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Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines

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Horticultural Plant Journal 2021年第6期7卷 539-551页

作者： Sampath Perumal Nomar Espinosa Waminal Jonghoon Lee Hyun-jin Koo Boem-soon Choi Jee Young Park Kyounggu Ahn tae-jin yang Department of Agriculture Forestry and BioresourcesPlant Genomics and Breeding Instituteand Research Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Global Institute for Food Security University of Saskatchewan421 Downey RoadSaskatoonSK S7N 4L8Canada Agriculture and Agri-Food Canada 107 Science PlaceSaskatoon S7N 0X2Canada Chromosome Research Institute Department of Life ScienceSahmyook UniversitySeoul 01795Republic of Korea Joeun Seeds.Co. LtdGoesan-GunChungcheongbuk-Do 367-833Republic of Korea Phyzen Genomics Institute 13Seongnam-daero 331beon-gilBundang-guSeongnam-siGyeonggi-do 13558Republic of Korea

Whole-genome shogun sequence(WGS)data generated by next-generation sequencing(NGS)platforms are a valuable resource for crop *** produced 5–6×WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes:cabbage,broccoli,cauliflower,kailan,kale,Brussels sprout,and kohlrabi to systematically evaluate the nuclear and chloroplast(Cp)diversity in the 44 *** breeding *** then exploited the impact of low-coverage NGS by evaluating nuclear genome diversity and assembly,annotation of complete chloroplast(Cp)genomes and 45 S nuclear ribosomal DNA(45S nrDNA)sequences,and copy number variation for major *** genome diversity analysis has revealed a total of 496463 SNPs and 37493 indels in the nuclear genome across the 44 ***,some SNPs showed subspecies enrichment at certain chromosomal *** assembly of complete Cp genomes contained 153361–153372 bp with 37 variants including SNPs and *** 45S nrDNA transcription unit was 5802 bp long with a total of 31 SNPs from the 44 *** phylogenetic tree inferred from the nuclear and Cp genomes coincided and clustered broccoli,cauliflower,and kailan in one group and cabbage,Brussels sprout,kale,and kohlrabi in another *** morphotypes diverged during the last 0.17 million *** Cp genome diversity reflected the unique cytoplasm of each subspecies,and revealed that the cytoplasm of many breeding lines was replaced and intermingled via inter-subspecies crosses during the breeding process *** polymorphic Cp markers provide a classification system for the cytoplasm types in ***,copy numbers of major transposable elements(TEs)showed high diversity among the 44 accessions,indicating that many TEs have become active ***,we demonstrated a comprehensive utilization of low-coverage NGS data and might shed light on the genetic diversity and evolution of diverse *** morphotypes.

关键词： Brassica oleracea subspecies Chloroplast genome Nuclear ribosomal DNA Genetic diversity Phylogeny

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Whole-genome,transcriptome,and methylome analyses provide insights into the evolution of platycoside biosynthesis in Platycodon grandiflorus,a medicinal plant

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Horticulture Research 2020年第1期7卷 1536-1547页

作者： Jungeun Kim Sang-Ho Kang Sin-Gi Park tae-jin yang Yi Lee Ok tae Kim Oksung Chung Jungho Lee Jae-Pil Choi Soo-jin Kwon Keunpyo Lee Byoung-Ohg Ahn Dong jin Lee Seung-il Yoo In-Gang Shin Yurry Um Dae Young Lee Geum-Soog Kim Chang Pyo Hong Jong Bhak Chang-Kug Kim Personal Genomics Institute Genome Research FoundationOsong 28160Korea Genomics Division National Institute of Agricultural Sciences(NAS)Jeonju 54874Korea Theragen Etex Bio Institute Suwon 16229Korea Department of Plant Science Plant Genomics and Breeding Instituteand Research Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Korea Department of Industrial Plant Science&Technology Chungbuk National UniversityCheongju 28644Korea Department of Herbal Crop Research National Institute of Horticultural and Herbal ScienceRural Development Administration(RDA)Eumseong 27709Korea Clinomics Inc Ulsan 44919Korea Green Plant Institute Yongin 16954Korea Korean Genomics Center(KOGIC) Ulsan National Institute of Science and Technology(UNIST)Ulsan 44919Korea Department of Biomedical Engineering School of Life SciencesUlsan National Institute of Science and Technology(UNIST)Ulsan 44919Korea

Triterpenoid saponins(TSs)are common plant defense phytochemicals with potential pharmaceutical *** grandiflorus(Campanulaceae)has been traditionally used to treat bronchitis and asthma in East *** oleanane-type TSs,platycosides,are a major component of the *** root *** studies show that platycosides exhibit anti-inflammatory,antiobesity,anticancer,antiviral,and antiallergy ***,the evolutionary history of platycoside biosynthesis genes remains *** this study,we sequenced the genome of *** and investigated the genes involved in platycoside *** draft genome of *** is 680.1 Mb long and contains 40,017 protein-coding *** analysis revealed that the CYP716 family genes play a major role in platycoside *** CYP716 gene family of *** was much larger than that of other Asterid *** gene annotation also revealed the expansion ofβ-amyrin synthases(bASs)in ***,which was confirmed by tissue-specific gene *** these expanded gene families,we identified key genes showing preferential expression in roots and association with platycoside *** addition,wholegenome bisulfite sequencing showed that CYP716 and bAS genes are hypomethylated in ***,suggesting that epigenetic modification of these two gene families affects platycoside *** whole-genome,transcriptome,and methylome data of *** provide novel insights into the regulation of platycoside biosynthesis by CYP716 and bAS gene families.

关键词： properties insight roots

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High-throughput discovery of plastid genes causing albino phenotypes in ornamental chimeric plants

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Horticulture Research 2023年第1期10卷 249-259页

作者： Hyun-Seung Park Jae-Hyeon Jeon Woohyeon Cho Yeonjeong Lee Jee Young Park Jiseok Kim Young Sang Park Hyun Jo Koo Jung Hwa Kang taek Joo Lee Sang Hoon Kim jin-Baek Kim Hae-Yun Kwon Suk-Hwan Kim Nam-Chon Paek Geupil Jang Jeong-Yong Suh tae-jin yang Department of Agriculture Forestry and BioresourcesResearch Institute of Agriculture and Life Sciencesand Plant Genomics and Breeding InstituteCollege of Agriculture and Life SciencesSeoul National UniversitySeoul08826Republic of Korea Department of Integrative Biological Sciences and Industry Sejong UniversitySeoul 05006Korea Hantaek Botanical Garden YonginGyeonggi-do17183Republic of Korea Radiation Breeding Research Team Advanced Radiation Technology InstituteKorea Atomic Energy Research InstituteJeongeup 56212Korea Special Forest Resources Division National Institute of Forest ScienceSuwon 16631Korea School of Biological Sciences and Technology Chonnam National UniversityGwangjuSouth Korea Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National UniversitySeoul 08826Korea

Chimeric plants composed of green and albino tissues have great ornamental *** unveil the functional genes responsible for albino phenotypes in chimeric plants,we inspected the complete plastid genomes(plastomes)in green and albino leaf tissues from 23 ornamental chimeric plants belonging to 20 species,including monocots,dicots,and *** nine chimeric plants,plastomes were identical between green and albino ***,another 14 chimeric plants were heteroplasmic,showing a mutation between green and albino *** identified 14 different point mutations in eight functional plastid genes related to plastid-encoded RNA polymerase(rpo)or photosystems which caused albinism in the chimeric *** them,12 were deleterious mutations in the target genes,in which early termination appeared due to small deletion-mediated frameshift or single nucleotide *** was single nucleotide substitution in an intron of the ycf3 and the other was a missense mutation in coding region of the rpoC2 *** inspected chlorophyll structure,protein functional model of the rpoC2,and expression levels of the related genes in green and albino tissues of Reynoutria japonica.A single amino acid change,histidine-to-proline substitution,in the rpoC2 protein may destabilize the peripheral helix of plastid-encoded RNA polymerase,impairing the biosynthesis of the photosynthesis system in the albino tissue of *** chimera plant.

关键词： plast substitution ornamental

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Ultra‑Transparent and Multifunctional IZVO Mesh Electrodes for Next‑Generation Flexible Optoelectronics

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Nano-Micro Letters 2025年第1期17卷 293-309页

作者： Kiran A.Nirmal Tukaram D.Dongale Atul C.Khot Chenjie Yao Nahyun Kim tae Geun Kim School of Electrical Engineering Korea UniversityAnam‑ro 145Seongbuk‑guSeoulRepublic of Korea Computational Electronics and Nanoscience Research Laboratory School of Nanoscience and BiotechnologyShivaji UniversityKolhapur 416004India

Mechanically durable transparent electrodes are essential for achieving long-term stability in flexible optoelectronic ***,they are crucial for applications in the fields of energy,display,healthcare,and soft *** meshes represent a promising alternative to traditional,brittle,metal oxide conductors due to their high electrical conductivity,optical transparency,and enhanced mechanical *** this paper,we present a simple method for fabricating an ultra-transparent conducting metal oxide mesh electrode using selfcracking-assisted *** this method,we produced an electrode with ultra-transparency(97.39%),high conductance(Rs=21.24Ωsq^(−1)),elevated work function(5.16 eV),and good mechanical *** also evaluated the effectiveness of the fabricated electrodes by integrating them into organic photovoltaics,organic light-emitting diodes,and flexible transparent memristor devices for neuromorphic computing,resulting in exceptional device *** addition,the unique porous structure of the vanadium-doped indium zinc oxide mesh electrodes provided excellent flexibility,rendering them a promising option for application in flexible optoelectronics.

关键词： Self-cracking template Vanadium-doped indium zinc oxide mesh Organic solar cells Organic light-emitting diodes Flexible transparent memory

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Machine learning empowers efficient design of ternary organic solar cells with PM6 donor

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Journal of Energy Chemistry 2025年第1期100卷 337-347页

作者： Kiran A.Nirmal Tukaram D.Dongale Santosh S.Sutar Atul C.Khot tae Geun Kim School of Electrical Engineering Korea University Computational Electronics and Nanoscience Research Laboratory School of Nanoscience and Biotechnology Shivaji University Yashwantrao Chavan School of Rural Development Shivaji University

Organic solar cells(OSCs) hold great potential as a photovoltaic technology for practical ***, the traditional experimental trial-and-error method for designing and engineering OSCs can be complex, expensive, and time-consuming. Machine learning(ML) techniques enable the proficient extraction of information from datasets, allowing the development of realistic models that are capable of predicting the efficacy of materials with commendable accuracy. The PM6 donor has great potential for high-performance OSCs. However, it is crucial for the rational design of a ternary blend to accurately forecast the power conversion efficiency(PCE) of ternary OSCs(TOSCs) based on a PM6 ***, we collected the device parameters of PM6-based TOSCs and evaluated the feature importance of their molecule descriptors to develop predictive models. In this study, we used five different ML algorithms for analysis and prediction. For the analysis, the classification and regression tree provided different rules, heuristics, and patterns from the heterogeneous dataset. The random forest algorithm outperforms other prediction ML algorithms in predicting the output performance of PM6-based TOSCs. Finally, we validated the ML outcomes by fabricating PM6-based TOSCs. Our study presents a rapid strategy for assessing a high PCE while elucidating the substantial influence of diverse descriptors.

关键词： Random forests

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Prominent cycling reversibility and kinetics enabled by CaTiO3 protective layer on Zn metal for aqueous Zn-ion batteries

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Journal of Energy Chemistry 2025年第1期100卷 245-258页

作者： Gaeun Lee Yong Nam Ahn Seongjoon So Chanwoo Park Jong-Seong Bae taehyun Park Il tae Kim Jaehyun Hur School of Chemical Biological and Battery Engineering Gachon University Seongnam Busan Center Korea Basic Science Institute

Aqueous Zn-ion batteries （AZIBs） have received considerable attention owing to their various advantages such as safety,low cost,simple battery assembly conditions,and high ionic ***,they still suffer from serious problems,including uncontrollable dendrite growth,corrosion,hydrogen evolution reaction （HER） from water decomposition,electrode passivation,and unexpected *** creation of a uniform artificial nanocrystal layer on the Zn anode surface is a promising strategy for resolving these ***,we propose the use of a perovskite CaTiO3（CTO） protective layer on Zn（CTO@Zn） as a promising approach for improving the performance of *** CTO artificial layer provides an efficient pathway for Zn ion diffusion towards the Zn metal because of the high dielectric constant （εr=180） and ferroelectric characteristics that enable the alignment of dipole moments and redistribute the Zn2+ions in the CTO *** avoiding the direct contact of the Zn anode with the electrolyte solution,the uneven dendrite growth,corrosion,parasitic side reactions,and HER are mitigated,while CTO retains its mechanical and chemical robustness during ***,CTO@Zn demonstrates an improved lifespan in a symmetric cell configuration compared with bare ***@Zn shows steady overpotential （～68 m V） for 1500 h at 1 mA cm-2/0.5 mA h cm-2,excelling bare ***,when paired with the V2O5-C cathode,the CTO@Zn//V2O5-C full battery delivers 148.4 mA h g-1（based on the mass of the cathode） after 300 *** study provides new insights into Zn metal anodes and the development of high-performance AZIBs.

关键词： Perovskite

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Optimization of an Artificial Intelligence Database and Camera Installation for Recognition of Risky Passenger Behavior in Railway Vehicles

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Computers, Materials & Continua 2025年第1期82卷 1277-1293页

作者： Min-kyeong Kim Yeong Geol Lee Won-Hee Park Su-hwan Yun tae-Soon Kwon Duckhee Lee Railroad Test&Certification Division Korea Railroad Research Institute(KRRI)Cheoldo BangmulgwanroUiwang-si16105Republic of Korea Railroad Safety Division Korea Railroad Research Institute(KRRI)Cheoldo BangmulgwanroUiwang-si16105Republic of Korea

Urban railways are vital means of public transportation in *** than 30%of metropolitan residents use the railways,and this proportion is expected to *** enhance safety,the government has mandated the installation of closed-circuit televisions in all carriages by ***,cameras still monitored *** address this limitation,we developed a dataset of risk factors and a smart detection system that enables an immediate response to any abnormal behavior and intensive monitoring *** created an innovative learning dataset that takes into account seven unique risk factors specific to Korean railway *** data collection was conducted across the Shinbundang Line of the Incheon Transportation Corporation,and the Ui-Shinseol *** observed several behavioral characteristics and assigned unique annotations to *** also considered carriage *** performance was evaluated by camera placement and *** the camera installation plan was *** dataset will find immediate applications in domestic railway *** artificial intelligence algorithms will be verified shortly.

关键词： AI railway vehicle risk factor smart detection AI training data

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Comprehensive molecular characterization to predict immunotherapy response in advanced biliary tract cancer:a phase II trial of pembrolizumab

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Oncology Research 2025年第1期33卷 57-65页

作者： RYUL KIM JOO KYUNG PARK MINSUK KWON MINAE AN JUNG YONG HONG JOON OH PARK SUNG HEE LIM SEUNG tae KIM Division of Hematology-Oncology Department of MedicineSamsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea Division of Gastroenterology Department of MedicineSamsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea Department of Hematology-Oncology Ajou University School of MedicineSuwon-siGyeonggi-doKorea Samsung Advanced Institute of Health Science and Technology Sungkyunkwan University School of MedicineSeoulKorea

Background:Immune checkpoint inhibitors(ICIs)are effective in a subset of patients with metastatic solid ***,the patients who would benefit most from ICIs in biliary tract cancer(BTC)are still *** and methods:We molecularly characterized tissues and blood from 32 patients with metastatic BTC treated with the ICI pembrolizumab as second-line ***:All patients had microsatellite stable(MSS)type *** of the 32 patients achieved partial response(PR),with an objective response rate(ORR)of 9.4%(95%confidence interval[CI],2.0–25.2)and nine showed stable disease(SD),exhibiting a disease control rate(DCR)of 37.5%(95%CI,21.1–56.3).For the 31 patients who had access to PD-1 ligand 1(PD-L1)combined positive score(CPS)testing(cut-off value≥1%),the ORR was not different between those who had PD-L1-positive(PD-L1+;1/11,9.1%)and PDL1-(2/20,10.0%)tumors(p=1.000).The tumor mutational burden(TMB)of PD-L1+BTC was comparable to that of PD-L1-BTC(p=0.630).TMB and any exonic somatic mutations were also not predictive of pembrolizumab *** analysis of blood and tumor samples demonstrated a relatively high natural killer(NK)cell proportion in the peripheral blood before pembrolizumab treatment in patients who achieved tumor ***,the tumors of these patients presented high enrichment scores for NK cells,antitumor cytokines,and Th1 signatures,and a low enrichment score for cancer-associated ***:This study shows the molecular characteristics associated with the efficacy of pembrolizumab in BTC of the MSS type.

关键词： Pembrolizumab Whole-exome sequencing Whole-transcriptome sequencing Biliary tract cancer

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Homeostasis and regulation of autoreactive B cells

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Cellular & Molecular Immunology 2020年第6期17卷 561-569页

作者： Sujin Lee Yeunjung Ko tae jin Kim Department of Immunology Sungkyunkwan University School of MedicineSuwon 16419Republic of Korea

In contrast to the previous belief that autoreactive B cells are eliminated from the normal repertoire of B cells,many autoreactive B cells actually escape clonal deletion and develop into mature B *** autoreactive B cells in healthy individuals perform some beneficial functions in the host and are homeostatically regulated by regulatory T and B cells or other mechanisms to prevent autoimmune *** B-1 cells constitutively produce polyreactive natural antibodies for tissue ***,autoreactive follicular B cells were reported to participate actively in the germinal center ***,the selection and usefulness of autoreactive marginal zone(MZ)B cells found in autoimmune diseases are not well understood,although the repertoire of MZ B-cell receptors(BCRs)is presumed to be biased to detect bacterial *** this review,we discuss the autoreactive B-cell populations among all three major B-cell subsets and their regulation in immune responses and diseases.

关键词： B-cell autoreactivity polyreactivity autoreactive antibody B-cell receptor B-1 lymphocyte autoreactive germinal center autoreactive marginal zone B cell

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Comparison of postoperative corneal changes between dry eye and non-dry eye in a murine cataract surgery model

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International Journal of Ophthalmology(English edition) 2016年第2期9卷 218-224页

作者： jin Woo Kwon Yeon Woong Chung jin A Choi tae Yoon La Dong Hyun Jee yang Kyung Cho Department of Ophthalmology St.Vincent's HospitalCollege of Medicine The Catholic University of Korea

AIM： To compare the effects of the surgical insult of cataract surgery on corneal inflammatory infiltration, neovascularization （NV） and lymphangiogenesis （LY） between the dry eye and non-dry eye in murine cataract surgery models.METHODS： We established two groups of animals, one with normal eyes （non-dry eye） and the second with induced dry eyes. In both groups, we used surgical insults to mimic human cataract surgery, which consisted of lens extraction, corneal incision and suture. After harvesting of corneas on the 9th postoperative day and immunohistochemical staining, we compared NV, LY and CD11b＋ cell infiltration in the corneas.RESULTS： Dry eye group had significantly more inflammatory infiltration （21.75%±7.17% r/s 3.65%±1.49%; P=0.049）. The dry eye group showed significantly more NV （48.21% ±4.02% ys 26.24% ±6.01% ; P =0.016） and greater levels of LY （9.27%±0.48% ys 4.84%±1.15%; P= 0.007）. In corneas on which no surgery was performed, there was no induction of NV in both the dry and non- dry group, but dry eye group demonstrated more CD11b＋ cells infiltration than the non-dry eye group （0.360%± 0.160% vs 0.023%±0.006%; P=0.068）. Dry eye group showed more NV than non-dry eye group in both topical PBS application and subconjunctival PBS injection （P= 0.020 and 0.000, respectively）.

关键词： angiogenesis cataract surgery dry eyedisease inflammation

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