• 천문학회보
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• 제45권1호
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• pp.38.2-38.2
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• 2020

Horizon Run 5 (HR5) is a cosmological hydrodynamical simulation which captures the properties of the Universe on a Gpc scale while achieving a resolution of 1 kpc. This enormous dynamic range allows us to simultaneously capture the physics of the cosmic web on very large scales and account for the formation and evolution of dwarf galaxies on much smaller scales. Inside the simulation box. we zoom-in on a high-resolution cuboid region with a volume of 1049 × 114 × 114 Mpc3. The subgrid physics chosen to model galaxy formation includes radiative heating/cooling, reionization, star formation, supernova feedback, chemical evolution tracking the enrichment of oxygen and iron, the growth of supermassive black holes and feedback from active galactic nuclei (AGN) in the form of a dual jet-heating mode. For this simulation we implemented a hybrid MPI-OpenMP version of the RAMSES code, specifically targeted for modern many-core many thread parallel architectures. For the post-processing, we extended the Friends-of-Friend (FoF) algorithm and developed a new galaxy finder to analyse the large outputs of HR5. The simulation successfully reproduces many observations, such as the cosmic star formation history, connectivity of galaxy distribution and stellar mass functions. The simulation also indicates that hydrodynamical effects on small scales impact galaxy clustering up to very large scales near and beyond the baryonic acoustic oscillation (BAO) scale. Hence, caution should be taken when using that scale as a cosmic standard ruler: one needs to carefully understand the corresponding biases. The simulation is expected to be an invaluable asset for the interpretation of upcoming deep surveys of the Universe.

• Genomics & Informatics
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• 제21권3호
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• pp.36.1-36.19
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• 2023

The LIM domain-containing proteins are dominantly found in plants and play a significant role in various biological processes such as gene transcription as well as actin cytoskeletal organization. Nevertheless, genome-wide identification as well as functional analysis of the LIM gene family have not yet been reported in the economically important plant sorghum (Sorghum bicolor L.). Therefore, we conducted an in silico identification and characterization of LIM genes in S. bicolor genome using integrated bioinformatics approaches. Based on phylogenetic tree analysis and conserved domain, we identified five LIM genes in S. bicolor (SbLIM) genome corresponding to Arabidopsis LIM (AtLIM) genes. The conserved domain, motif as well as gene structure analyses of the SbLIM gene family showed the similarity within the SbLIM and AtLIM members. The gene ontology (GO) enrichment study revealed that the candidate LIM genes are directly involved in cytoskeletal organization and various other important biological as well as molecular pathways. Some important families of regulating transcription factors such as ERF, MYB, WRKY, NAC, bZIP, C2H2, Dof, and G2-like were detected by analyzing their interaction network with identified SbLIM genes. The cis-acting regulatory elements related to predicted SbLIM genes were identified as responsive to light, hormones, stress, and other functions. The present study will provide valuable useful information about LIM genes in sorghum which would pave the way for the future study of functional pathways of candidate SbLIM genes as well as their regulatory factors in wet-lab experiments.

• 한국도서관정보학회지
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• 제54권4호
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• pp.255-279
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• 2023

이 연구의 목적은 미국 공공도서관과 국내 공공도서관의 목록 보강콘텐츠 서비스 제공 현황 비교를 통하여 시사점을 도출하고 향후 국내 공공도서관을 위한 목록 보강콘텐츠 서비스에 대한 개선방안을 모색하는 것이다. 2023년 9월 초부터 10월 중순까지 미국과 국내 공공도서관 홈페이지에서 특정 도서를 검색한 후, 검색결과에 나타난 보강콘텐츠 서비스 기능을 비교하였으며, 그 결과는 다음과 같다. 첫째, 국내 공공도서관 보강콘텐츠 서비스는 별도의 업체에서 보강콘텐츠 서비스 솔루션을 개발 후, 제공하는 방식이 필요하다. 둘째, 보강콘텐츠 서비스 솔루션은 도서중심정보, 도서추천정보, 이용자참여정보 영역에서 활용할 수 있는 국내 정보원을 발굴해야 한다. 셋째, 도서관정보 나루와 같은 공공데이터를 활용한 보강콘텐츠 개발이 필요하다. 넷째, 각 통합도서관은 지역커뮤니티 참여 서비스에서 생성되는 데이터를 보강콘텐츠 서비스로 활용할 수 있도록 해야 한다.

• 대한한의학회지
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• 제45권1호
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• pp.114-125
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• 2024

Objectives: Network pharmacology is an analysis method that explores drug-centered efficacy and mechanism by constructing a compound-target-disease network based on system biology, and is attracting attention as a methodology for studying herbal medicine that has the characteristics for multi-compound therapeutics. Thus, we investigated the potential functions and pathways of Myrrha on Allergic Rhinitis (AR) via network pharmacology analysis and molecular docking. Methods: Using public databases and PubChem database, compounds of Myrrha and their target genes were collected. The putative target genes of Myrrha and known target genes of AR were compared and found the correlation. Then, the network was constructed using STRING database, and functional enrichment analysis was conducted based on the Gene Ontology (GO) Biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways. Binding-Docking stimulation was performed using CB-Dock. Results: The result showed that total 3 compounds and 55 related genes were gathered from Myrrha. 33 genes were interacted with AR gene set, suggesting that the effects of Myrrha are closely related to AR. Target genes of Myrrha are considerably associated with various pathways including 'Fc epsilon RI signaling pathway' and 'JAK-STAT signaling pathway'. As a result of blinding docking, AKT1, which is involved in both mechanisms, had high binding energies for abietic acid and dehydroabietic acid, which are components of Myrrha. Conclusion: Through a network pharmacological method, Myrrha was predicted to have high relevance with AR by regulating AKT1. This study could be used as a basis for studying therapeutic effects of Myrrha on AR.

• 생명과학회지
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• 제19권8호
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• pp.1159-1163
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• 2009

ER stress에 관련된 유전자의 기능변화와 전사조절인자 분석하기 위해 ER stress를 유도한 간세포에서 expression microarray로 유전자 발현을 확보한 후 GSECA로 분석하였다. ER stress가 유도되면, ER에 주어지는 과도한 부하를 감소시키는 기능들이 증가하는 반면, ER stress가 더 증가함에 따라 ATP 생성이나 DNA repair, 더 나아가 세포분열의 기능이 감소하는 등 세포가 damage을 받음을 알 수 있었다. ER stress에 관련된 전사조절인자로는 FOX04, AP-1, FOX03, HNF4, IRF-1, GATA 등의 전사조절인자들이 ER stress에 의해 발현이 증가하는 유전자들의 promoter에 공통적으로 존재하였으며, E2F, Nrf-1, Elk-1, YY1, CREB, MTF-1, STAT-1, ATF 등의 전사인자들이 발현이 감소하는 유전자들의 promoter에서 공통적으로 존재하여, 이들의 전사인자들이 ER stress에 의한 유전자의 발현조절에 중요한 역할을 하는 전사조절인자임을 알 수 있었다.

• Asian-Australasian Journal of Animal Sciences
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• 제29권3호
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• pp.343-351
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• 2016

Although the chemical, physical, and nutritional properties of bovine milk have been extensively studied, only a few studies have attempted to characterize milk-synthesizing genes using RNA-seq data. RNA-seq data was collected from 21 Holstein samples, along with group information about milk production ability; milk yield; and protein, fat, and solid contents. Meta-analysis was employed in order to generally characterize genes related to milk production. In addition, we attempted to investigate the relationship between milk related traits, parity, and lactation period. We observed that milk fat is highly correlated with lactation period; this result indicates that this effect should be considered in the model in order to accurately detect milk production related genes. By employing our developed model, 271 genes were significantly (false discovery rate [FDR] adjusted p-value<0.1) detected as milk production related differentially expressed genes. Of these genes, five (albumin, nitric oxide synthase 3, RNA-binding region (RNP1, RRM) containing 3, secreted and transmembrane 1, and serine palmitoyltransferase, small subunit B) were technically validated using quantitative real-time polymerase chain reaction (qRT-PCR) in order to check the accuracy of RNA-seq analysis. Finally, 83 gene ontology biological processes including several blood vessel and mammary gland development related terms, were significantly detected using DAVID gene-set enrichment analysis. From these results, we observed that detected milk production related genes are highly enriched in the circulation system process and mammary gland related biological functions. In addition, we observed that detected genes including caveolin 1, mammary serum amyloid A3.2, lingual antimicrobial peptide, cathelicidin 4 (CATHL4), cathelicidin 6 (CATHL6) have been reported in other species as milk production related gene. For this reason, we concluded that our detected 271 genes would be strong candidates for determining milk production.

• Asian Pacific Journal of Cancer Prevention
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• 제15권23호
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• pp.10513-10524
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• 2015

Background: Metastasis is a major reason for poor prognosis in patients with cancer, including hepatocellular carcinoma (HCC). A salient feature is the ability of cancer cells to colonize different organs. Long non-coding RNAs (lncRNAs) play important roles in numerous cellular processes, including metastasis. Materials and Methods: In this study, the lncRNA expression profiles of two HCC cell lines, one with high potential for metastasis to the lung (HCCLM3) and the other to lymph nodes (HCCLYM-H2) were assessed using the Arraystar Human LncRNA Array v2.0, which contains 33,045 lncRNAs and 30,215 mRNAs. Coding-non-coding gene co-expression (CNC) networks were constructed and gene set enrichment analysis (GSEA) was performed to identify lncRNAs with potential functions in organ-specific metastasis. Levels of two representative lncRNAs and one representative mRNA, RP5-1014O16.1, lincRNA-TSPAN8 and TSPAN8, were further detected in HCC cell lines with differing metastasis potential by qRT-PCR. Results: Using microarray data, we identified 1,482 lncRNAs and 1,629 mRNAs that were differentially expressed (${\geq}1.5$ fold-change) between the two HCC cell lines. The most upregulated lncRNAs in H2 were RP11-672F9.1, RP5-1014O16.1, and RP11-501G6.1, while the most downregulated ones were lincRNA-TSPAN8, lincRNA-CALCA, C14orf132, NCRNA00173, and CR613944. The most upregulated mRNAs in H2 were C15orf48, PSG2, and PSG8, while the most downregulated ones were CALCB, CD81, CD24, TSPAN8, and SOST. Among them, lincRNA-TSPAN8 and TSPAN8 were found highly expressed in high lung metastatic potential HCC cells, while lowly expressed in no or low lung metastatic potential HCC cells. RP5-1014O16.1 was highly expressed in high lymphatic metastatic potential HCC cell lines, while lowly expressed in no lymphatic metastatic potential HCC cell lines. Conclusions: We provide the first detailed description of lncRNA expression profiles related to organ-specific metastasis in HCC. We demonstrated that a large number of lncRNAs may play important roles in driving HCC cells to metastasize to different sites; these lncRNAs may provide novel molecular biomarkers and offer a new basis for combating metastasis in HCC cases.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• 제30권2호
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• pp.100-107
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• 2004

Schwann cell, one of important components of peripheral nervous system, interact with neurons to mutually support the growth and replication of embryonal nerves and to maintain the different functions of adult nerves. The Ara-C, known as an antimitotic agent, have been used to have high effectiveness in eliminating fibroblasts during Schwann cell culture period. This enrichment effect is also known to be cummulative with each successive pulse of Ara-C applied and is due to a progressive loss of fibroblasts. But the cytotoxicity by Ara-C is also cummulative and noticeable over the period. To determine the most effective application time and interval of Ara-C in the Schwann cell culture, we observed the Schwann cell purity and density with the Ara-C treatment in plain and three-dimensional culture from dorsal root ganglion of new born rat. By culturing dispersed dorsal root ganglia, we can repeatedly generate homogenous Schwann cells, and cellular morphology and cell count with mean percentages were evaluated in the plain culture dishes and in the immunostainings of S-100 and GFAP in the three-dimensional culture. The Ara-C treated cultures showed a higher Schwann cell percentage ($31.0%{\pm}8.09%$ in P4 group to $65.5%{\pm}24.08%$ in P2 group), compared with that obtained in the abscence of Ara-C ($17.6%{\pm}6.03%$) in the plain culture after 2 weeks. And in the three-dimensional culture, S-100 positive cells increased to $56.22%{\pm}0.67%$ and GFAP positive cells to $66.46%{\pm}1.83%$ in G2 group (p<0.05), higher yield than other groups with Ara-C application. Therefore, we concluded that the Ara-C treatment is effective for the proliferation of Schwann cells contrast to the fibroblasts in vitro culture, and the first application after 24 hours from cell harvesting and subsequent 2 pulse treatment (P2 group in plain culture and G2 group in three-dimensional culture) was more effective than other application protocols.

• Journal of Plant Biotechnology
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• 제44권3호
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• pp.264-270
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• 2017

식물의 유일한 활성 스테로이드 호르몬인 Brassinosteroid (BR)는 다양한 내재적 또는 외부 신호 전달 경로와의 통합적인 결합을 통해 식물의 생장 및 발달 과정에서 중요한 기능을 하는 것으로 알려져 있다. 최근 식물학 연구들은 종자의 발아와 초기 발달과정에서 BR과 ABA 사이의 필수적인 상호작용 메커니즘이 존재하고 있음을 보고하고 있다. 하지만 이들 두 호르몬의 중요한 신호전달 상호작용에 대한 분자 메커니즘은 거의 알려지지 않았다. 식물의 초기 발달과정에서 BR에 의해 매개되는 ABA 신호전달과의 기능학적, 생물학적 상호작용 네트워크를 이해하기 위해 Agilent Arabidopsis $4{\times}44K$ 올리고 칩을 사용하여 비교 전사체 분석을 수행하였다. ABA에 반응하지 않는 bes1-D 돌연변이체에서의 ABA 처리에 따른 다양한 유전자의 발현 패턴을 야생형 식물과 비교 분석하였다. 그 결과 발현의 변화가 발생하는 유전자(DEGs) 2,353개를 확인하였다. GO 분석을 통해 ABA 신호전달 및 대사에 관여하는 유전자들이 BR 신호전달 경로에 의해 하향 조절되는 것으로 확인되었다. 뿐만 아니라, BR 신호전달 경로는 다양한 비생물학적/생물학적 스트레스, 오옥신 및 ROS 등 다양한 신호전달 체계와 밀접하게 연관되어 있음을 확인하였다. 본 연구를 통해 BR 신호전달의 활성화는 ABA 신호전달에 관여하는 다양한 유전자들의 발현을 억제함을 확인하였다. 또한 본 연구는 다양한 신호 경로 사이의 상호작용이 다양한 환경요인에 대한 식물의 적응 반응에 중요하게 작용할 수 있음을 보여주고 있다.

• 한국미생물·생명공학회지
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• 제33권3호
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• pp.169-177
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• 2005

본 연구는 어업이나 농업 등의 인간활동에 의하여 상당한 영향을 받고 있는 순천만 갈대의 근권에서 이루어지는 정화작용에 있어 미생물의 역할을 조사하는 것에 중점을 두었다. 일반적으로 만은 환경 스트레스로 인한 갑작스런 충격을 감소시키는 완충지역으로서의 역할을 하는 것으로 알려져 있다. 갈대근권에서 이루어지는 정화기능에 있어 미생물의 역할을 밝히기 위한 첫 번째 노력의 일환으로 벤젠, 톨루엔, 또는 자일렌이 단일 탄소 및 에너지원으로 첨가된 농화배양법을 사용하여 BTEX를 분해할 수 있는 두 종류의 그람양성 세균을 순수분리하였다. 다양한 온도조건의 BTEX배지에서 이들 세균을 배양하는 동안 BTEX의 분해율 및 성장률을 주기적으로 조사한 결과 $37^{\circ}C$에서 가장 빠른 기질 분해율을 보였고 $42^{\circ}C$의 고온에서도 두 균 모두 잘 성장하는 것으로 나타났다. 본 연구에서 시험한 수은, 카드뮴, 납, 바륨, 철 대부분의 중금속에 강한 내성뿐만 아니라 ampicillin을 비롯한 시험한 5종류의 항생제 모두에 강한 내성을 나타냈다. 16S rRNA 유전자 서열과 다양한 표현형 및 형태학적 특성을 기초로 한 동정의 결과 BTEX를 분해할 수 있는 두 균주는 $95{\%}$상의 신뢰도로 Microbacterium sp.와 Rhodococcus sp.로 나타났고, 각 균주는 Microbacterium sp. EMB-1과 Rhodococcus sp. EMB-2로 명명하였다. 이러한 결과는 주요한 염습지 식물중의 하나인 갈대의 근권에서 살아가는 이들 균주들이 BTEX와 같은 석유로 오염된 근권 환경의 정화작용에 중요한 역할을 할 수 있음을 제시해주었다.