shoot morphological growth in a cultivated wild-type tomato (Solanum lycopersicum cv. BGA) and a BR biosynthetic mutant [Micro Tom (MT)]. We observed that the canonical BR signaling pathway was essential for xylem differentiation and sequential wood formation by facilitating plant secondary growth. The gradual retardation of xylem development phenotypes during shoot vegetative growth in the BR-deficient MT tomato mutant recovered completely in response to exogenous BR treatment or genetic complementation of the BR biosynthetic DWARF (D) gene. By contrast, overexpression of the tomato Glycogen synthase kinase 3 (SlGSK3) or CRISPR-Cas9 (CR)-mediated knockout of the tomato Brassinosteroid-insensitive 1 (SlBRI1) impaired BR signaling and resulted in severely defective xylem differentiation and secondary growth. Genetic modulation of the transcriptional activity of the tomato Brassinazole-resistant 1/2 (SlBZR1/SlBZR2) confirmed the positive roles of BR signaling pathways for xylem differentiation and secondary growth. Our data indicate that BR signaling pathways directly promote xylem differentiation and wood formation by canonical BR-activated SlBZR1/SlBZR2.
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Affiliation(s)
- Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Seahee Han
- National Agrobiodiversity Center, National Academy of Agricultural Science RDA, Jeonju, 54875, Republic of Korea
| | - Hwa-Yong Lee
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Bomi Jeong
- Department of Information and Statistics, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Tae-Young Heo
- Department of Information and Statistics, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Tae Kyung Hyun
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Kyunghwan Kim
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Byoung Il Je
- Department of Horticultural Bioscience, College of Natural Resource and Life Science, Pusan National University, Miryang, 50467, Republic of Korea
| | - Horim Lee
- Department of Biotechnology, Duksung Women's University, Seoul, 01369, Republic of Korea
| | - Donghwan Shim
- Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Soon Ju Park
- Division of Biological Sciences, Research Institute for Basic Science, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Shin WR, Sekhon SS, Kim SG, Rhee SJ, Yang GN, Won K, Rhee SK, Ryu H, Kim K, Min J, Ahn JY, Kim YH. Aptamer-Based Pathogen Monitoring for Salmonella enterica ser. Typhimurium. J Biomed Nanotechnol 2019; 14:1992-2002. [PMID: 30165934 DOI: 10.1166/jbn.2018.2634] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Salmonella enterica ser. Typhimurium is a foodborne pathogen that causes salmonellosis. Symptoms of salmonellosis include fever, diarrhea, and gastroenteritis. Conventional culture methods for detecting foodborne bacterial pathogens require long incubation time, expensive immunoassay methods, and sample enrichment steps. The objective of this study was to develop an aptamer-based sandwich assay to detect S. enterica ser. Typhimurium. First, S. enterica ser. Typhimurium specific binding aptamers (S11 and S24) were obtained by whole-cell SELEX for high sensitivity and specificity detection using live S. enterica ser. Typhimurium. S11 and S24 aptamers were able to capture S. enterica ser. Typhimurium selectively and distinguish it from other species of Salmonella (S. enterica ser. Typhimurium, S. enterica ser. Choleraesuis, S. enterica ser. Dublin, and S. enterica ser. Enteritidis) and food-borne bacterial pathogens (Escherichia coli K12, Listeria monocytogenes, Shigella sonnei and Staphylococcus aureus) with KD values of 4.41×10-12 M and 3.75×10-11 M, respectively. S. enterica ser. Typhimurium. aptamer-based sandwich assay exhibited a linear response for sensing S. enterica ser. Typhimurium. cells at concentration ranging from 2×101 to 2×105 CFU/mL. This aptamer-based sandwich assay can be used for on-site detection of S. enterica ser. Typhimurium.
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Yoo SI, Lee HY, Markkandan K, Moon S, Ahn YJ, Ji S, Ko J, Kim SJ, Ryu H, Hong CP. Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes. BMC Genomics 2019; 20:121. [PMID: 30736734 PMCID: PMC6368761 DOI: 10.1186/s12864-019-5509-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 02/05/2019] [Indexed: 12/18/2022] Open
Abstract
Background Lentinula edodes is one of the most popular edible mushroom species in the world and contains useful medicinal components, such as lentinan. The light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process for ensuring the quantity and quality of this edible mushroom. To understand the molecular mechanisms underlying this critical developmental process in L. edodes, we characterized the morphological phenotypic changes in a strain, Chamaram, associated with abnormal brown film formation and compared its genome-wide transcriptional features. Results In the present study, we performed genome-wide transcriptome analyses of different vegetative mycelium growth phenotypes, namely, early white, normal brown, and defective dark yellow partial brown films phenotypes which were exposed to different light conditions. The analysis revealed the identification of clusters of genes specific to the light-induced brown film phenotypes. These genes were significantly associated with light sensing via photoreceptors such as FMN- and FAD-bindings, signal transduction by kinases and GPCRs, melanogenesis via activation of tyrosinases, and cell wall degradation by glucanases, chitinases, and laccases, which suggests these processes are involved in the formation of mycelial browning in L. edodes. Interestingly, hydrophobin genes such as SC1 and SC3 exhibited divergent expression levels in the normal and abnormal brown mycelial films, indicating the ability of these genes to act in fruiting body initiation and formation of dikaryotic mycelia. Furthermore, we identified the up-regulation of glycoside hydrolase domain-containing genes in the normal brown film but not in the abnormal film phenotype, suggesting that cell wall degradation in the normal brown film phenotype is crucial in the developmental processes related to the initiation and formation of fruiting bodies. Conclusions This study systematically analysed the expression patterns of light-induced browning-related genes in L. edodes. Our findings provide information for further investigations of browning formation mechanisms in L. edodes and a foundation for future L. edodes breeding. Electronic supplementary material The online version of this article (10.1186/s12864-019-5509-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seung-Il Yoo
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea
| | - Hwa-Yong Lee
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | | | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Yong Ju Ahn
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea
| | - Sumin Ji
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea
| | - Junsu Ko
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea
| | - Seong-Jin Kim
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea.,Precision Medicine Research Center, Advanced Institutes of Convergence Technology, Suwon, Korea.,Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University, Suwon, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Chang Pyo Hong
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea.
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Lee HY, Raveendar S, An H, Oh YL, Jang KY, Kong WS, Ryu H, So YS, Chung JW. Development of Polymorphic Simple Sequence Repeat Markers using High-Throughput Sequencing in Button Mushroom ( Agaricus bisporus). Mycobiology 2018; 46:421-428. [PMID: 30637151 PMCID: PMC6319473 DOI: 10.1080/12298093.2018.1538072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/05/2018] [Accepted: 08/14/2018] [Indexed: 06/09/2023]
Abstract
The white button mushroom (Agaricus bisporus) is one of the most widely cultivated species of edible mushroom. Despite its economic importance, relatively little is known about the genetic diversity of this species. Illumina paired-end sequencing produced 43,871,558 clean reads and 69,174 contigs were generated from five offspring. These contigs were subsequently assembled into 57,594 unigenes. The unigenes were annotated with reference genome in which 6,559 unigenes were associated with clusters, indicating orthologous genes. Gene ontology classification assigned many unigenes. Based on genome data of the five offspring, 44 polymorphic simple sequence repeat (SSR) markers were developed. The major allele frequency ranged from 0.42 to 0.92. The number of genotypes and the number of alleles ranged from 1 to 4, and from 2 to 4, respectively. The observed heterozygosity and the expected heterozygosity ranged from 0.00 to 1.00, and from 0.15 to 0.64, respectively. The polymorphic information content value ranged from 0.14 to 0.57. The genetic distances and UPGMA clustering discriminated offspring strains. The SSR markers developed in this study can be applied in polymorphism analyses of button mushroom and for cultivar discrimination.
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Affiliation(s)
- Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Sebastin Raveendar
- National Agrobiodiversity Center, National Institute of Agricultural Science, RDA, Jeonju, Republic of Korea
| | - Hyejin An
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Youn-Lee Oh
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, RDA, Eumseong, Republic of Korea
| | - Kab-Yeul Jang
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, RDA, Eumseong, Republic of Korea
| | - Won-Sik Kong
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, RDA, Eumseong, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
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Lee HY, Moon S, Koo CD, Chung JW, Ryu H. The complete mitochondrial genome of the edible and phytopathogenic fungus Desarmillaria tabescens. Mitochondrial DNA B Resour 2018; 4:33-34. [PMID: 33365409 PMCID: PMC7510627 DOI: 10.1080/23802359.2018.1535861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/20/2018] [Indexed: 10/27/2022]
Abstract
Desarmillaria tabescens is one of the most important edible, medicinal, and phytopathogenic basidiomycetes. The complete mitochondrial genome of this species was determined using next-generation sequencing technology. This mitogenome is a circular molecule of 93,439 bp with a GC content of 29.28% and contains 15 protein-coding, two rRNA (rnl and rns), and 24 tRNA genes. Phylogenetic analysis revealed that D. tabescens is genetically closest to Agrocybe aegerita. Desarmillaria tabescens mitogenome can contribute to our understanding of the phylogeny and evolution of this species.
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Affiliation(s)
- Hwa-Yong Lee
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea.,Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Chang-Duck Koo
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
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Park SG, Ryu D, Lee H, Ryu H, Ahn YJ, Yoo SI, Ko J, Hong CP. TaF: a web platform for taxonomic profile-based fungal gene prediction. Genes Genomics 2018; 41:337-342. [PMID: 30456524 DOI: 10.1007/s13258-018-0766-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 11/13/2018] [Indexed: 10/27/2022]
Abstract
INTRODUCTION The accurate prediction and annotation of gene structures from the genome sequence of an organism enable genome-wide functional analyses to obtain insight into the biological properties of an organism. OBJECTIVES We recently developed a highly accurate filamentous fungal gene prediction pipeline and web platform called TaF. TaF is a homology-based gene predictor employing large-scale taxonomic profiling to search for close relatives in genome queries. METHODS TaF pipeline consists of four processing steps; (1) taxonomic profiling to search for close relatives to query, (2) generation of hints for determining exon-intron boundaries from orthologous protein sequence data of the profiled species, (3) gene prediction by combination of ab inito and evidence-based prediction methods, and (4) homology search for gene models. RESULTS TaF generates extrinsic evidence that suggests possible exon-intron boundaries based on orthologous protein sequence data, thus reducing false-positive predictions of gene structure based on distantly related orthologs data. In particular, the gene prediction method using taxonomic profiling shows very high accuracy, including high sensitivity and specificity for gene models, suggesting a new approach for homology-based gene prediction from newly sequenced or uncharacterized fungal genomes, with the potential to improve the quality of gene prediction. CONCLUSION TaF will be a useful tool for fungal genome-wide analyses, including the identification of targeted genes associated with a trait, transcriptome profiling, comparative genomics, and evolutionary analysis.
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Affiliation(s)
- Sin-Gi Park
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea
| | - DongSung Ryu
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea
| | - Hyunsung Lee
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Yong Ju Ahn
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea
| | - Seung Il Yoo
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea
| | - Junsu Ko
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea.
| | - Chang Pyo Hong
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea.
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Lee MW, Kim N, Kim S, Joo M, Ryu H, Lee H. Chemokine receptor CXCR7 expression, function and clinical implications in head and neck squamous cell carcinoma. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy304.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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37
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Lee H, Lee KM, Han D, Ryu H. N-Myc and STAT interactor (NMI) as a key determinant of chemosensitivity in breast cancer: Proteomic-based computing network mapping and in vivo verification with a mouse model. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy304.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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38
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Ryu H, Han D, Lee KM, Kim K. Proteomic-based machine learning computational analysis discovered biomarkers of aberrant vesicle-exosomal trafficking to determine chemotherapeutic responses in breast cancer. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy303.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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39
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Ryu H, Galiguis J, Pham A, Le A. Blastocyst development and euploidy rate in single medium with continuous or renewal on day 3 using sibling embryos. Fertil Steril 2018. [DOI: 10.1016/j.fertnstert.2018.07.1008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Cho H, Cho HS, Nam H, Jo H, Yoon J, Park C, Dang TVT, Kim E, Jeong J, Park S, Wallner ES, Youn H, Park J, Jeon J, Ryu H, Greb T, Choi K, Lee Y, Jang SK, Ban C, Hwang I. Translational control of phloem development by RNA G-quadruplex-JULGI determines plant sink strength. Nat Plants 2018; 4:376-390. [PMID: 29808026 DOI: 10.1038/s41477-018-0157-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/19/2018] [Indexed: 05/24/2023]
Abstract
The emergence of a plant vascular system was a prerequisite for the colonization of land; however, it is unclear how the photosynthate transporting system was established during plant evolution. Here, we identify a novel translational regulatory module for phloem development involving the zinc-finger protein JULGI (JUL) and its targets, the 5' untranslated regions (UTRs) of the SUPPRESSOR OF MAX2 1-LIKE4/5 (SMXL4/5) mRNAs, which is exclusively conserved in vascular plants. JUL directly binds and induces an RNA G-quadruplex in the 5' UTR of SMXL4/5, which are key promoters of phloem differentiation. We show that RNA G-quadruplex formation suppresses SMXL4/5 translation and restricts phloem differentiation. In turn, JUL deficiency promotes phloem formation and strikingly increases sink strength per seed. We propose that the translational regulation by the JUL/5' UTR G-quadruplex module is a major determinant of phloem establishment, thereby determining carbon allocation to sink tissues, and that this mechanism was a key invention during the emergence of vascular plants.
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Affiliation(s)
- Hyunwoo Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Hyun Seob Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Hoyoung Nam
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Joonseon Yoon
- Crop Seed Development Team, Seed Business Division, FarmHannong Co. Ltd., Daejeon, Korea
| | - Chanyoung Park
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Tuong Vi T Dang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Eunah Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Jongmin Jeong
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Soyoung Park
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Eva-Sophie Wallner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Hyungjun Youn
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Jongmin Park
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Jinseong Jeon
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, Korea
| | - Thomas Greb
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Kyuha Choi
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Yoontae Lee
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Sung Key Jang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea.
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Lee J, Shim D, Moon S, Kim H, Bae W, Kim K, Kim YH, Rhee SK, Hong CP, Hong SY, Lee YJ, Sung J, Ryu H. Genome-wide transcriptomic analysis of BR-deficient Micro-Tom reveals correlations between drought stress tolerance and brassinosteroid signaling in tomato. Plant Physiol Biochem 2018; 127:553-560. [PMID: 29723826 DOI: 10.1016/j.plaphy.2018.04.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/18/2018] [Accepted: 04/24/2018] [Indexed: 05/03/2023]
Abstract
Brassinosteroids (BRs) are plant steroid hormones that play crucial roles in a range of growth and developmental processes. Although BR signal transduction and biosynthetic pathways have been well characterized in model plants, their biological roles in an important crop, tomato (Solanum lycopersicum), remain unknown. Here, cultivated tomato (WT) and a BR synthesis mutant, Micro-Tom (MT), were compared using physiological and transcriptomic approaches. The cultivated tomato showed higher tolerance to drought and osmotic stresses than the MT tomato. However, BR-defective phenotypes of MT, including plant growth and stomatal closure defects, were completely recovered by application of exogenous BR or complementation with a SlDWARF gene. Using genome-wide transcriptome analysis, 619 significantly differentially expressed genes (DEGs) were identified between WT and MT plants. Several DEGs were linked to known signaling networks, including those related to biotic/abiotic stress responses, lignification, cell wall development, and hormone responses. Consistent with the higher susceptibility of MT to drought stress, several gene sets involved in responses to drought and osmotic stress were differentially regulated between the WT and MT tomato plants. Our data suggest that BR signaling pathways are involved in mediating the response to abiotic stress via fine-tuning of abiotic stress-related gene networks in tomato plants.
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Affiliation(s)
- Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon 16631, Republic of Korea.
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Hyemin Kim
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Kyunghwan Kim
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Yang-Hoon Kim
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Chang Pyo Hong
- TheragenEtex Bio Institute, Suwon 16229, Republic of Korea.
| | - Suk-Young Hong
- Division of Soil and Fertilizer, National Academy of Agricultural Science, RDA, Wanju, 27715, Republic of Korea.
| | - Ye-Jin Lee
- Division of Soil and Fertilizer, National Academy of Agricultural Science, RDA, Wanju, 27715, Republic of Korea.
| | - Jwakyung Sung
- Division of Soil and Fertilizer, National Academy of Agricultural Science, RDA, Wanju, 27715, Republic of Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea.
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42
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Ha B, Kim S, Kim M, Moon YJ, Song Y, Ryu JS, Ryu H, Ro HS. Diversity of A mating type in Lentinula edodes and mating type preference in the cultivated strains. J Microbiol 2018; 56:416-425. [PMID: 29858830 DOI: 10.1007/s12275-018-8030-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/02/2018] [Accepted: 04/12/2018] [Indexed: 10/14/2022]
Abstract
Diversity of A mating type in Lentinula edodes has been assessed by analysis of A mating loci in 127 strains collected from East Asia. It was discovered that hypervariable sequence region with an approximate length of 1 kb in the A mating locus, spanning 5' region of HD2-intergenic region-5' region of HD1, could represent individual A mating type as evidenced by comprehensive mating analysis. The sequence analysis revealed 27 A mating type alleles from 96 cultivated strains and 48 alleles from 31 wild strains. Twelve of them commonly appeared, leaving 63 unique A mating type alleles. It was also revealed that only A few A mating type alleles such as A1, A4, A5, and A7 were prevalent in the cultivated strains, accounting for 62.5% of all A mating types. This implies preferred selection of certain A mating types in the process of strain development and suggests potential role of A mating genes in the expression of genes governing mushroom quality. Dominant expression of an A mating gene HD1 was observed from A1 mating locus, the most prevalent A allele, in A1-containing dikaryons. However, connections between HD1 expression and A1 preference in the cultivated strains remain to be verified. The A mating type was highly diverse in the wild strains. Thirty-six unique A alleles were discovered from relatively small and confined area of mountainous region in Korean peninsula. The number will further increase because no A allele has been recurrently observed in the wild strains and thus newly discovered strain will have good chances to contain new A allele. The high diversity in small area also suggests that the A mating locus has evolved rapidly and thus its diversity will further increase.
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Affiliation(s)
- Byeongsuk Ha
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Sinil Kim
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Minseek Kim
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Yoon Jung Moon
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Yelin Song
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Jae-San Ryu
- Department of Mushroom, Korea National College of Agriculture and Fisheries, Jeonju, 54874, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Hyeon-Su Ro
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea. .,Division of Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.
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43
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Lim B, Hwang M, Song JS, Ryu AJ, Joung B, Shim EB, Ryu H, Pak HN. 1008Effectiveness of atrial fibrillation rotor ablation is dependent on conduction velocity: an in-silico 3-dimensional modeling study. Europace 2018. [DOI: 10.1093/europace/euy015.557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- B Lim
- Yonsei University , Seoul, Korea Republic of
| | - M Hwang
- Yonsei University , Seoul, Korea Republic of
| | - J S Song
- Yonsei University , Seoul, Korea Republic of
| | - A J Ryu
- Kangwon National University Hospital, Chuncheon, Korea Republic of
| | - B Joung
- Yonsei University , Seoul, Korea Republic of
| | - E B Shim
- Kangwon National University Hospital, Chuncheon, Korea Republic of
| | - H Ryu
- NVIDIA, Seoul, Korea Republic of
| | - H N Pak
- Yonsei University , Seoul, Korea Republic of
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44
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Lee H, Ryu H, Han D. High-throughput proteome identifies ANHAK as a novel biomarker for bladder urothelial carcinoma diagnosis in liquid-based cytology. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx653.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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45
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Ryu H, Han D. Next generation proteomic profiling to predict the response to neoadjuvant chemotherapy in breast cancer. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx653.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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46
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Park SG, Yoo SI, Ryu DS, Lee H, Ahn YJ, Ryu H, Ko J, Hong CP. Long-read transcriptome data for improved gene prediction in Lentinula edodes. Data Brief 2017; 15:454-458. [PMID: 29845094 PMCID: PMC5961913 DOI: 10.1016/j.dib.2017.09.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 11/28/2022] Open
Abstract
Lentinula edodes is one of the most popular edible mushrooms in the world and contains useful medicinal components such as lentinan. The whole-genome sequence of L. edodes has been determined with the objective of discovering candidate genes associated with agronomic traits, but experimental verification of gene models with correction of gene prediction errors is lacking. To improve the accuracy of gene prediction, we produced 12.6 Gb of long-read transcriptome data of variable lengths using PacBio single-molecule real-time (SMRT) sequencing and generated 36,946 transcript clusters with an average length of 2.2 kb. Evidence-driven gene prediction on the basis of long- and short-read RNA sequencing data was performed; a total of 16,610 protein-coding genes were predicted with error correction. Of the predicted genes, 42.2% were verified to be covered by full-length transcript clusters. The raw reads have been deposited in the NCBI SRA database under accession number PRJNA396788.
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Affiliation(s)
- Sin-Gi Park
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Seung Il Yoo
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Dong Sung Ryu
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Hyunsung Lee
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Yong Ju Ahn
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Junsu Ko
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Chang Pyo Hong
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
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Jo IH, Lee J, Hong CE, Lee DJ, Bae W, Park SG, Ahn YJ, Kim YC, Kim JU, Lee JW, Hyun DY, Rhee SK, Hong CP, Bang KH, Ryu H. Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome. Genes (Basel) 2017; 8:E228. [PMID: 28914759 PMCID: PMC5615361 DOI: 10.3390/genes8090228] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/17/2017] [Accepted: 09/12/2017] [Indexed: 11/17/2022] Open
Abstract
Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness. Of those unigenes, 67.5% were predicted to be complete full-length (FL) open reading frames (ORFs) and exhibited a high gene annotation rate. Furthermore, we successfully identified unique full-length genes involved in triterpenoid saponin synthesis and plant hormonal signaling pathways, including auxin and cytokinin. Studies on the functional genomics of P. ginseng seedlings have confirmed the rapid upregulation of negative feed-back loops by auxin and cytokinin signaling cues. The conserved evolutionary mechanisms in the auxin and cytokinin canonical signaling pathways of P. ginseng are more complex than those in Arabidopsis thaliana. Our analysis also revealed a more detailed view of transcriptome-wide alternative isoforms for 88 genes. Finally, transposable elements (TEs) were also identified, suggesting transcriptional activity of TEs in P. ginseng. In conclusion, our results suggest that long-read, full-length or partial-unigene data with high-quality assemblies are invaluable resources as transcriptomic references in P. ginseng and can be used for comparative analyses in closely related medicinal plants.
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Affiliation(s)
- Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Chi Eun Hong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | | | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Sin-Gi Park
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Yong Ju Ahn
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Young Chang Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jang Uk Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jung Woo Lee
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Dong Yun Hyun
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea.
| | | | - Kyong Hwan Bang
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
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48
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Kim H, Lee SJ, Jo IH, Lee J, Bae W, Kim H, Won K, Hyun TK, Ryu H. Characterization of the Rosellinia necatrix Transcriptome and Genes Related to Pathogenesis by Single-Molecule mRNA Sequencing. Plant Pathol J 2017; 33:362-369. [PMID: 28811753 PMCID: PMC5538440 DOI: 10.5423/ppj.oa.03.2017.0046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/31/2017] [Accepted: 04/09/2017] [Indexed: 06/03/2023]
Abstract
White root rot disease, caused by the pathogen Rosellinia necatrix, is one of the world's most devastating plant fungal diseases and affects several commercially important species of fruit trees and crops. Recent global outbreaks of R. necatrix and advances in molecular techniques have both increased interest in this pathogen. However, the lack of information regarding the genomic structure and transcriptome of R. necatrix has been a barrier to the progress of functional genomic research and the control of this harmful pathogen. Here, we identified 10,616 novel full-length transcripts from the filamentous hyphal tissue of R. necatrix (KACC 40445 strain) using PacBio single-molecule sequencing technology. After annotation of the unigene sets, we selected 14 cell cycle-related genes, which are likely either positively or negatively involved in hyphal growth by cell cycle control. The expression of the selected genes was further compared between two strains that displayed different growth rates on nutritional media. Furthermore, we predicted pathogen-related effector genes and cell wall-degrading enzymes from the annotated gene sets. These results provide the most comprehensive transcriptomal resources for R. necatrix, and could facilitate functional genomics and further analyses of this important phytopathogen.
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Affiliation(s)
- Hyeongmin Kim
- Department of Biology, Chungbuk National University, Cheongju 28644,
Korea
| | - Seung Jae Lee
- Bioinformatics Team, DNA Link, Inc., Seoul 03721,
Korea
| | - Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709,
Korea
| | - Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju 28644,
Korea
| | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju 28644,
Korea
| | - Hyemin Kim
- Department of Biology, Chungbuk National University, Cheongju 28644,
Korea
| | - Kyungho Won
- Pear Research Institute, National Institute of Horticultural & Herbal Science, Rural Development Administration, Naju 58126,
Korea
| | - Tae Kyung Hyun
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644,
Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644,
Korea
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49
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Moon S, Lee HY, Shim D, Kim M, Ka KH, Ryoo R, Ko HG, Koo CD, Chung JW, Ryu H. Development and Molecular Characterization of Novel Polymorphic Genomic DNA SSR Markers in Lentinula edodes. Mycobiology 2017; 45:105-109. [PMID: 28781544 PMCID: PMC5541145 DOI: 10.5941/myco.2017.45.2.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/03/2017] [Accepted: 06/12/2017] [Indexed: 05/15/2023]
Abstract
Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.
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Affiliation(s)
- Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
| | - Hwa-Yong Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea
| | - Donghwan Shim
- Division of Forest Genetic Resources, National Institute of Forest Science, Suwon 16631, Korea
| | - Myungkil Kim
- Division of Wood Chemistry & Microbiology, National Institute of Forest Science, Seoul 02455, Korea
| | - Kang-Hyeon Ka
- Division of Wood Chemistry & Microbiology, National Institute of Forest Science, Seoul 02455, Korea
| | - Rhim Ryoo
- Division of Wood Chemistry & Microbiology, National Institute of Forest Science, Seoul 02455, Korea
| | - Han-Gyu Ko
- Forest Mushroom Research Center, National Forestry Cooperative Federation, Yeoju 12653, Korea
| | - Chang-Duck Koo
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea
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Lee HY, Moon S, Shim D, Hong CP, Lee Y, Koo CD, Chung JW, Ryu H. Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars. Genes (Basel) 2017; 8:genes8040109. [PMID: 28338645 PMCID: PMC5406856 DOI: 10.3390/genes8040109] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/28/2017] [Accepted: 03/21/2017] [Indexed: 11/16/2022] Open
Abstract
The shiitake mushroom (Lentinulaedodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms. In this study, we developed 44 novel polymorphic simple sequence repeat (SSR) markers for the determination of shiitake mushroom cultivars based on a whole genome sequencing database of L. edodes. These markers were found to be polymorphic and reliable when screened in 23 shiitake mushroom cultivars. For the 44 SSR markers developed in this study, the major allele frequency ranged from 0.13 to 0.94; the number of genotypes and number of alleles were each 2-11; the observed and expected heterozygosity were 0.00-1.00 and 0.10-0.90, respectively; and the polymorphic information content value ranged from 0.10 to 0.89. These new markers can be used for molecular breeding, the determination of cultivars, and other applications.
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Affiliation(s)
- Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea.
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon 16631, Korea.
| | | | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea.
| | - Chang-Duck Koo
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
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