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Single-cell and spatial omics:exploring hypothalamic heterogeneity

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Neural Regeneration Research 2025年第6期20卷 1525-1540页

作者： Muhammad Junaid eun Jeong Lee su Bin Lim Department of Biochemistry&Molecular Biology Ajou University School of MedicineSuwonSouth Korea Department of Biomedical Sciences Graduate School of Ajou UniversitySuwonSouth Korea Department of Brain Science Ajou University School of MedicineSuwonSouth Korea

Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.

关键词： cellular diversity hypothalamus multi-omics single-cell transcriptomics spatial transcriptomics

Metabolic relationships between marine red algae and algae‑associated bacteria

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Marine Life Science & Technology 2024年第2期6卷 298-314页

作者： Kyung Hyun Kim Jeong Min Kim Ju Hye Baek Sang eun Jeong Hocheol Kim Hwan su Yoon Che Ok Jeon Department of Biological Sciences and Biotechnology Hannam UniversityDaejon 34054Republic of Korea Department of Life Science Chung-Ang UniversitySeoul 06974Republic of Korea Department of Biological Sciences Sungkyunkwan UniversitySuwon 16419Republic of Korea

Mutualistic interactions between marine phototrophs and associated bacteria are an important strategy for their success-ful survival in the ocean,but little is known about their metabolic ***,bacterial communities in the algal sphere(AS)and bulk solution(BS)of nine marine red algal cultures were analyzed,and Roseibium and Phycisphaera were identified significantly more abundantly in AS than in *** metabolic features of Roseibium RMAR6-6(isolated and genome-sequenced),Phycisphaera MAG 12(obtained by metagenomic sequencing),and a marine red alga,Porphyridium purpureum CCMP1328(from GenBank),were analyzed ***6-6 has the genetic capability to fix nitrogen and produce B vitamins(B1,B2,B5,B6,B9,and B12),bacterioferritin,dimethylsulfoniopropionate(DMSP),and phenylacetate that may enhance algal growth,whereas MAG 12 may have a limited metabolic capability,not producing vitamins B9 and B12,DMSP,phenylacetate,and siderophores,but with the ability to produce bacitracin,possibly modulating algal *** CCMP1328 lacks the genetic capability to fix nitrogen and produce vitamin B12,DMSP,phenylacetate,and *** was shown that the nitrogen-fixing ability of RMAR6-6 promoted the growth of ***-pureum,and DMSP reduced the oxidative stress of *** metabolic interactions between strain RMAR6-6 and *** CCMP1328 were also investigated by the transcriptomic analyses of their monoculture and *** together,potential metabolic relationships between Roseibium and *** were *** study provides a bet-ter understanding of the metabolic relationships between marine algae and algae-associated bacteria for successful growth.

关键词： Metabolic relationship Marine red algae Symbiotic bacteria Roseibium Phycisphaera Porphyridium

Degradation and resynthesis of chlorophyll during increased oxidative stress and prolonged darkness differ between annual and perennial flax(Linum L.)

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Oil Crop Science 2024年第2期9卷 121-130页

作者： Kenyon J. Nisbett Abida Alokozai su Hyun Elizabeth ko G. Adam Mott Jason C.L. Browna Department of Biological Sciences University of Toronto ScarboroughTorontoONCanada Department of Cell&Systems Biology University of TorontoTorontoONCanada Centre for the Analysis of Genome Evolution&Function University of TorontoTorontoONCanada

Among plants,there is considerable variation in lifespan:annuals live less than one year,whereas perennials live for several years,with the longest-living perennial having survived 43,600 *** proposed by the Disposable Soma Theory,this lifespan variation among plants likely reflects differential investment of limited energy and nutrient resources,with perennials investing more energy and nutrients into biomolecular maintenance compared to annuals in order to ensure persistence over multiple *** differential investment may be particularly important during periods of exogenous stress,which are known to accelerate biomolecular *** present study evaluated this hypothesis using annual and perennial flax(Linum L.)subjected to two exogenous stressors—increased oxidative stress(i.e.,foliar H2O2spraying)and complete prolonged *** chlorophyll has been shown to exhibit degradation in response to changes in environmental conditions,we utilized changes in chlorophyll levels during and after periods of exogenous stress to evaluate our *** predicted that i)perennials would exhibit a slower rate of chlorophyll degradation during exposure to exogenous stressors compared to annuals,and ii)perennials would exhibit a faster rate of chlorophyll resynthesis following such exposure compared to *** levels before,during,and after exposure to both exogenous stressors were measured in two separate trails,once using image colour analysis and once using *** chlorophyll degradation rates in response to oxidative stress did not differ between annuals and perennials,contrary to our predictions,chlorophyll resynthesis rates following such exposure were significantly higher in perennials,as *** plants were subjected to complete prolonged darkness,chlorophyll degradation rates were significantly lower in perennials than annuals,as predicted;however,when plants were subsequently reintroduced to natural photoperiod,ch

关键词： Ageing Life history Maximum lifespan Oxidative stress Somatic maintenance

Organic X-Ray Image Sensors Using a Medium Bandgap Polymer Donor with Low Dark Current

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ENERGY & ENVIRONMENTAL MATERIALS 2024年第6期7卷 230-237页

作者： Ha, Jong-Woon Eom, Seung Hun Cha, Bo Kyung Song, Seyeong eun, Hyeong Ju Kim, Jong H. Park, Jong Mok Kim, Bongsoo Park, Byoungwook ko, Seo-Jin Yoon, sung Cheol Lee, Changjin Jung, In Hwan Hwang, Do-Hoon Pusan Natl Univ Chem Inst Funct Mat Dept Chem Busan 46241 South Korea korea Res Inst Chem Technol KRICT Div Adv Energy Mat Res Ctr Daejeon 34114 South Korea korea Electrotechnol Res Inst KERI Electromed Device Res Ctr Ansan 15588 South Korea Ulsan Natl Inst Sci & Technol UNIST Grad Sch Carbon Neutral Sch Energy & Chem Engn Ulsan 44919 South Korea Ajou Univ Dept Mol Sci & Technol Suwon 16449 South Korea korea Res Inst Chem Technol Res Ctr Adv Specialty Chem Ulsan 44412 South Korea Ulsan Natl Inst Sci & Technol UNIST Dept Chem Ulsan 44919 South Korea Hanyang Univ Dept Organ & Nano Engn Human Tech Convergence Program 222 Wangsimni Ro Seoul 04763 South Korea

The development of portable X-ray detectors is necessary for diagnosing fractures in unconscious patients in emergency situations. However, this is quite challenging because of the heavy weight of the scintillator and silicon photodetectors. The weight and thickness of X-ray detectors can be reduced by replacing the silicon layer with an organic photodetectors. This study presents a novel bithienopyrroledione-based polymer donor that exhibits excellent photodetection properties even in a thick photoactive layer (similar to 700 nm), owing to the symmetric backbone and highly soluble molecular structure of bithienopyrroledione. The ability of bithienopyrroledione-based polymer donor to strongly suppress the dark current density (J(d) similar to 10(-10) A cm(-2)) at a negative bias (-2.0 V) while maintaining high responsivity (R = 0.29 A W-1) even at a thickness of 700 nm results in a maximum shot-noise-limited specific detectivity of D-sh* = 2.18 x 10(13) Jones in the organic photodetectors. Printed organic photodetectors are developed by slot-die coating for use in X-ray detectors, which exhibit D-sh* = 2.73 x 10(12) Jones with clear rising (0.26 s) and falling (0.29 s) response times upon X-ray irradiation. Detection reliability is also proven by linear response of the X-ray detector, and the X-ray detection limit is 3 mA.

关键词： low dark current low detection limit organic photodetector printable X-ray DETECTORS PHOTOCONDUCTORS SENSITIVITY

Effect of Asiasari radix on osteoblastic differentiation of stem cells derived from gingiva

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Journal of Traditional Chinese Medicine 2016年第6期36卷 756-759页

作者： su-Hyeon Jeong Ji-eun Lee Seong-Ho Jin Youngkyung ko Jun-Beom Park Department of Rehabilitation Medicine of korean Medicine Chungju Hospital of Korean MedicineCollege of Korean Medicine Semyung University Development of Periodontics College of MedicineThe Catholic University of Korea

OBJECTIVE: To examine the dose-dependent impact of Asiasari Radix(A. radix) on the cell viability,differentiation and mineralization of stem cells derived from ***: Stem cells that were derived from gingiva were grown in the presence of A. radix at final concentrations that ranged from 0.001 to 10 μg/m L. The morphology of the cells was viewed under an inverted microscope and the analysis of cell proliferation was performed by using Cell Counting Kit-8(CCK-8) on day 1. The alkaline phosphatase activity test was used to assess differentiation and Alizarin red S staining was used to assess mineralization of treated ***: The control group showed spindleshaped, fibroblast-like morphology and the shapesof the cells in 0.001, 0.01, 0.1, 1 and 10 μg/mL of *** were similar to that of the control group at day 1. The cultures growing in the presence of0.001 μg/m L of A. radix at day 1 showed an increase in the CCK-8 value(P 0.05). Mineralized extracellular deposits were observed after Alizarin Red S staining and the cultures grown in the presence of 0.001 μg/m L of A. radix showed the highest value for quantitative results for bound dye(P < 0.05).CONCLUSION: Within the limits of this study, A. radix influenced the proliferation of stem cells derived from the gingiva and low concentrations of *** might enhance osteogenic differentiation of the stem cells.

关键词： Cell differentiation Plant roots Plant extracts Stem cells Drugs,Chinese herbal

Anti-senescence and anti-wrinkle activities of 3-bromo-4,5-dihydroxybenzaldehyde from Polysiphonia morrowii Harvey in human dermal fibroblasts

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Asian Pacific Journal of Tropical Biomedicine 2021年第2期11卷 74-80页

作者： su-Hyeon Cho eun-Yi ko Soo-Jin Heo Seo-Young Kim Juhee Ahn Kil-Nam Kim Chuncheon Center Korea Basic Science InstituteChuncheon 24341Republic of Korea Bio research Center DermaproJeju 63309Republic of Korea Jeju Marine Research Center Korea Institute of Ocean Science&TechnologyJeju 63349Republic of Korea Department of Medical Biomaterials Engineering College of Biomedical SciencesKangwon National UniversityChuncheon 24341Republic of Korea

Objective:To investigate the anti-senescence effect of 3-bromo-4,5-dihydroxybenzaldehyde(BDB)from Polysiphonia morrowii Harvey in human dermal fibroblasts(HDF).Methods:HDF were subjected to treatment of BDB and then treated with hydrogen peroxide(H2O2)to induce premature ***-associatedβ-galactosidase(SA-β-gal)activity in HDF was determined using the SA-β-gal staining *** reactive oxygen species(ROS)production was measured using the 2’,7’-dichlorodihydrofluorescein diacetate *** blotting assay was performed to assess the level of antioxidant enzyme glutathione peroxidase 1(GPX1).In addition,intracellular collagen and collagenase contents were analyzed using the respective ELISA *** activity in HDF supernatants was measured from p-nitroaniline release and normalized using total protein ***:Treatment of HDF with H2O2 increased the activity of SA-β-gal,but BDB pre-treatment resulted in the reduction of SA-β-gal ***,BDB significantly reduced H2O2-induced intracellular ROS *** also markedly increased the level of GPX1,which was inhibited by 400μM of ***,in in vitro study,BDB significantly increased intracellular collagen content and decreased matrix metalloproteinase-1 and elastase activities in ***:Our results demonstrate that BDB shows antisenescence and anti-wrinkle activities in vitro.

关键词： Polysiphonia morrowii Harvey 3-bromo-4,5-dihydroxybenzaldehyde Oxidative stress Human dermal fibroblast Anti-senescence activity Anti-wrinkle activity

Effect of friction on the contact stress of a coated polymer gear

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Friction 2020年第6期8卷 1169-1177页

作者： su-Min BAE Kuk-Jin SEO Dae-eun KIM Department of Mechanical Engineering Yonsei UniversitySeoul 03722Republic of Korea

Polymer gears are used extensively in various ***,durability issues have been emerging because of friction at gear tooth contact *** extend the lifetime of polymer gears,a low-frictional coating has been considered as a possible *** this study,a finite element simulation method was performed to investigate the contact stress between a pair of coated polymer *** simulation included various friction coefficients(COFs)for studying the effects of friction during the *** results revealed that the friction causes the contact stress to shift over the roll angle,which is attributed to the direction of the sliding friction based on a free-body *** also investigated the effects of coating and found that a thin coating has little effect on the bulk deformation behavior of the ***,the stress distribution in the coating at the pitch point was investigated as the COF *** zero friction,three notable stress regions were observed:1)the center of the surface,2)the end of the contact,and 3)the overall contact *** COF was increased in the micro-slip region of the contact interface,both tensile and compressive stresses in the coating *** study provides significant aid to engineers for understanding the stress response of the coating applied to polymer gears to achieve an optimal design.

关键词： coating contact stress finite element method(FEM) friction polymer gear

SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA-and tRNA-derived Small RNAs

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Genomics, Proteomics & Bioinformatics 2018年第2期16卷 144-151页

作者： Junchao Shi eun-A ko Kenton M.Sanders Qi Chen Tong Zhou Department of Physiology and Cell Biology University of Nevada Reno School of Medicine

High-throughput RNAoseq has revolutionized the process of small RNA （sRNA） discovery, leading to a rapid expansion of sRNA categories. In addition to the previously wellcharacterized sRNAs such as microRNAs （miRNAs）, piwi-interacting RNAs （piRNAs）, and small nucleolar RNA （snoRNAs）, recent emerging studies have spotlighted on tRNA-derived sRNAs （tsRNAs） and rRNA-derived sRNAs （rsRNAs） as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipeline _optimized for rRNA- and tRNA-derived s_RNAs （SPORTS 1 .0）. SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users＇ input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate, which is consistent with their highly modified nature. SPORTS1.0 is an opensource software and can be publically accessed at https：//***/junchaoshi/sports1.0.

关键词： Small RNA RNA-seq data analysistsRNA rsRNA Annotation pipeline

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