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Article: Asymbiotic Seed Germination and In Vitro Seedling Development of the Endangered Orchid Species

Park, Hyeong Bin / An, Jiae / Bae, Kee-Hwa / Hong, Seung Hyo / Park, Hwan Joon / Kim, Seongjun / Lee, Chang Woo / Lee, Byoung-Doo / Baek, Ju Hyoung / Kim, Nam Young / Hwang, Jung Eun

Plants (Basel, Switzerland)

2023 Volume 12, Issue 22

Abstract: Cypripedium ... ...

Abstract	Cypripedium guttatum
Language	English
Publishing date	2023-11-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants12223788
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Deep Learning-Based End-to-End Language Development Screening for Children Using Linguistic Knowledge

Byoung-Doo Oh / Yoon-Kyoung Lee / Jong-Dae Kim / Chan-Young Park / Yu-Seop Kim

Applied Sciences, Vol 12, Iss 4651, p

2022 Volume 4651

Abstract: Language development is inextricably linked to the development of fundamental human abilities. A language problem can result from abnormal language development in childhood, which has a severe impact on other elements of life. As a result, early ... ...

Abstract	Language development is inextricably linked to the development of fundamental human abilities. A language problem can result from abnormal language development in childhood, which has a severe impact on other elements of life. As a result, early treatment of language impairments in children is critical. However, because it is difficult for parents to identify atypical language development in their children, optimal diagnosis and treatment periods are frequently missed. Furthermore, the diagnosis process necessitates a significant amount of time and work. As a consequence, in this study, we present a deep learning-based language development screening model based on word and part-of-speech and investigate the effectiveness of a large-scale language model. For the experiment, we collected data from Korean children by transcribing the utterances of children aged 2, 4, and 6 years. Convolutional neural networks and the notion of Siamese networks, as well as word and part-of-speech information, were used to determine the language development level of children. We also investigated the effectiveness of employing KoBERT and KR-BERT among Korean-specific large-scale language models. In 5-fold cross-validation study, the proposed model has an average accuracy of 78.0%. Furthermore, contrary to predictions, the large-scale language models were shown to be ineffective for representing children’s utterances.
Keywords	language development screening for children ; linguistic knowledge ; Siamese networks ; convolutional neural networks ; large-scale language model ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	410
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: CONSTITUTIVE PHOTOMORPHOGENIC 1 promotes seed germination by destabilizing RGA-LIKE 2 in Arabidopsis.

Lee, Byoung-Doo / Yim, Yehyun / Cañibano, Esther / Kim, Suk-Hwan / García-León, Marta / Rubio, Vicente / Fonseca, Sandra / Paek, Nam-Chon

Plant physiology

2022 Volume 189, Issue 3, Page(s) 1662–1676

Abstract: Under favorable moisture, temperature, and light conditions, gibberellin (GA) biosynthesis is induced and triggers seed germination. A major mechanism by which GA promotes seed germination is by promoting the degradation of the DELLA protein RGA-LIKE 2 ( ... ...

Abstract	Under favorable moisture, temperature, and light conditions, gibberellin (GA) biosynthesis is induced and triggers seed germination. A major mechanism by which GA promotes seed germination is by promoting the degradation of the DELLA protein RGA-LIKE 2 (RGL2), a major repressor of germination in Arabidopsis (Arabidopsis thaliana) seeds. Analysis of seed germination phenotypes of constitutive photomorphogenic 1 (cop1) mutants and complemented COP1-OX/cop1-4 lines in response to GA and paclobutrazol (PAC) suggested a positive role for COP1 in seed germination and a relation with GA signaling. cop1-4 mutant seeds showed PAC hypersensitivity, but transformation with a COP1 overexpression construct rendered them PAC insensitive, with a phenotype similar to that of rgl2 mutant (rgl2-SK54) seeds. Furthermore, cop1-4 rgl2-SK54 double mutants showed a PAC-insensitive germination phenotype like that of rgl2-SK54, identifying COP1 as an upstream negative regulator of RGL2. COP1 interacted directly with RGL2, and in vivo this interaction was strongly enhanced by SUPPRESSOR OF PHYA-105 1. COP1 directly ubiquitinated RGL2 to promote its degradation. Moreover, GA stabilized COP1 with consequent RGL2 destabilization. By uncovering this COP1-RGL2 regulatory module, we reveal a mechanism whereby COP1 positively regulates seed germination and controls the expression of germination-promoting genes.
MeSH term(s)	Arabidopsis/metabolism ; Arabidopsis Proteins/metabolism ; Gene Expression Regulation, Plant ; Germination ; Gibberellins/metabolism ; Gibberellins/pharmacology ; Repressor Proteins/metabolism ; Seeds/metabolism ; Transcription Factors/metabolism ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Arabidopsis Proteins ; Gibberellins ; RGA protein, Arabidopsis ; Repressor Proteins ; Transcription Factors ; AT2G32950 protein, Arabidopsis (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2022-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	208914-2
ISSN	1532-2548 ; 0032-0889
ISSN (online)	1532-2548
ISSN	0032-0889
DOI	10.1093/plphys/kiac060
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Endangered plant species under differing anthropogenic interventions: how to preserve

Kim, Seongjun / Park, Hwan-Joon / Lee, Chang Woo / Kim, Nam Young / Hwang, Jung Eun / Lee, Byoung-Doo / Park, Hyeong Bin / An, Jiae / Baek, JuHyoung

PeerJ

2022 Volume 10, Page(s) e14050

Abstract: Endangered wetland plants are important as the potential keystone species and mediators for plant-soil interactions. Establishing conservation strategies for endangered plants is also prioritized because of the elevating extinction risk by human-induced ... ...

Abstract	Endangered wetland plants are important as the potential keystone species and mediators for plant-soil interactions. Establishing conservation strategies for endangered plants is also prioritized because of the elevating extinction risk by human-induced wetland disturbances. The present study examined the factors controlling the incidence of
Language	English
Publishing date	2022-09-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.14050
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Effects of Different Growth Media on In Vitro Seedling Development of an Endangered Orchid Species

An, Jiae / Kim, Pyoung Beom / Park, Hyeong Bin / Kim, Seongjun / Park, Hwan Joon / Lee, Chang Woo / Lee, Byoung-Doo / Kim, Nam Young / Hwang, Jung Eun

Plants (Basel, Switzerland)

2021 Volume 10, Issue 6

Abstract: ... Sedirea ... ...

Abstract	Sedirea japonica
Language	English
Publishing date	2021-06-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants10061193
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Article ; Online: Endangered plant species under differing anthropogenic interventions

Seongjun Kim / Hwan-Joon Park / Chang Woo Lee / Nam Young Kim / Jung Eun Hwang / Byoung-Doo Lee / Hyeong Bin Park / Jiae An / JuHyoung Baek

PeerJ, Vol 10, p e

how to preserve Pterygopleurum neurophyllum in Wondong wetland?

2022 Volume 14050

Abstract	Endangered wetland plants are important as the potential keystone species and mediators for plant-soil interactions. Establishing conservation strategies for endangered plants is also prioritized because of the elevating extinction risk by human-induced wetland disturbances. The present study examined the factors controlling the incidence of Pterygopleurum neurophyllum, the endangered wetland plant experiencing severe habitat loss throughout Northeast Asia. Here, P. neurophyllum populations and their surrounding environments were addressed in the last natural Korean habitat to assess the possible influential factors (vegetation coverage, species richness, exotic plant species, coarse rock content, soil bulk density, and soil electroconductivity and pH) under anthropogenic wetland interventions (with or without soil disturbance). Our results showed that P. neurophyllum occurred 6 out of 32 plots in the study area. All P. neurophyllum were found in Miscanthus-dominated area, but preferred microhabitats featuring reduced vegetation coverage, increased species richness, and undisturbed soils under vegetation removal. Multimodel inference also indicated that vegetation coverage (relative importance = 1.00) and coarse rock content (relative importance = 0.70) were the major influential factors for P. neurophyllum population size, and the surviving P. neurophyllum were strictly limited to where both of them were kept lowered. Furthermore, the wetland intervention with soil disturbance had a negative effect on P. neurophyllum by creating the rocky and compacted soil surface as a result of land reclamation treatments. Conversely, the wetland intervention without soil disturbance enhanced the P. neurophyllum incidence by decreasing vegetation coverage of the overcrowding competitive plants. Overall findings reflect that the strategies to counteract habitat loss and manage the overly dense competitive plants should be necessary for conserving P. neurophyllum, as well as other wetland plants threatened by the human-induced ...
Keywords	Conservation ecology ; Influential factor ; Soil compaction ; Threatened species ; Vegetation coverage ; Wetland disturbance ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	580 ; 630
Language	English
Publishing date	2022-09-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: BAP1 controls mesenchymal stem cell migration by inhibiting the ERK signaling pathway.

Kim, Seobin / Lee, Eun-Woo / Oh, Doo-Byoung / Seo, Jinho

BMB reports

2023

Abstract: Mesenchymal stem cells (MSCs) have remarkable potential in regenerative medicine owing to their stem-like characteristics and immunosuppressive properties. Much effort has been devoted to enhancing the efficacy of MSC therapy by enhancing MSC migration. ... ...

Abstract	Mesenchymal stem cells (MSCs) have remarkable potential in regenerative medicine owing to their stem-like characteristics and immunosuppressive properties. Much effort has been devoted to enhancing the efficacy of MSC therapy by enhancing MSC migration. In this study, we identified deubiquitinase BRCA1-associated protein 1 (BAP1) as an inhibitor of MSC migration. Using deubiquitinase siRNA library screening based on an in vitro wound healing assay, we found that silencing BAP1 significantly augmented MSC migration. Conversely, BAP1 overexpression reduced the migration and invasion capabilities of MSCs. BAP1 depletion in MSCs upregulates ERK phosphorylation, thereby increasing the expression of the migration factor osteopontin. Further examination revealed that BAP1 interacts with phosphorylated ERK1/2, deubiquitinating their ubiquitins, and thus attenuating the ERK signaling pathway. Overall, our study highlights the critical role of BAP1 in regulating MSC migration through its deubiquitinase activity and suggests a novel approach to improve the therapeutic potential of MSCs in regenerative medicine.
Language	English
Publishing date	2023-11-14
Publishing country	Korea (South)
Document type	News
ZDB-ID	2410389-5
ISSN	1976-670X ; 1976-6696
ISSN (online)	1976-670X
ISSN	1976-6696
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: GIGANTEA Shapes the Photoperiodic Rhythms of Thermomorphogenic Growth in Arabidopsis

Park, Young-Joon / Kim, Jae Young / Lee, June-Hee / Lee, Byoung-Doo / Paek, Nam-Chon / Park, Chung-Mo

Molecular plant. 2020 Mar. 02, v. 13, no. 3

2020

Abstract: Plants maintain their internal temperature under environments with fluctuating temperatures by adjusting their morphology and architecture, an adaptive process termed thermomorphogenesis. Notably, the rhythmic patterns of plant thermomorphogenesis are ... ...

Abstract	Plants maintain their internal temperature under environments with fluctuating temperatures by adjusting their morphology and architecture, an adaptive process termed thermomorphogenesis. Notably, the rhythmic patterns of plant thermomorphogenesis are governed by day-length information. However, it remains elusive how thermomorphogenic rhythms are regulated by photoperiod. Here, we show that warm temperatures enhance the accumulation of the chaperone GIGANTEA (GI), which thermostabilizes the DELLA protein, REPRESSOR OF ga1-3 (RGA), under long days, thereby attenuating PHYTOCHROME INTERACTING FACTOR 4 (PIF4)-mediated thermomorphogenesis. In contrast, under short days, when GI accumulation is reduced, RGA is readily degraded through the gibberellic acid-mediated ubiquitination-proteasome pathway, promoting thermomorphogenic growth. These data indicate that the GI–RGA–PIF4 signaling module enables plant thermomorphogenic responses to occur in a day-length-dependent manner. We propose that the GI-mediated integration of photoperiodic and temperature information shapes thermomorphogenic rhythms, which enable plants to adapt to diel fluctuations in day length and temperature during seasonal transitions.
Keywords	Arabidopsis ; internal temperature ; photoperiod ; phytochrome
Language	English
Dates of publication	2020-0302
Size	p. 459-470.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2393618-6
ISSN	1752-9867 ; 1674-2052
ISSN (online)	1752-9867
ISSN	1674-2052
DOI	10.1016/j.molp.2020.01.003
Database	NAL-Catalogue (AGRICOLA)

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Article: Effects of Light Condition on Growth and Physiological Characteristics of the Endangered Species

Lee, Kyeong Cheol / An, Jiae / Hwang, Jung Eun / Kim, Pyoung Beom / Park, Hyeong Bin / Kim, Seongjun / Park, Hwan Joon / Lee, Chang Woo / Lee, Byoung-Doo / Kim, Nam Young

Plants (Basel, Switzerland)

2021 Volume 10, Issue 9

Abstract: This study was conducted to evaluate the physiological and growth responses ... ...

Abstract	This study was conducted to evaluate the physiological and growth responses of
Language	English
Publishing date	2021-09-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants10091891
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Article ; Online: The Rice Basic Helix–Loop–Helix 79 ( OsbHLH079 ) Determines Leaf Angle and Grain Shape

Hyoseob Seo / Suk-Hwan Kim / Byoung-Doo Lee / Jung-Hyun Lim / Sang-Ji Lee / Gynheung An / Nam-Chon Paek

International Journal of Molecular Sciences, Vol 21, Iss 6, p

2020 Volume 2090

Abstract: Changes in plant architecture, such as leaf size, leaf shape, leaf angle, plant height, and floral organs, have been major factors in improving the yield of cereal crops. Moreover, changes in grain size and weight can also increase yield. Therefore, ... ...

Abstract	Changes in plant architecture, such as leaf size, leaf shape, leaf angle, plant height, and floral organs, have been major factors in improving the yield of cereal crops. Moreover, changes in grain size and weight can also increase yield. Therefore, screens for additional factors affecting plant architecture and grain morphology may enable additional improvements in yield. Among the basic Helix-Loop-Helix (bHLH) transcription factors in rice ( Oryza sativa ), we found an enhancer-trap T-DNA insertion mutant of OsbHLH079 (termed osbhlh079-D ). The osbhlh079-D mutant showed a wide leaf angle phenotype and produced long grains, similar to the phenotypes of mutants with increased brassinosteroid (BR) levels or enhanced BR signaling. Reverse transcription-quantitative PCR analysis showed that BR signaling-associated genes are largely upregulated in osbhlh079-D , but BR biosynthesis-associated genes are not upregulated, compared with its parental japonica cultivar ‘Dongjin’. Consistent with this, osbhlh079-D was hypersensitive to BR treatment. Scanning electron microscopy revealed that the expansion of cell size in the adaxial side of the lamina joint was responsible for the increase in leaf angle in osbhlh079-D . The expression of cell-elongation-associated genes encoding expansins and xyloglucan endotransglycosylases/hydrolases increased in the lamina joints of leaves in osbhlh079-D . The regulatory function of OsbHLH079 was further confirmed by analyzing 35S::OsbHLH079 overexpression and 35S::RNAi-OsbHLH079 gene silencing lines. The 35S::OsbHLH079 plants showed similar phenotypes to osbhlh079-D , and the 35S::RNAi-OsbHLH079 plants displayed opposite phenotypes to osbhlh079-D . Taking these observations together, we propose that OsbHLH079 functions as a positive regulator of BR signaling in rice.
Keywords	bhlh transcription factor ; lamina joint ; leaf angle ; long grain ; brassinosteroid signaling ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	580
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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