• Journal of Animal Science and Technology
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• 제65권4호
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• pp.890-893
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• 2023

Lactobacillus johnsonii 7409N31 was isolated from the feces of a healthy 11-day-old Hanwoo calf from a farm in Geochang-gun, Gyeongsangnam-do, Korea. The genome of the strain was completely sequenced using the PacBio RSII sequencing system, and it was confirmed that it was composed of one circular chromosome. The size of the entire genome was 2,198,442 bp, and it had 35.01 mol% guanine + cytosine (G + C) content and 2,222 protein-coding sequences, 24 rRNA, 3 ncRNA, and 112 tRNA genes. Strain 7409N31 possessed genes encoding enzymes involved in the hydrolysis of both fibrous and non-fibrous carbohydrates. These data provide a comprehensive theoretical understanding for developing industrial probiotic feed additives that improve nutrient digestibility.

• BMB Reports
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• 제57권1호
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• pp.2-11
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• 2024

Advancements in gene and cell therapy have resulted in novel therapeutics for diseases previously considered incurable or challenging to treat. Among the various contributing technologies, genome editing stands out as one of the most crucial for the progress in gene and cell therapy. The discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and the subsequent evolution of genetic engineering technology have markedly expanded the field of target-specific gene editing. Originally studied in the immune systems of bacteria and archaea, the CRISPR system has demonstrated wide applicability to effective genome editing of various biological systems including human cells. The development of CRISPR-based base editing has enabled directional cytosine-to-thymine and adenine-to-guanine substitutions of select DNA bases at the target locus. Subsequent advances in prime editing further elevated the flexibility of the edit multiple consecutive bases to desired sequences. The recent CRISPR technologies also have been actively utilized for the development of in vivo and ex vivo gene and cell therapies. We anticipate that the medical applications of CRISPR will rapidly progress to provide unprecedented possibilities to develop novel therapeutics towards various diseases.

• International Journal of Stem Cells
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• 제16권2호
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• pp.234-243
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• 2023

The recent advances in human pluripotent stem cells (hPSCs) enable to precisely edit the desired bases in hPSCs to be used for the establishment of isogenic disease models and autologous ex vivo cell therapy. The knock-in approach based on the homologous directed repair with Cas9 endonuclease, causing DNA double-strand breaks (DSBs), produces not only insertion and deletion (indel) mutations but also deleterious large deletions. On the contrary, due to the lack of Cas9 endonuclease activity, base editors (BEs) such as adenine base editor (ABE) and cytosine base editor (CBE) allow precise base substitution by conjugated deaminase activity, free from DSB formation. Despite the limitation of BEs in transition substitution, precise base editing by BEs with no massive off-targets is suggested to be a prospective alternative in hPSCs for clinical applications. Considering the unique cellular characteristics of hPSCs, a few points should be considered. Herein, we describe an updated and optimized protocol for base editing in hPSCs. We also describe an improved methodology for CBE-based C to T substitutions, which are generally lower than A to G substitutions in hPSCs.

• Journal of Animal Science and Technology
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• 제66권1호
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• pp.232-236
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• 2024

Ligilactobacillus is a genus of Gram-positive lactobacilli commonly found in the intestinal tracts of vertebrates. It has been granted a Qualified Presumption of Safety (QPS) status from the European Food Safety Authority (EFSA). One specific strain, Ligilactobacillus salivarius B4311, was isolated from fecal samples of broiler chickens from a farm associated with Chung-Ang University (Anseong, Korea). This strain was observed to have inhibitory effects against Listeria monocytogenes. In this paper, we present the complete genome sequence of Lig. salivarius B4311. The whole genome of strain B4311 comprises 2,071,255 bp assembled into 3 contigs representing a chromosome, repA-type megaplasmid, and small plasmid. The genome contains 1,963 protein-coding sequences, 22 rRNA genes, and 78 tRNA genes, with a guanine + cytosine (GC) content of 33.1%. The megaplasmid of strain B4311 was found to contain the bacteriocin gene cluster for salivaricin P, a two-peptide bacteriocin belonging to class IIb.

• 한국임상수의학회지
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• 제31권3호
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• pp.226-232
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• 2014

8개월령의 단모종 집고양이가 감소된 식욕과 활력 저하로 내원하였다. 진단을 위한 영상 검사에서 종격동의 종괴와 종격동 림프절의 비대 소견을 확인할 수 있었다. 이어서 진행한 세침흡인술 검사로, 악성 림프구를 다수 확인할 수 있었으며, 이 고양이는 다발성 림프종 (병기 V-b)로 진단되었다. 치료는 COP 프로토콜을 사용하였으며, 완전 완화를 확인할 수 있었지만, 항암 치료를 시작한 후 314일 째 재발과 함께 중추신경계로 전이된 소견을 확인할 수 있었다. 구조화학 요법을 실시하여, 단기적으로는 임상증상의 큰 개선을 확인할 수 있었지만, 부분완화만이 관찰되었으며, 처음 내원 부터 약 383일 정도 생존하였다. 부검과 조직병리학적 검사를 통해, 다발성의 T 세포 림프종으로 확인하였으며, 뇌에서도 병변을 확인할 수 있었다.

• 한국인터넷방송통신학회논문지
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• 제16권6호
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• pp.135-140
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• 2016

본 논문에서는 유전정보 DNA 표준 코드인 [UC;AG]를 64괘로 분석했다. 인간의 유전정보를 담고 있는 DNA는 인산과 당에 A(아데닌) C(시토신) G(구아닌) T(티민) 등 네 종류의 염기가 30억쌍 이어 붙여진 형태이다. DNA 표준 코드를 64괘로 나타내고, 이 코드를 Kronecker product를 이용하여 $16{\times}4$행렬로 나타냈다. 이 $16{\times}4$ 행렬은 이중나선의 중복성을 가지고 있으며, 이 중복성을 제거하면 RNA코드 $4{\times}4$ 행렬을 얻는다. $16{\times}4$행렬은 Kronecker product를 이용하여 소 행렬로 분해되었다. DNA 이중나선을 행렬로 표시하고 유전정보 괘 배열 코드를 분석하였으며 그 예를 예 5, 6에 나타냈다.

• 한국지능시스템학회논문지
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• 제11권6호
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• pp.538-542
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• 2001

DNA computing 은 Adleman 실험 이후에 많은 여러 가지 최적화 문제에 적용되어 왔다. DNA computing의 장점은 스트링의 길이가 가변적이고 4가지 염기를 이용하기 때문에 복잡한 문제에 전역 최적점을 찾는데 기존의 다른 방법보다는 효율적이라는것이다. 본 논문에서는 이진 스트링의 개체 지단 위에서 모의진화를 일으켜 효율적으로 최적 해를 탐색하는 GA(Genetic Algorithms)와 생체 분자와 DNA를 계산의 도구 및 정보 저장도구로 사용하여 A(Adenine). C(Cytosine), G(Guanine), T(Thymine)등의 4가지 염기를 사용하는 DNA 코딩방법을 이용하여multi-modal 함수의 전역 최적점을 탐색하는 문제에서의 각각의 성능을 조사하였다. Selection, crossover, mutation등의 GA연산자를 DNA를 코딩에 동일하게 적용하였으며 최적의 해를 탐색하는데 걸리는 시간과 찾아낸 최적해의 값을 평가한다.을 평가한다.

• 대한수의학회지
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• 제43권3호
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• pp.439-448
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• 2003

The VP2 gene of infectious bursal disease virus (IBDV) Chinju which was previously detected in Chinju, Korea was cloned and sequenced to establish the information for the development of genetically engineered vaccines and diagnostic reagents against IBDV. The nucleotide sequence of the entire Chinju VP2 gene consisted of 1,356 bases long encoding 452 amino acids in a single open reading frame (ORF). It consisted of 368 adenine (27.1%), 363 cytosine (26.8%), 339 guanine (25.0%) and 286 thymine (21.1%) residues. The predicted $M_r$ of the Chinju VP2 protein was 48 kDa, and the protein contained 13 phosphorylation sites by protein kinase C, casein kinase II or tyrosine kinase, whereas 3 asparagine-linked glycosylation sites were recognized. The nucleotide sequence of Chinju VP2 ORF had a very close phylogenetic relationship with 98-99% homology to that of the very virulent IBDVs (vvIBDVs) HK46, OKYM, D6948, UK661, UPM97/61 and BD3/99. Also, the Chinju VP2 protein revealed a very close phylogenetic relationship with 99-100% homology to that of these vvIBDVs. The Chinju VP2 protein had 100% amino acid identity in the variable region of residues 206-360 with that of the D6948, HK46, OKYM and UK661, as well as 100% identity in two hypervariable regions of residues 212-224 and 314-324 with those of the D6948, HK46, OKYM, UK661, UPM97/61 and BD3/99. The amino acid sequence of the chinju VP2 protein contained a serine-rich heptapeptide of SWSASGS as in these vvIBDVs.

• 한국가축번식학회지
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• 제27권4호
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• pp.309-315
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• 2003

DNA methylation at CpG sites, which is a epigenetic modification, is associated with gene expression without change of DNA sequences. During early mouse embryogenesis, dynamic changes of DNA methylation occur. In this study, DNA methylation patterns of porcine embryos produced in vivo and in vitro were examined at various developmental stages by the immunocytochemical staining method. Interestingly, active demethylation was not observed on the paternal pronucleus of porcine zygotes. However, differences were detected in the passive demethylation process between in vivo and in vitro embryos. There was no change in the DNA methylation state until the blastocyst stage of in vivo embryos, whereas partial demethylation was observed in several blastomeres from a 4 cell stage to a morula stage of in vitro embryos. The whole genome of inner cell mass (ICM) and trophectoderm (TE) cells in porcine blastocysts were evenly methylated without de novo methylation. Our findings demonstrate that genome-wide demethylation does not occur in pig embryos during preimplantation development unlike murine and bovine embryos. It indicates that the machinery regulating epigenetic reprogramming may be different between species.

• 미생물학회지
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• 제23권1호
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• pp.1-8
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• 1985

일산화 탄소를 이용한 enrichment 배양 방법을 통하여 흙으로부터 일산화탄소를 이용하여 성장 할 수 있는 세가지 종류 (JC1, JC2, HY1)의 호기성 Acinetobacter 들을 분리했다. 이세균들은 모두Gramdma성 세균들로 운동성이 없었으며, 지수성장기에는 간균의 형태를 나타내었으나 성장이 정지되었을 때에는 구균으로 변하였다. 이들은 페니실린에 대해 내성이 있었고 $42^{\circ}C$에서도 성장을 할 수 있었다. DNA의 G+C함량은 43%-44.5%이였고 모든 세균에서 oxidase의 활성이 나타나지 않았다. 이 세균들의 coloy들은 모두 둥글고 매끄러웠으며 연한 노란색을 띄었다. 이들은 또 여러가지 종류의 당이나 유기산, 아미노산. 알코올 등을 이용하여 생장할 수 있였다. JC1과 J JC2 벚 HY1이 30%의 일산화탄소를 이용하여 $30^{\circ}C$에서 성장할 때의 doubling time은 각각 19시간. 25시간, 그리 고 35시간 이었다. JC1의 자가영양적 성장을 위한 최적조건은 pH가 6.8이였L 온도는 $42^{\circ}C$ 그리고 일산화탄소의 농도는 30%이였다. JC1 의 자가영양적 성장에는 몰리브데늄이 필요치 않았고, 또 이 세균은 100ppm의 CO만으로도 성장할 수 있는 것으로 밝혀졌다.