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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] [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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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. THE PLANT PATHOLOGY JOURNAL 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] [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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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] [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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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] [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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Ryu H, Laffont C, Frugier F, Hwang I. MAP Kinase-Mediated Negative Regulation of Symbiotic Nodule Formation in Medicago truncatula. Mol Cells 2017; 40:17-23. [PMID: 28152300 PMCID: PMC5303885 DOI: 10.14348/molcells.2017.2211] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/22/2016] [Accepted: 12/27/2016] [Indexed: 11/29/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) signaling cascades play critical roles in various cellular events in plants, including stress responses, innate immunity, hormone signaling, and cell specificity. MAPK-mediated stress signaling is also known to negatively regulate nitrogen-fixing symbiotic interactions, but the molecular mechanism of the MAPK signaling cascades underlying the symbiotic nodule development remains largely unknown. We show that the MtMKK5-MtMPK3/6 signaling module negatively regulates the early symbiotic nodule formation, probably upstream of ERN1 (ERF Required for Nodulation 1) and NSP1 (Nod factor Signaling Pathway 1) in Medicago truncatula. The overexpression of MtMKK5 stimulated stress and defense signaling pathways but also reduced nodule formation in M. truncatula roots. Conversely, a MAPK specific inhibitor, U0126, enhanced nodule formation and the expression of an early nodulation marker gene, MtNIN. We found that MtMKK5 directly activates MtMPK3/6 by phosphorylating the TEY motif within the activation loop and that the MtMPK3/6 proteins physically interact with the early nodulation-related transcription factors ERN1 and NSP1. These data suggest that the stress signaling-mediated MtMKK5/MtMPK3/6 module suppresses symbiotic nodule development via the action of early nodulation transcription factors.
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Lee S, Kim JY, Cheon S, Kim S, Kim D, Ryu H. Stimuli-responsive magneto-/electro-chromatic color-tunable hydrophobic surface modified Fe3O4@SiO2 core–shell nanoparticles for reflective display approaches. RSC Adv 2017. [DOI: 10.1039/c6ra27540k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Magneto-/electro-chromatic reflective color tunability is confirmed using hydrophobic surface modified magnetite nanoparticles. The optical reflective color spectra and color gamut demonstrate the promising applications in reflective displays.
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Ryu H, Song I, Choi Y, Baek S, Moon J, Lee H, Yun H, Kim S, Jo D. 337O The changes in the treatment of elderly AML patients in Korea: A single center experience. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw586.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Ryu H, Han D, Kim J, Lee H. 555P Systems-wide bioinformatics analysis using next generation transcriptome and proteomics reveals nicotinamide transforms molecular signaling networks toward an antitumor growth: A novel anti-cancer agent in triple negative breast cancer. Ann Oncol 2016. [DOI: 10.1016/s0923-7534(21)00713-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Moon J, Baek SW, Ryu H, Choi Y, Song IC, Yun HJ, Jo DY, Kim S, Lee H. 512P VIP (etoposide, ifosfamide, and cisplatin) in patients with previously treated soft tissue sarcoma. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw597.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Moon J, Baek SW, Ryu H, Choi Y, Song IC, Yun HJ, Jo DY, Kim S, Lee H. 512P VIP (etoposide, ifosfamide, and cisplatin) in patients with previously treated soft tissue sarcoma. Ann Oncol 2016. [DOI: 10.1016/s0923-7534(21)00670-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Ryu H, Han D, Kim J, Lee H. 555P Systems-wide bioinformatics analysis using next generation transcriptome and proteomics reveals nicotinamide transforms molecular signaling networks toward an anti-tumor growth: A novel anti-cancer agent in triple negative breast cancer. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw601.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Jo IH, Kim YC, Kim DH, Kim KH, Hyun TK, Ryu H, Bang KH. Applications of molecular markers in the discrimination of Panax species and Korean ginseng cultivars ( Panax ginseng). J Ginseng Res 2016; 41:444-449. [PMID: 29021689 PMCID: PMC5628328 DOI: 10.1016/j.jgr.2016.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 09/19/2016] [Indexed: 01/09/2023] Open
Abstract
The development of molecular markers is one of the most useful methods for molecular breeding and marker-based molecular associated selections. Even though there is less information on the reference genome, molecular markers are indispensable tools for determination of genetic variation and identification of species with high levels of accuracy and reproducibility. The demand for molecular approaches for marker-based breeding and genetic discriminations in Panax species has greatly increased in recent times and has been successfully applied for various purposes. However, owing to the existence of diverse molecular techniques and differences in their principles and applications, there should be careful consideration while selecting appropriate marker types. In this review, we outline the recent status of different molecular marker applications in ginseng research and industrial fields. In addition, we discuss the basic principles, requirements, and advantages and disadvantages of the most widely used molecular markers, including restriction fragment length polymorphism, random amplified polymorphic DNA, sequence tag sites, simple sequence repeats, and single nucleotide polymorphisms.
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Inkinen J, Jayaprakash B, Santo Domingo J, Keinänen-Toivola M, Ryu H, Pitkänen T. Diversity of ribosomal 16S DNA- and RNA-based bacterial community in an office building drinking water system. J Appl Microbiol 2016; 120:1723-38. [DOI: 10.1111/jam.13144] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 01/27/2016] [Accepted: 02/01/2016] [Indexed: 12/14/2022]
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Shim D, Park SG, Kim K, Bae W, Lee GW, Ha BS, Ro HS, Kim M, Ryoo R, Rhee SK, Nou IS, Koo CD, Hong CP, Ryu H. Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes. J Biotechnol 2016; 223:24-5. [PMID: 26924240 DOI: 10.1016/j.jbiotec.2016.02.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 02/24/2016] [Indexed: 12/22/2022]
Abstract
Lentinula edodes, the popular shiitake mushroom, is one of the most important cultivated edible mushrooms. It is used as a food and for medicinal purposes. Here, we present the 46.1 Mb draft genome of L. edodes, comprising 13,028 predicted gene models. The genome assembly consists of 31 scaffolds. Gene annotation provides key information about various signaling pathways and secondary metabolites. This genomic information should help establish the molecular genetic markers for MAS/MAB and increase our understanding of the genome structure and function.
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Ryu H, Cho A, Seong M, Park S, Lee J, Lim B, Kim K, Hwang Y, Chae J. Mutation spectrum of the dystrophin gene in 507 Korean Duchenne/Becker muscular dystrophy patients. Neuromuscul Disord 2015. [DOI: 10.1016/j.nmd.2015.06.254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Ryu H, Lee J, Je S, Chung T. 233 Administration of Adipose-Derived Mesenchymal Stem Cells After Transient Global Cerebral Ischemia has an Additory Stimulating Effect on Intrinsic Neurogenesis. Ann Emerg Med 2015. [DOI: 10.1016/j.annemergmed.2015.07.266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lee BD, Dutta S, Ryu H, Yoo SJ, Suh DS, Park K. Induction of systemic resistance in Panax ginseng against Phytophthora cactorum by native Bacillus amyloliquefaciens HK34. J Ginseng Res 2015; 39:213-20. [PMID: 26199552 PMCID: PMC4506372 DOI: 10.1016/j.jgr.2014.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 12/18/2014] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Korean ginseng (Panax ginseng Meyer) is a perennial herb prone to various root diseases, with Phytophthora cactorum being considered one of the most dreaded pathogens. P. cactorum causes foliar blight and root rot. Although chemical pesticides are available for disease control, attention has been shifted to viable, eco-friendly, and cost-effective biological means such as plant growth-promoting rhizobacteria (PGPR) for control of diseases. METHODS Native Bacillus amyloliquefaciens strain HK34 was isolated from wild ginseng and assessed as a biological control agent for ginseng. Leaves from plants treated with HK34 were analyzed for induced systemic resistance (ISR) against P. cactorum in square plate assay. Treated plants were verified for differential expression of defense-related marker genes using quantitative reverse transcription polymerase chain reaction. RESULTS A total of 78 native rhizosphere bacilli from wild P. ginseng were isolated. One of the root-associated bacteria identified as B. amyloliquefaciens strain HK34 effectively induced resistance against P. cactorum when applied as soil drench once (99.1% disease control) and as a priming treatment two times in the early stages (83.9% disease control). A similar result was observed in the leaf samples of plants under field conditions, where the percentage of disease control was 85.6%. Significant upregulation of the genes PgPR10, PgPR5, and PgCAT in the leaves of plants treated with HK34 was observed against P. cactorum compared with untreated controls and only pathogen-treated plants. CONCLUSION The results of this study indicate HK34 as a potential biocontrol agent eliciting ISR in ginseng against P. cactorum.
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Lee J, Ryu H, Keum G, Yoon YJ, Kowall NW, Ryu H. Therapeutic targeting of epigenetic components in amyotrophic lateral sclerosis (ALS). Curr Med Chem 2015; 21:3576-82. [PMID: 25005187 DOI: 10.2174/0929867321666140706131825] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/24/2014] [Accepted: 07/01/2014] [Indexed: 11/22/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is an adult-onset motor neuron disease characterized by degeneration of motor neuron and glial activation followed by the progressive muscle loss and paralysis. Numerous distinct therapeutic interventions have been examined but currently ALS does not have a cure or an efficacious treatment for the disorder. Glutamate- induced excitotoxicity, inflammation, mitochondrial dysfunction, oxidative stress, protein aggregation, transcription deregulation, and epigenetic modifications are associated with the pathogenesis of ALS and known to be therapeutic targets in ALS. In this review, we discuss translational pharmacological studies targeting epigenetic components to ameliorate ALS. Understanding of the epigenetic mechanisms will provide novel insights that will further identify potential biological markers and therapeutic approaches for treating ALS. A combination of treatments that modulate epigenetic components and multiple targets may prove to be the most effective therapy for ALS.
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Kwon JW, Park EJ, Jung SY, Sohn H, Ryu H, Suh H. A Large National Cohort Study of the Association between Bisphosphonates and Osteonecrosis of the Jaw in Patients with Osteoporosis. J Dent Res 2015; 94:212S-9S. [DOI: 10.1177/0022034515587862] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The purpose of this study was to examine the association between bisphosphonate exposure and osteonecrosis of the jaw (ONJ) in Korean patients with osteoporosis. A nested case-control study was performed using the claims database during 2002 to 2010 provided by the National Health Insurance Service. We identified a cohort of individuals with diagnosis of osteoporosis during 2002 to 2010. Cases and controls were identified during 2004 to 2010, and the date of potential cases of ONJ was defined as the index date. Bisphosphonate exposure was evaluated during 2 y prior to the index date. The association between bisphosphonate exposure and ONJ was tested by performing a conditional logistic regression analysis for matched data, and odds ratios (ORs) with 95% confidence intervals (CIs) were presented. Subjects were classified as nonuser, recent user, past user, or continuous user, depending on the prescription of bisphosphonates in 2 periods (1 to 2 y and 0 to 1 y prior to the index date). Continuous users were defined as patients who were exposed to bisphosphonate in both periods. We also examined the impact of bisphosphonate medication compliance by measuring the cumulative duration of exposure (CDE) on the risk of ONJ. A total of 212 cases with ONJ and 2,120 controls matched by sex, age, income level, and insurance type were identified among 109,787 patients with osteoporosis out of 1,025,340 enrollees in the sample cohort. The odds of having ONJ after adjusting for patient comorbidities significantly increased in continuous users of bisphosphonates (OR, 3.9; 95% CI, 2.4 to 6.2) compared to nonusers. Increased odds of ONJ were observed as CDE increased. The adjusted OR in patients with 1.5 y < CDE ≤ 2 y prior to the index date was 7.8 (95% CI, 4.0 to 15.5) versus nonusers. Our study results support significantly increased occurrences of potential ONJ in patients with osteoporosis who were exposed to bisphosphonates compared to those without exposure.
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Ryu H, Park I, Kim H, Jung Y. A novel potential prognostic marker SIRT1 on tumor invasion and metastasis, and tumor recurrence in triple negative breast cancer. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv117.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Furuichi T, Sanz C, Koops K, Sakamaki T, Ryu H, Tokuyama N, Morgan D. Why do wild bonobos not use tools like chimpanzees do? BEHAVIOUR 2015. [DOI: 10.1163/1568539x-00003226] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
One of the most conspicuous behavioural differences among great apes is the paucity of tool use among wild bonobos (Pan paniscus) in comparison to chimpanzees (Pan troglodytes) who are one of the most prolific and skilled tool users in the animal kingdom. This is in spite of the fact that bonobo tool use repertories are as large and diverse as chimpanzees’ in captive settings. In this study, we compared tool using behaviours and potential drivers of these behaviours in the Wamba bonobo population located in central Democratic Republic of Congo with the Goualougo chimpanzee population of northern Republic of Congo. The tool use repertoire of wild bonobos was comprised of only 13 behaviours, compared to 42 for chimpanzees. However, the number of tool behaviours observed in each study site was similar between bonobos and chimpanzees, and many types of tool use for social, self-grooming/stimulation, and comfort/protection functions were commonly used by both species. A marked difference is that 25 of 42 tool behaviours exhibited by chimpanzees are performed for feeding, in contrast to a single report of bonobos using a leaf sponge to drink water. We examined whether the differences in tool use repertoires can be explained by the necessity, opportunity, relative profitability, or invention hypotheses. We found that habitat composition and fluctuation of fruit production at these two sites were similar, particularly when compared with variation observed between sites within each species. Thus it was unlikely that the necessity hypothesis explains the lack of tool use for feeding in bonobos. Though further study at Wamba is needed, we did not identify any obvious differences in prey availability that would indicate differences in tool using opportunities between the sites. This study could not test the relative profitability hypothesis, and further research is needed on whether tool use is the most efficient means of calorie or protein intake for wild apes. Bonobos at Wamba formed much larger and stable parties than chimpanzees at Goualougo, which was contrary to the prediction by the invention hypothesis. Another explanation is that differences in tool use behaviour between bonobos and chimpanzees might not be explained by the current ecological or social conditions, but rather by circumstances during the Pleistocene Epoch. The observed species differences might also reflect divergent behavioural predispositions, rather than actual differences in cognitive abilities.
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Liu Y, Ryu H, Ge B, Pan G, Sun L, Park K, Zhang K. Improvement of Wuyiencin Biosynthesis in Streptomyces wuyiensis CK-15 by Identification of a Key Regulator, WysR. J Microbiol Biotechnol 2014; 24:1644-53. [DOI: 10.4014/jmb.1405.05017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Byun J, Son SM, Cha MY, Shong M, Hwang YJ, Kim Y, Ryu H, Moon M, Kim KS, Mook-Jung I. CR6-interacting factor 1 is a key regulator in Aβ-induced mitochondrial disruption and pathogenesis of Alzheimer's disease. Cell Death Differ 2014; 22:959-73. [PMID: 25361083 PMCID: PMC4423180 DOI: 10.1038/cdd.2014.184] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 08/25/2014] [Accepted: 09/25/2014] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial dysfunction, often characterized by massive fission and other morphological abnormalities, is a well-known risk factor for Alzheimer's disease (AD). One causative mechanism underlying AD-associated mitochondrial dysfunction is thought to be amyloid-β (Aβ), yet the pathways between Aβ and mitochondrial dysfunction remain elusive. In this study, we report that CR6-interacting factor 1 (Crif1), a mitochondrial inner membrane protein, is a key player in Aβ-induced mitochondrial dysfunction. Specifically, we found that Crif1 levels were downregulated in the pathological regions of Tg6799 mice brains, wherein overexpressed Aβ undergoes self-aggregation. Downregulation of Crif1 was similarly observed in human AD brains as well as in SH-SY5Y cells treated with Aβ. In addition, knockdown of Crif1, using RNA interference, induced mitochondrial dysfunction with phenotypes similar to those observed in Aβ-treated cells. Conversely, Crif1 overexpression prevented Aβ-induced mitochondrial dysfunction and cell death. Finally, we show that Aβ-induced downregulation of Crif1 is mediated by enhanced reactive oxygen species (ROS) and ROS-dependent sumoylation of the transcription factor specificity protein 1 (Sp1). These results identify the ROS-Sp1-Crif1 pathway to be a new mechanism underlying Aβ-induced mitochondrial dysfunction and suggest that ROS-mediated downregulation of Crif1 is a crucial event in AD pathology. We propose that Crif1 may serve as a novel therapeutic target in the treatment of AD.
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Ryu H, Cho H, Bae W, Hwang I. Control of early seedling development by BES1/TPL/HDA19-mediated epigenetic regulation of ABI3. Nat Commun 2014; 5:4138. [PMID: 24938150 DOI: 10.1038/ncomms5138] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/16/2014] [Indexed: 12/23/2022] Open
Abstract
Seed germination and young seedling establishment should be tightly regulated to maximize plant survival and thereby enable successful propagation. Plants have evolved developmental signalling networks to integrate environmental cues for proper control of these critical processes, in which brassinosteroids are known to attenuate ABA-mediated arrest of early seedling development; however, the underlying regulatory mechanism remains elusive. Here we reveal that a BES1/TPL/HDA19 repressor complex mediates the inhibitory action of brassinosteroids on ABA responses during early seedling development. BR-activated BES1 forms a transcriptional repressor complex with TPL-HDA19, which directly facilitates the histone deacetylation of ABI3 chromatin. This event leads to the transcriptional repression of ABI3 and consequently ABI5, major ABA signalling regulators in early seedling development. Our data reveal that the BR-activated BES1-TPL-HDA19 repressor complex controls epigenetic silencing of ABI3 and thereby suppresses the ABA signalling output during early seedling development.
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Ryu H, Park H, Suh DS, Jung GH, Park K, Lee BD. Biological control of Colletotrichum panacicola on Panax ginseng by Bacillus subtilis HK-CSM-1. J Ginseng Res 2014; 38:215-9. [PMID: 25378997 PMCID: PMC4213823 DOI: 10.1016/j.jgr.2014.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 04/15/2014] [Accepted: 04/29/2014] [Indexed: 12/05/2022] Open
Abstract
Background Biological control of plant pathogens using benign or beneficial microorganisms as antagonistic agents is currently considered to be an important component of integrated pest management in agricultural crops. In this study, we evaluated the potential of Bacillus subtilis strain HK-CSM-1 as a biological control agent against Colletotrichum panacicola. Methods The potential of B. subtilis HK-CSM-1 as a biological control agent for ginseng anthracnose was assessed. C. panacicola was inoculated to ginseng plants and the incidence and severity of disease was assessed to examine the efficacy of the bacterium as a biological control against C. panacicola. Results Inoculation of Panax ginseng plants with B. subtilis significantly suppressed the number of disease lesions of C. panacicola and was as effective as the chemical fungicide iminoctadine tris(albesilate). The antifungal activity of B. subtilis against C. panacicola was observed on a co-culture medium. Interestingly, treatment with B. subtilis did not significantly affect the diameter of the lesions, suggesting that the mechanism of protection was through the reduction in the incidence of infection related to the initial events of the infection cycle, including penetration and infection via spore germination and appressorium formation rather than by the inhibition of invasive growth after infection. Conclusion Our results suggest that B. subtilis HK-CSM-1 can be used as an effective and ecologically friendly biological control agent for anthracnose in P. ginseng.
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