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PagMYB128 regulates secondary cell wall formation by direct activation of cell wall biosynthetic genes during wood formation in poplar

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Journal of Integrative Plant Biology 2024年第8期66卷 1658-1674页

作者： Yuanyuan Hao Fachuang Lu Seung-Won Pyo Min-Ha Kim jae-heung ko Xiaojing Yan John Ralph Quanzi Li State Key Laboratory of Tree Genetics and Breeding Chinese Academy of ForestryBeijing 100091China Department of Biochemistry and DOE Great Lakes Bioenergy Research Center Wisconsin Energy InstituteUniversity of Wisconsin-MadisonWisconsin 53726USA Department of Plant&Environmental New Resources Kyung Hee UniversityYongin 17104Korea

The biosynthesis of cellulose,lignin,and hemicelluloses in plant secondary cell walls(SCWs)is regulated by a hierarchical transcriptional regulatory *** network features orthologous transcription factors shared between poplar and Arabidopsis,highlighting a foundational similarity in their genetic ***,knowledge on the discrepant behavior of the transcriptional-level molecular regulatory mechanisms between poplar and Arabidopsis remains *** this study,we investigated the function of PagMYB128 during wood formation and found it had broader impacts on SCW formation compared to its Arabidopsis ortholog,*** poplar trees overexpressing PagMYB128 exhibited significantly enhanced xylem development,with fiber cells and vessels displaying thicker walls,and an increase in the levels of cellulose,lignin,and hemicelluloses in the *** contrast,plants with dominant repression of PagMYB128 demonstrated the opposite *** sequencing and reverse transcription–quantitative polymerase chain reaction showed that PagMYB128 could activate SCW biosynthetic gene expression,and chromatin immunoprecipitation along with yeast one-hybrid,and effector–reporter assays showed this regulation was *** analysis revealed that PagSND1(SECONDARY WALL-ASSOCIATED NAC-DOMAIN PROTEIN1)directly regulates PagMYB128 but not cell wall metabolic genes,highlighting the pivotal role of PagMYB128 in the SND1-driven regulatory network for wood development,thereby creating a feedforward loop in SCW biosynthesis.

关键词： cellulose hemicellulose lignin PagMYB128 Populus transcription factor wood formation

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MYB46-Mediated Transcriptional Regulation of Secondary Wall Biosynthesis

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Molecular Plant 2012年第5期5卷 961-963页

作者： jae-heung ko Won-Chan Kim Joo-Yeol Kim Sung-Ju Ahn Kyung-Hwan Han Department of Plant and Environmental New Resources Kyung Hee University Yongin Korea Bioenergy Center Kyung Hee University Yongin Korea Department of Horticulture and Department of Forestry Michigan State University East Lansing MI 48824-1222 USA DOE-Great Lakes Bioenergy Research Center Michigan State University East Lansing MI 48824-1222 USA Department of Bioenergy Science and Technology (WCU) Chonnam National University 333 Yongbongro Buk-gu Gwangju 500-757 Korea

Formation of secondary wall requires coordinated transcrip- tional regulation of the genes involved in the biosynthesis of major secondary wall components （e.g. cellulose, hemicellu- lose, and lignin）. Even though many aspects of plant biology have been extensively elucidated using various model spe- cies, our current understanding of secondary wall formation is limited.

关键词： Biosynthesis Regulation Wall

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An improved draft genome sequence of hybrid Populus alba×Populus glandulosa

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Journal of Forestry Research 2021年第4期32卷 1663-1672页

作者： Xiong Huang Song Chen Xiaopeng Peng Eun-Kyung Bae Xinren Dai Guiming Liu Guanzheng Qu jae-heung ko Hyoshin Lee Su Chen Quanzi Li Mengzhu Lu State Key Laboratory of Tree Genetics and Breeding Chinese Academy of ForestryBeijing 100091People’s Republic of China Research Institute of Forestry Chinese Academy of ForestryBeijing 100091People’s Republic of China State Key Laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040People’s Republic of China Division of Forest Biotechnology National Institute of Forest ScienceSuwon 441847Republic of Korea Agro-Biotechnology Research Center Beijing Academy of Agriculture and Forestry SciencesBeijing 100097People’s Republic of China Department of Plant&Environmental New Resources Kyung Hee UniversityYongin 446701Republic of Korea

Populus alba × *** clone 84 K,derived from South korea,is widely cultivated in China and used as a model in the molecular research of woody plants because of hi gh gene transformation ***,we combined63-fold coverage Illumina short reads and 126-fold coverage PacBio long reads to assemble the *** to the hi gh heterozygosity level at 2.1% estimated by k-mer analysis,we exploited TrioCanu for genome *** PacBio clean subreads of *** × *** were separated into two parts according to the similarities,compared with the parental genomes of *** and *** two parts of the subreads were assembled to two sets of subgenomes comprising subgenome A(405.31 Mb,from ***)and subgenome G(376.05 Mb,from ***) with the contig N50 size of 5.43 Mb and 2.15 Mb,respectively.A high-quality *** × *** genome assembly was *** genome size was 781.36 Mb with the contig N50 size of 3.66 Mb and the longest contig was 19.47 *** addition,a total of 176.95 Mb(43.7%),152.37 Mb(40.5%)of repetitive elements were identified and a total of 38,701 and 38,449 protein-coding genes were predicted in subgenomes A and G,*** functional annotation,96.98% of subgenome A and 96.96% of subgenome G genes were annotated with public *** de novo assembled genome will facilitate systematic and comprehensive study,such as multi-omics analysis,in the model tree *** X ***.

关键词： Genome assembly Gene annotation Hybrid poplar Populus alba×p.glandulosa cl.84 K

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Interplay between ABA and GA Modulates the Timing of Asymmetric Cell Divisions in the Arabidopsis Root Ground Tissue

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Molecular Plant 2016年第6期9卷 870-884页

作者： Shin Ae Lee Sejeong Jang Eun Kyung Yoon Jung-Ok Heo Kwang Suk Chang Ji Won Choi Souvik Dhar Gyuree Kim Jeong-Eun Choe jae Bok Heo Chian Kwon jae-heung ko Yong-Sic Hwang Jun Lim Department of Systems Biotechnology Konkuk University Seour 05029 Korea Department of Molecular Biotechnology Dong-A University Busan 49201 Korea Department of Molecular Biology Dankook University Yongin 16890 Korea Department of Plant and Environmental New Resources Kyung Hee University Yongin 17104 Korea These authors contributed equally to this article. Present address: The Sainsbury Laboratory University of Cambridge Cambridge CB2 1LR United Kingdom Present address: Department of Life Science Research Institute for Natural Sciences Hanyang University Seoul 04763 Korea

In multicellular organisms, controlling the timing and extent of asymmetric cell divisions （ACDs） is crucial for correct patterning. During post-embryonic root development in Arabidopsis thaliana, ground tissue （GT） maturation involves an additional ACD of the endodermis, which generates two different tissues： the endo- dermis （inner） and the middle cortex （outer）. It has been reported that the abscisic acid （ABA） and gibberellin （GA） pathways are involved in middle cortex （MC） formation. However, the molecular mechanisms under- lying the interaction between ABA and GA during GT maturation remain largely unknown. Through transcriptome analyses, we identified a previously uncharacterized C2H2-type zinc finger gene, whose expression is regulated by GA and ABA, thus named GAZ （GA- AND ABA-RESPONSIVE ZINC FINGER）. Seedlings ectopically overexpressing GAZ （GAZ-OX） were sensitive to ABA and GA during MC formation, whereas GAZ-SRDX and RNAi seedlings displayed opposite phenotypes. In addition, our results indicated that GAZ was involved in the transcriptional regulation of ABA and GA homeostasis. In agreement with pre- vious studies that ABA and GA coordinate to control the timing of MC formation, we also confirmed the unique interplay between ABA and GA and identified factors and regulatory networks bridging the two hor- mone pathways during GT maturation of the Arabidopsis root.

关键词： ABA GA GRAS ground tissue root development transcription factor

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A molecular framework for seasonal growth-dormancy regulation in perennial plants

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Horticulture Research 2014年第1期1卷 22-30页

作者： Donghwan Shim jae-heung ko Won-Chan Kim Qijun Wang Daniel E Keathley Kyung-Hwan Han Schatz Center for Tree Molecular Genetics Pennsylvania State UniversityUniversity ParkPA16802USA Department of Plant&Environmental New Resources College of Life ScienceKyung Hee UniversityYongin-siGyeonggi-do 446-701Republic of Korea Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Department of Forestry Michigan State UniversityEast LansingMI 48824USA konjac Research Center College of Horticulture and Landscape ArchitectureSouthwest UniversityChongqing 400715China

The timing of the onset and release of dormancy impacts the survival,productivity and spatial distribution of temperate horticultural and forestry perennials and is mediated by at least three main regulatory programs involving signal perception and processing by phytochromes(PHYs)and PHY-interacting transcription factors(PIFs).PIF4 functions as a key regulator of plant growth in response to both external and internal *** poplar,the expression of PIF4 and PIF3-LIKE1 is upregulated in response to short days,while PHYA and PHYB are not regulated at the transcriptional *** of light and environmental signals is achieved by gating the expression and transcriptional activity of *** this annual cycle,auxin promotes the degradation of Aux/IAA transcriptional repressors through the SKP–Cullin-F–boxTIR1 complex,relieving the repression of auxin-responsive genes by allowing auxin response factors(ARFs)to activate the transcription of auxin-responsive genes involved in growth *** of transcriptome changes during dormancy transitions have identified MADS-box transcription factors associated with endodormancy *** studies show that poplar dormancy-associated MADS-box(DAM)genes PtMADS7 and PtMADS21 are differentially regulated during the growth-dormancy *** may be regulated by internal factors,which are specifically localized in ***7/PtMADS21 may function as an internal regulator in *** control of flowering time shares certain regulatory hierarchies with control of the dormancy/growth ***,the particularities of different stages of the dormancy/growth cycle warrant comprehensive approaches to identify the causative genes for the entire cycle.A growing body of knowledge also indicates epigenetic regulation plays a role in these processes in perennial horticultural and forestry *** increased knowledge contributes to better understanding of the dormancy process and consequently to pr

关键词： seasonal knowledge temperate

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Mixed-dimensional stacked nanocomposite structures for a specific wavelength-selectable ambipolar photoresponse

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Nano Research 2024年第6期17卷 5549-5558页

作者： Young jae Park jaeho Shim Joo Song Lee Kyu Seung Lee Ji-Yeon Kim Kang Bok ko Sang-Youp Yim Seongjun Kim Hoon-Kyu Shin Donghee Park Yong Ju Yun Dong Ick Son Institute of Advanced Composite Materials Korea Institute of Science and TechnologyJeollabuk-do 55324Republic of Korea National Institute for Nanomaterials Technology Pohang University of Science and TechnologyGyeongsangbuk-do 37673Republic of Korea Department of Semiconductor Science and Technology Semiconductor Physics Research CenterJeonbuk National UniversityJeonju 54896Republic of Korea Advanced Photonics Research Institute Gwangju Institute of Science and TechnologyGwangju 61005Republic of Korea Center for Opto-Electronic Materials and Devices Post-Silicon Semiconductor InstituteKorea Institute of Science and TechnologySeoul 02792Republic of Korea Graduate School of Energy and Environment(KU-KIST Green School) Korea UniversitySeoul 02841Republic of Korea KIST School Department of Nanomaterials and Nano ScienceUniversity of Science and Technology(UST)Daejeon 34113Republic of Korea

Mixed-dimensional composite structures using zero-dimensional(0D)quantum dots(QDs)and two-dimensional(2D)transition metal dichalcogenides(TMDs)materials are expected to attract great interest in optoelectronics due to the potential to generate new optical ***,we report on the unique optical characteristics of a devices with mixed dimensional vertically stacked structures based on tungsten diselenide(WSe_(2))/CdSeS QDs monolayer/molybdenum disulfide(MoS_(2))(2D/0D/2D).Specifically,it exhibits an ambipolar photoresponse characteristic,with a negative photoresponse observed in the 400-600 nm wavelength range and a positive photoresponse appeared at 700 nm *** resulted in the high negative responsivity of up to 52.22 mA·W^(−1)under 400 nm,which is 163 times higher than that of the photodetector without CdSeS *** also demonstrated the negative photoresponse,which could be due to increased carrier collision probability and non-radiative *** modeling and simulation reveal that Auger recombination among the types of non-radiative recombination is the main cause of negative photocurrent ***,we discovered ambipolar photoresponse near a specific wavelength corresponding to the energy of quantum *** study revealed interesting phenomenon in the mixed low-dimensional stacked structure and paved the way to exploit it for the development of innovative photodetection materials as well as for optoelectronic applications.

关键词： mixed-dimension quantum dot heterostructure photodetector ambipolar photoresponse

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Effect of smoking on the risk of gastrointestinal cancer after cholecystectomy: A national population-based cohort study

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World Journal of Gastrointestinal Surgery 2024年第9期16卷 2796-2807页

作者： Minseob Kim Kyung-Do Han Seung-Hyun ko Yoonkyung Woo jae Hyun Han Department of Surgery Graduate School of MedicineThe Catholic University of KoreaSeoul 06591South Korea Department of Statistics and Actuarial Science Soongsil UniversitySeoul 06978South Korea Division of Endocrinology and Metabolism Department of Internal MedicineSt Vincent’s HospitalCollege of MedicineThe Catholic University of KoreaSuwon 16247South Korea Division of Hepatobiliary-Pancreas Surgery and Liver Transplantation Department of SurgerySt Vincent’s HospitalCollege of MedicineThe Catholic University of KoreaSuwon 16247South Korea

BACKGROUND The role of smoking in the incidence of colorectal cancer(CRC)or gastric cancer(GC)in populations undergoing cholecystectomy has not been *** To evaluate the effect of smoking on CRC or GC development in cholecystectomy *** A total of 174874 patients who underwent cholecystectomy between January 1,2010 and December 31,2017 were identified using the korean National Health Insurance Service claims *** patients were matched 1:1 with mem-bers of a healthy population according to age and *** or GC risk after cholecystectomy and the association between smoking and CRC or GC risk in cholecystectomy patients were evaluated using adjusted hazard ratios(HRs)and 95%*** The risks of CRC(adjusted HR:1.15;95%CI:1.06-1.25;P=0.0013)and GC(adjusted HR:1.11;95%CI:1.01-1.22;P=0.0027)were significantly higher in cholecystectomy *** the population who underwent cholecystectomy,both CRC and GC risk were higher in those who had smoked compared to those who had never *** both cancers,the risk tended to increase in the order of non-smokers,ex-smokers,and current *** addition,a positive correlation was observed between the amount of smoking and the risks of both CRC and *** Careful follow-up and screening should be performed,focusing on the increased risk of gastrointestinal cancer in the cholecystectomy group,particularly considering the individual smoking habits.

关键词： Cholecystectomy Smoking,Gastric cancer Colon cancer Risk factor Hazard ratio

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Current status and trends in forest genomics

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Forestry Research 2022年第1期2卷 99-120页

作者： Dulal Borthakur Victor Busov Xuan Hieu Cao Qingzhang Du Oliver Gailing Fikret Isik jae-heung ko Chenghao Li Quanzi Li Shihui Niu Guanzheng Qu Thi Ha Giang Vu Xiao-Ru Wang Zhigang Wei Lin Zhang Hairong Wei Department of Molecular Biosciences and Bioengineering University of Hawaii at Manoa1955 East-West RoadHonoluluHI 96822USA College of Forest Resources and Environmental Science Michigan Technological UniversityHoughtonMI 49931USA Forest Genetics and Forest Tree Breeding Faculty for Forest Sciences and Forest EcologyUniversity of GöttingenBüsgenweg 237077 GöttingenGermany National Engineering Research Center of Tree Breeding and Ecological Restoration College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083P.R.China Cooperative Tree Improvement Program North Carolina State UniversityRaleighNC 27695USA Department of Plant&Environmental New Resources Kyung Hee University1732 Deogyeong-daeroYongin 17104Republic of Korea State Key Laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040P.R.China State Key Laboratory of Tree Genetics and Breeding Chinese Academy of ForestryBeijing 100093P.R.China Department of Ecology and Environmental Science UmeåPlant Science CentreUmeåUniversityUmeå90187Sweden College of Life Sciences Heilongjiang UniversityHarbin 150080P.R.China Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees Ministry of EducationCentral South University of Forestry and TechnologyChangsha 410004Hunan ProvinceP.R.China

Forests are not only the most predominant of the Earth's terrestrial ecosystems,but are also the core supply for essential products for human ***,global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest *** genomics has great potential of increasing forest productivity and adaptation to the changing *** the last two decades,the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies,single cell RNA-seq,clustered regularly interspaced short palindromic repeats(CRISPR)-mediated genome editing,and spatial transcriptomes,as well as bioinformatics analysis technologies,which have led to the generation of multidimensional,multilayered,and spatiotemporal gene expression *** technologies,together with basic technologies routinely used in plant biotechnology,enable us to tackle many important or unique issues in forest biology,and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and *** this review,we recapitulated the advancement and current status of 12 research branches of forest genomics,and then provided future research directions and focuses for each ***,a shift from simple biotechnology-based research to advanced and integrative genomics research,and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge.

关键词： forest routine biotechnology

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koNA:korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 161-167页

作者： Gunhwan ko jae Ho Lee Young Mi Sim Wangho Song Byung-Ha Yoon Iksu Byeon Bang Hyuck Lee Sang-Ok Kim Jinhyuk Choi Insoo Jang Hyerin Kim Jin Ok Yang Kiwon Jang Sora Kim Jong-Hwan Kim Jongbum Jeon jaeeun Jung Seungwoo Hwang Ji-Hwan Park Pan-Gyu Kim Seon-Young Kim Byungwook Lee korea Bioinformation Center Korea Research Institute of Bioscience&BiotechnologyDaejeon 34141Republic of Korea

During the last decade,the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges,including access to human data,as well as transfer,storage,and sharing of enormous amounts of *** promote data-driven biological research,the korean government announced that all biological data generated from government-funded research projects should be deposited at the korea BioData Station(K-BDS),which consists of multiple databases for individual data ***,we introduce the korean Nucleotide Archive(koNA),a repository of nucleotide sequence *** of July 2022,the korean Read Archive in koNA has collected over 477 TB of raw next-generation sequencing data from national genome *** ensure data quality and prepare for international alignment,a standard operating procedure was adopted,which is similar to that of the International Nucleotide Sequence Database *** standard operating procedure includes quality control processes for submitted data and metadata using an automated pipeline,followed by manual *** ensure fast and stable data transfer,a high-speed transmission system called GBox is used in ***,the data uploaded to or downloaded from koNA through GBox can be readily processed using a cloud computing service called *** seamless coupling of koNA,GBox,and Bio-Express enhances the data experience,including submission,access,and analysis of raw nucleotide *** not only satisfies the unmet needs for a national sequence repository in korea but also provides datasets to researchers globally and contributes to advances in *** koNA is available at https://***/kona/.

关键词： korea BioData Station Nucleotide sequence Next-generation sequencing repository Genomics Deposition and access of big data

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Small-scale analysis of brittle-to-ductile transition behavior in pure tungsten

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Journal of Materials Science & Technology 2022年第10期105卷 242-258页

作者： Yeonju Oh Won-Seok ko Nojun Kwak jae-il Jang Takahito Ohmura heung Nam Han Department of Materials Science and Engineering&Research Institute of Advanced Materials Seoul National UniversitySeoul 08826South Korea School of Materials Science and Engineering University of UlsanUlsan 44610South Korea Division of Materials Science and Engineering Hanyang UniversitySeoul04763South Korea National Institute for Materials Science 1-2-1 SengenTsukubaIbaraki 305-0047Japan

Tungsten as a material exhibits broad and increasingly important applications;however,the characterization of its ductile-to-brittle transition(BDT)is currently limited to large-scale scenarios and destructive *** this study,we overcome this challenge by implementing small-scale techniques to provide a comprehensive understanding of the BDT behavior of pure *** order to predict the failure mode at various temperature ranges,the practical fracture analysis diagram has been proposed to describe the resistance to shear flow and cracking behavior with *** temperature nano-indentation tests have provided the inherent mechanical responses corresponding to the maximum shear stress at various temperatures,which is required for dislocation activities in an atomic scaled activation *** one hand,atomistic simulations have provided the temperature dependence of brittle fracture stress,where the atomic bonds break due to intergranular or intragranular *** considered four tungsten specimens having various microstructures prepared using different processing conditions of cold-rolling and post-annealing,and their BDT ranges were inferred using the obtained fracture analysis diagram with the statistical data *** fracture analysis diagram of each specimen obtained were compared with the direct observation of fracture responses in macroscopic mechanical tests,which conclusively indicated that the small-scale inherent mechanical properties are greatly relevant to the macroscopic BDT behavior in pure *** on the BDT estimations by small-scale characterization,we provided further insights into the factors affecting the BDT behavior of tungsten,focusing on the contributions of different types of dislocations.

关键词： Brittle-to-ductile transition Nano-indentation Molecular dynamics Dislocation Tungsten

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