• Applied Microscopy
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• 제50권
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• pp.6.1-6.6
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• 2020

The cerebellum is a region of the brain that plays an important role in motor control. It is classified phylogenetically into archicerebellum, paleocerebellum and neocerebellum. The Purkinje cells are lined in a row called Purkinje cell layer and it has a unique dendritic branches with many spines. The previous study reported that there is a difference of synapse density according to the lobules based on large two-dimensional data. However, recent study with high voltage electron microscopy showed there was no differences in dendritic spine density of the Purkinje cell according to its phylogenetic lobule. We analyzed Purkinje cell density in the II, VI and X lobules by stereological modules and synaptic density was estimated by double disector based on Purkinje cell density in the molecular layer of each lobule. The results showed that there was significant difference in the Purkinje cell density and synapse number according to their phylogenetic lobules. The number of Purkinje cell in a given volume was larger in the archicerebellum, but synapse density was higher in the neocerebellum. These data suggest that cellular and synaptic organization of the Purkinje cell is different according to their phylogenetic background.

• 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.

• Genomics & Informatics
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• 제21권4호
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• pp.51.1-51.5
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• 2023

The genus Neoarius, known as marine catfish, is a group of the family Ariidae, composed of 10 species found in Oceania. None of the species in this genus have their mitochondrial genome described, which is highly valuable in phylogenetic and molecular evolution studies. For the present work, eight species from the Neoarius genus were selected: Neoarius utarus, Neoarius midgleyi, Neoarius graeffei, Neoarius leptaspis, Neoarius berenyi, Neoarius paucus, Neoarius pectoralis, and Neoarius aff. graeffei. DNA sequences of the eight species were obtained through the NCBI Sequence Read Archive (SRA) database, and the mitochondrial genomes were assembled using the NOVOplasty tool on the Galaxy platform, subsequently annotated with the MitoAnnotator tool. We then utilized the protein-coding genes from the mitogenomes to estimate the phylogenetic relationships within the group, including seven additional mitogenomes available in the NCBI. In all species, the mitochondrial genomes presented 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 D-loop.

• 한국미생물·생명공학회지
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• 제45권3호
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• pp.226-235
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• 2017

Phytoene, lycopene, ${\beta}-carotene$과 같은 카로티노이드는 식품의 착색제나 영양보조제, 사료첨가제, 화장품의 원료로 사용된다. 이전 연구에서 본 연구진은 분홍색의 색소를 생산하는 새로운 해양 세균인 K. gwangalliensis를 분리 동정하였다. Phytoene desaturase (CrtI) 효소는 crtI 유전자에 암호화되어 있으며, phytoene을 lycopene으로 전환하며, 카로티노이드 합성 초기 단계에 있어서 필수적이다. CrtI는 카로티노이드 생합성 조절의 주요 효소 중 하나이며, 다양한 카로티노이드를 생합성하는 생물들의 카로티노이드 생합성 경로에 있어서 속도 조절 단계에 관련이 있다. 본 논문에서는 K. gwangalliensis로부터 lycopene 생합성을 담당하는 crtI 유전자를 클로닝 하였으며, 이 유전자는 1,584개의 염기서열을 가지며, 527개의 아미노산을 암호화하고 있다. crtI 유전자의 염기 서열을 Kocuria rhizophila와 Myxococcus xanthus를 포함한 다른 종의 염기 서열과 비교한 결과, 진화 과정에서 잘 보존되어 있음을 확인하였다. crtI 유전자를 포함하는 발현 플라스미드를 구축하여 발현시킨 결과, 이 플라스미드를 함유하는 대장균은 약 57 kDa의 재조합 단백질을 생산화였으며, 이는 phytoene desaturase의 분자량에 해당한다. lycopene의 생합성은 lycopene 생합성에 필요한 crtE, crtB 유전자를 포함한 pRScrtEB plasmid를 E. coli에 형질전환 했을 때, Escherichia coli에서 합성되는 것을 확인하였다. 이 연구의 결과는 분자 수준에서 K. gwangalliensis CrtI의 1차 구조에 대한 폭 넓은 지식 기반을 제공할 것이다.

• ALGAE
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• 제32권4호
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• pp.359-377
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• 2017

Pyropia haitanensis (T. J. Chang et B. F. Zheng) N. Kikuchi et M. Miyata is one of the most commercially useful macroalgae cultivated in southeastern China. In red algae, the biosynthesis of terpenoids through 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway can produce a direct influence on the synthesis of many biologically important metabolites. In this study, two genes of cDNAs, 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and 1-deoxy-D-xylulose-5-phosphate reductase (DXR), which encoding the first two rate-limiting enzymes among MEP pathway were cloned from P. haitanensis. The cDNAs of P. haitanensis DXS (PhDXS) and DXR (PhDXR) both contained complete open reading frames encoding polypeptides of 764 and 426 amino acids residues, separately. The expression analysis showed that PhDXS was significant differently expressed between leafy thallus and conchocelis as PhDXR been non-significant. Additionally, expression of PhDXR and its downstream gene geranylgeranyl diphosphate synthase were both inhibited by fosmidomycin significantly. Meanwhile, we constructed types of phylogenetic trees through different algae and higher plants DXS and DXR encoding amino acid sequences, as a result we found tree clustering consequences basically in line with the "Cavalier-Smith endosymbiotic theory." Whereupon, we speculated that in red algae, there existed only complete MEP pathway to meet needs of terpenoids synthesis for themselves; Terpenoids synthesis of red algae derivatives through mevalonate pathway came from two or more times endosymbiosis of heterotrophic eukaryotic parasitifer. This study demonstrated that PhDXS and PhDXR could play significant roles in terpenoids biosynthesis at molecular levels. Meanwhile, as nuclear genes among MEP pathway, PhDXS and PhDXR could provide a new way of thinking to research the problem of chromalveolata biological evolution.

• 대한의생명과학회지
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• 제16권2호
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• pp.75-82
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• 2010

The molecular epidemiological characteristics of methicillin-resistant Staphylococcus aureus (MRSA) isolates have demonstrated their genetic diversity and evolution. A total of 137 strains of MRSA clinical isolates was collected from Korean healthcare facility in 2007. The MRSA clinical isolates were analyzed by molecular typings (SCCmec element and agr locus typing), virule nce factor gene detections {(Panton-Valentine leukocidin (PVL), enterotoxin, exfoliative toxin and toxic shock syndrome toxin-1), and amplified fragment length polymorphism (AFLP)}. The MRSA clinical isolates were classified as SCCmec type II-agr type 1 (2 strains), type II-agr type 2 (79 strains), type III-agr type 1 (24 strains), type III-agr type 2 (2 strains), type IV-agr type 1 (27 strains), type IV-agr type 2 (2 strains), and non-typable (1 strain, agr type 3). Based on SCCmec types, SCCmec type II (95.1%) and III (88.5%) indicated higher multidrug resistance rate than SCCmec type IV (10.3%) (P<0.001). The most common enterotoxin genes were seg (83.8%), sei (83.1%), and sec (80.2%). The tst gene was present in 86 out of 137 (62.8%) MRSA isolates. All MRSA isolates were negative for PVL and exfoliative toxin genes. The combinations of toxin genes were observed in particular SCCmec types; 97.6% of SCCmec type II strains carried sec, seg, sei and tst genes, 73.0% of SCCmec type III strains carried sea gene, and 89.7% of SCCmec type IV strains carried sec, seg and sei genes. Each of the SCCmec types of MRSA isolates had distinct AFLP profile. In conclusion, SCCmec type II, agr type 1 and 2 have demonstrated to be the most common types in Korea, and the results indicated that the virulence factors are closely associated with their molecular types (SCCmec and agr types).

• 대한전자공학회논문지SD
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• 제41권6호
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• pp.25-31
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• 2004

본 논문에서는 나노 스케일 확산 공정 모사를 위한 방법으로 동력학적 몬테칼로(kinetic Monte Carlo)를 소개하고자 한다. 먼저 동력학적 몬테칼로의 이론과 배경을 살펴보고 실제적인 이해를 돕기 위하여 실리콘 기판에 이온(전자) 주입 후 열처리과정에서 일어나는 점결함의 확산을 동력학적 몬테칼로를 이용하여 모사하는 간단한 예를 보여주고 있다. 동력학적 몬테칼로는 몬테칼로의 일종이지만 기존의 몬테칼로에서 구현하지 못하였던 물리적인 시간을 포아송 확률 과정을 통하여 구현하였다. 동력학적 몬테칼로 확산 공정 모사에서는 연속 확산 미분 방정식의 해를 구하는 기존의 유한 요소 수치 해석적 방법과 달리원자 상호간 혹은 원자와 결함 또는 결함들 간의 화학적 반응과 입자들의 확산 과정을 포아송 확률 과정에 따라 일어나는 화학적 반응, 입자들의 확산 사건의 연속으로 본다. 사건마다 고유의 사건 발생 확률을 갖고 이 사건 발생 확률에 따라 일어나는 확률적 사건의 연속적 발생으로 실제의 반도체 확산 공정을 시간에 따라 직접적으로 모사할 수 있다. 입자들 간의 화학적 반응 사건 확률과 입자들의 확산 공정에 필요한 확률적 인자들은 분자 동역학, 양자 역학적 계산, 흑은 실험으로 얻어진다.

• 대한미생물학회지
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• 제35권3호
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• pp.263-271
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• 2000

A clinical isolate of Klebsiella pneumoniae K7746 produced the extended-spectrum ${\beta}$-lactamase (ESBL) SHV-12. A 6.6 kb BamHI fragment containing the $bla_{SHV-12}$ gene of K7746 strain was cloned into pCRScriptCAM vector resulting in the recombinant plasmid p7746-Cl. The restriction map of 3.6 kb inserted DNA and sequences immediately surrounding $bla_{SHV-12}$ of p7746-C1 were homologous to plasmid pMPA2a carrying $bla_{SHV-2a}$. In addition, both $bla_{SHV-12}$ and $bla_{SHV-2a}$ were expressed from a common hybrid promoter made of the -35 region derived from the left inverted repeat of IS26 and the -10 region from the $bla_{SHV}$ promoter itself. The results indicate that $bla_{SHV-12}$ and $bla_{SHV-2a}$ may have evolved from a common ancestor in the sequential order of $bla_{SHV-2a}$ first, followed by $bla_{SHV-12}$. Furthermore, by the PCR mapping method using primers corresponding to the IS26 and $bla_{SHV}$, the association between IS26 and $bla_{SHV}$ was studied in 12 clinical isolates carrying $bla_{SHV-2a}$, 27 clinical isolates carrying $bla_{SHV-12}$, and 5 reference strains carrying $bla_{SHV-1}$ to $bla_{SHV-5}$. All 39 strains carrying $bla_{SHV-2a}$ or $bla_{SHV-12}$ were positive by the PCR, providing confirmative evidence that IS26 has been involved in the evolution and dissemination of $bla_{SHV-2a}$ and $bla_{SHV-12}$. But 5 reference strains carrying $bla_{SHV-1}$ to $bla_{SHV-5}$ were negative by the PCR. Therefore, we concluded that the molecular evolutionary pathway of $bla_{SHV-2a}$ and $bla_{SHV-12}$ may be different from that of other $bla_{SHV-ESBL}$, e.g., $bla_{SHV-2}$, $bla_{SHV-3}$, $bla_{SHV-4}$, and $bla_{SHV-5}$.

• Molecules and Cells
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• 제38권11호
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• pp.950-958
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• 2015

BCS1L gene encodes mitochondrial protein and is a member of conserved AAA protein family. This gene is involved in the incorporation of Rieske FeS and Qcr10p into complex III of respiratory chain. In our previous study, AluYRa2-derived alternative transcript in rhesus monkey genome was identified. However, this transcript has not been reported in human genome. In present study, we conducted evolutionary analysis of AluYRa2-exonized transcript with various primate genomic DNAs and cDNAs from humans, rhesus monkeys, and crabeating monkeys. Remarkably, our results show that AluYRa2 element has only been integrated into genomes of Macaca species. This Macaca lineage-specific integration of AluYRa2 element led to exonization event in the first intron region of BCS1L gene by producing a conserved 3' splice site. Intriguingly, in rhesus and crabeating monkeys, more diverse transcript variants by alternative splicing (AS) events, including exon skipping and different 5' splice sites from humans, were identified. Alignment of amino acid sequences revealed that AluYRa2-exonized transcript has short N-terminal peptides. Therefore, AS events play a major role in the generation of various transcripts and proteins during primate evolution. In particular, lineage-specific integration of Alu elements and species-specific Alu-derived exonization events could be important sources of gene diversification in primates.

• 한국신재생에너지학회:학술대회논문집
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• 한국신재생에너지학회 2010년도 춘계학술대회 초록집
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• pp.87-87
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• 2010

Photoelectrochemical (PEC) systems are promising methods of producing H2 gas using solar energy in an aqueous solution. The photoelectrochemical properties of numerous metal oxides have been studied. Among them, the PEC systems based on TiO2 have been extensively studied. However, the drawback of a PEC system with TiO2 is that only ultraviolet (UV) light can be absorbed because of its large band gap (3.2 - 3.4 eV). Two approaches have been introduced in order to use PEC cells in the visible light region. The first method includes doping impurities, such as nitrogen, into TiO2, and this technique has been extensively studied in an attempt to narrow the band gap. In comparison, research on the second method, which includes visible light water splitting in molecular photosystems, has been slow. Mallouk et al. recently developed electrochemical water-splitting cells using the Ru(II) complex as the visible light photosensitizer. the dye-sensitized PEC cell consisted of a dye-sensitized TiO2 layer, a Pt counter electrode, and an aqueous solution between them. Under a visible light (< 3 eV) illumination, only the dye molecule absorbed the light and became excited because TiO2 had the wide band gap. The light absorption of the dye was followed by the transfer of an electron from the excited state (S*) of the dye to the conduction band (CB) of TiO2 and its subsequent transfer to the transparent conducting oxide (TCO). The electrons moved through the wire to the Pt, where the water reduction (or H2 evolution) occurred. The oxidized dye molecules caused the water oxidation because their HOMO level was below the H2O/O2 level. Organic dyes have been developed as metal-free alternatives to the Ru(II) complexes because of their tunable optical and electronic properties and low-cost manufacturing. Recently, organic dye molecules containing multi-branched, multi-anchoring groups have received a great deal of interest. In this work, tri-branched tri-anchoring organic dyes (Dye 2) were designed and applied to visible light water-splitting cells based on dye-sensitized TiO2 electrodes. Dye 2 had a molecular structure containing one donor (D) and three acceptor (A) groups, and each ended with an anchoring functionality. In comparison, mono-anchoring dyes (Dye 1) were also synthesized. The PEC response of the Dye 2-sensitized TiO2 film was much better than the Dye 1-sensitized or unsensitized TiO2 films.