• Korean Journal of Plant Tissue Culture
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• v.27 no.6
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• pp.491-496
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• 2000

A RAG25 gene regulating flowering time was introduced into Codonopsis lanceolata through high efficiencies (ca. 90%) of plant regeneration. The leaf explants were immersed in YEP media containing Agrobacterium tumefaciens (pGA 1209) harboring RAG25 gene, and cocultivated for 3 days. After cocultivation, they were cultured in shoot inducing media (SIM), N2B2 (NAA 2 mg/L, BA 2 mg/L and kanamycin 20 mg/L) and N2B4 (NAA 2 mg/L, BA 4 mg/L and kanamycin 20 mg/L), and the putative transformants were regenerated. The introduction of nptII and RAG25 gene into Codonopsis lanceolata was confirmed by 0.7 kb and 0.6 kb bands from polymerase chain reaction and reconfirmed by Southern hybridization using PCR product of RAG25 gene.

• BMB Reports
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• v.40 no.3
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• pp.432-438
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• 2007

V(D)J recombination, a site-specific gene rearrangement process occurring during the lymphocyte development, begins with DNA double strand breaks by two recombination activating gene products (RAG1/2) and finishes with the repair process by several proteins including DNA-dependent protein kinase (DNA-PK). In this report, we found that RAG2 was specifically phosphorylated by DNA-PK at the $365^{th}$ serine residue, and this phosphorylated RAG2 affected the V(D)J recombination activity in cells in the GFP expression-based assay. While the V(D)J recombination activity between wild-type RAG2 and mutant S365A RAG2 in the assay using a signal joint substrate was undistinguishable in DNA-PK deficient cells (M059J), the activity with wild-type RAG2 was largely increased in DNA-PK proficient cells (M059K) in comparison with mutant RAG2, suggesting that RAG2 phosphorylation by DNA-PK plays a crucial role in the signal joint formation during V(D)J recombination.

• Laboraroty Animal Research
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• v.34 no.4
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• pp.166-175
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• 2018

Recombination activating gene-2 (RAG-2) plays a crucial role in the development of lymphocytes by mediating recombination of T cell receptors and immunoglobulins, and loss of RAG-2 causes severe combined immunodeficiency (SCID) in humans. Rag-2 knockout mice created using homologous recombination in ES cells have served as a valuable immunodeficient platform, but concerns have persisted on the specificity of Rag-2-related phenotypes in these animals due to the limitations associated with the genome engineering method used. To precisely investigate the function of Rag-2, we recently established a new Rag-2 knockout FVB mouse line ($Rag-2^{-/-}$) manifesting lymphopenia by employing a CRISPR/Cas9 system at Center for Mouse Models of Human Disease. In this study, we further characterized their phenotypes focusing on histopathological analysis of lymphoid organs. $Rag-2^{-/-}$ mice showed no abnormality in development compared to their WT littermates for 26 weeks. At necropsy, gross examination revealed significantly smaller spleens and thymuses in $Rag-2^{-/-}$ mice, while histopathological investigation revealed hypoplastic white pulps with intact red pulps in the spleen, severe atrophy of the thymic cortex and disappearance of follicles in lymph nodes. However, no perceivable change was observed in the bone marrow. Moreover, our analyses showed a specific reduction of lymphocytes with a complete loss of mature T cells and B cells in the lymphoid organs, while natural killer cells and splenic megakaryocytes were increased in $Rag-2^{-/-}$ mice. These findings indicate that our $Rag-2^{-/-}$ mice show systemic lymphopenia with the relevant histopathological changes in the lymphoid organs, suggesting them as an improved Rag-2-related immunodeficient model.

• BMB Reports
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• v.36 no.2
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• pp.201-206
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• 2003

Two lymphoid-specific proteins, RAG1 and RAG2, are required for the initiation of the V(D)J recombination in vitro. The V(D)J cleavage that is mediated by RAG proteins at the border between the coding and signal sequences results in the production of a hairpin at the coding end and a double-stranded break at the signal end. Two hairpin coding ends are re-opened, modified, and sealed; whereas, the signal ends are directly ligated. Here I report that only RAG1 can carry out a distinct endonucleolytic activity in vitro using an oligonucleotide substrate that is tethered by a short single-stranded DNA. The purified RAG1 protein alone formed a nick at the near position to the recombination signal sequence. This endonucleolytic activity was eliminated by immunoprecipitation using the RAG1-specific antibody, and required the 3'-hydroxy group. All of the RAG1 mutants that were incapable of the nick and hairpin formation in the V(D)J cleavage analysis also showed this new endonucleolytic activity. This suggests that the nicking activity that was observed might be functionally different from the nick formation in the V(D)J cleavage.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.57 no.3
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• pp.239-252
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• 2024

Recombination activating genes (RAGs) play a crucial role in initiating V(D)J recombination, which is essential for developing adaptive immunity in vertebrates. In this study, we cloned and characterized RAG1/2 cDNA from the marine medaka Oryzias dancena (OdRAG1/2) and investigated their mRNA expression patterns during ontogenetic developmental stages. The OdRAG1 and OdRAG2 cDNA contained open reading frames (ORFs) encoding proteins containing 1,078 and 531 amino acids, respectively. Multiple sequence alignment and phylogenetic analysis revealed that OdRAG1 and OdRAG2 are highly conserved with their corresponding orthologs, featuring distinct core and non-core regions. Notably, expression analysis showed that, in contrast to other fish RAGs studied, OdRAG1/2 expression peaked at 0 days post-hatching (DPH). Additionally, for the expression of T and B cell differentiation markers, CD3γ and CD20, also peaked at 0 DPH. Collectively, adaptive immunity in O. dancena potentially begins during embryonic development, which is critical for V(D)J recombination and essential immune component development, suggesting the early ontogenetic stage interactions between innate and adaptive immunity.

• Korean Journal of Remote Sensing
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• v.18 no.2
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• pp.107-116
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• 2002

A hybrid image segmentation algorithm is proposed which integrates edge-based and region-based techniques through the watershed algorithm. First, by using mean curvature diffusion coupled to min/max flow, noise is eliminated and thin edges are preserved. After images are segmented by watershed algorithm, the segmented regions are combined with neighbor regions. Region adjacency graph (RAG) is employed to analyze the relationship among the segmented regions. The graph nodes and edge costs in RAG correspond to segmented regions and dissimilarities between two adjacent regions respectively. After the most similar pair of regions is determined by searching minimum cost RAG edge, regions are merged and the RAG is updated. The proposed method efficiently reduces noise and provides one-pixel wide, closed contours.

• Proceedings of the Korea Information Processing Society Conference
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• 2024.05a
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• pp.600-601
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• 2024

본 논문은 RAG(Retrieval-Augmented Generation) End2End의 리소스(Resource) 과부하 문제를 해결하는 동시에 모델 성능을 향상 시키기 위해 PEFT(Parameters-Efficient Fine-Tuning)기술인 LoRA(Low Rank Adaptation)적용에 관한 연구이다. 본 논문에서는 RAG End2End 모델의 파라미터 값과 개수를 유지하면서, LRM(Low Rank Matrices)을 이용하여 추가적인 파라미터만을 미세 조정하는 방식으로, 전반적인 모델의 효율성을 극대화하는 방안을 제시하였다. 본 논문에서 다양한 도메인에 데이터 셋에 대한 제안 방식의 성능을 검증하고자 Conversation, Covid-19, News 데이터 셋을 사용하였다. 실험결과, 훈련에 필요한 파라미터의 크기가 약 6.4억개에서 180만개로 감소하였고, EM(Exact Match)점수가 유사하거나 향상되었다. 이는 LoRA를 통한 접근 법이 RAG End2End 모델의 효율성을 개선할 수 있는 효과적인 전략임을 증명하였다.

• Korean Journal of Ichthyology
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• v.26 no.1
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• pp.70-73
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• 2014

Interspecific hybrids between tiger grouper Epinephelus fuscoguttatus and giant grouper E. lanceolatus were genetically identified based on the partial sequence analysis of mitochondrial cytochrome c oxidase I (COX I) gene and nuclear recombination activating gene 2 (RAG 2) gene. Out of 585 base positions of RAG 2, a total of five nucleotide substitutions were detected between the two parental species (E. fuscoguttatus and E. lanceolatus). The hybrids had two distinct types of RAG 2 sequences corresponding to those of both parental species. Mitochondrial COX I gene sequencing showed that hybrids had sequences identical to E. fuscoguttatus. Molecular data clearly demonstrate that hybridization does occur between E. fuscoguttatus and E. lanceolatus, but with E. fuscoguttatus as the maternal parent.

• Annual Conference on Human and Language Technology
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• 2023.10a
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• pp.683-689
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• 2023

자연어 처리 분야는 최근에 큰 발전을 보였으며, 특히 초대규모 언어 모델의 등장은 이 분야에 큰 영향을 미쳤다. GPT와 같은 모델은 다양한 NLP 작업에서 높은 성능을 보이고 있으며, 특히 챗봇 분야에서 중요하게 다루어지고 있다. 하지만, 이러한 모델에도 여러 한계와 문제점이 있으며, 그 중 하나는 모델이 기대하지 않은 결과를 생성하는 것이다. 이를 해결하기 위한 다양한 방법 중, Retrieval-Augmented Generation(RAG) 방법이 주목받았다. 이 논문에서는 지식베이스와의 통합을 통한 도메인 특화형 질의응답 시스템의 효율성 개선 방안과 벡터 데이터 베이스의 수정을 통한 챗봇 답변 수정 및 업데이트 방안을 제안한다. 본 논문의 주요 기여는 다음과 같다: 1) QA Pair Passage RAG을 활용한 새로운 RAG 시스템 제안 및 성능 향상 분석 2) 기존의 LLM 및 RAG 시스템의 성능 측정 및 한계점 제시 3) RDBMS 기반의 벡터 검색 및 업데이트를 활용한 챗봇 제어 방법론 제안

• Journal of Microbiology and Biotechnology
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• v.18 no.12
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• pp.1890-1894
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• 2008

Apoemulsan is a biopolymer with potent emulsification activity, produced by Acinetobacter venetian us RAG-1 (RAG-1). The wee gene cluster is responsible for apoemulsan biosynthesis. The analysis of (i) a putative polysaccharide copolymerase mutant (${\Delta}wzc$), (ii) a putative polymerase mutant (${\Delta}wzy$), and (iii) an apoemulsan-deficient variant (${\Delta}2$) indicated that the wee gene cluster controls the synthesis of two polysaccharides: high molecular weight (HMW) and low molecular weight (LMW). LMW polysaccharide of wee origin was present in LPS isolated from RAG-1 cells, suggesting a link to the Lipid A-core of LPS molecules. SDS-PAGE analysis indicated that apoemulsan is copurified with LPS polysaccharide, with implications in the emulsification activity of RAG-1 polymer.