• Advances in environmental research
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• 제9권3호
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• pp.215-232
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• 2020

Crude oils are essential source of energy. It is majorly found in geographical locations beneath the earth's surface and crude oil is the main factor for the economic developments in the world. Natural crude oil contains unrefined petroleum composed of hydrocarbons of various molecular weights and it contains other organic materials like aromatic compounds, sulphur compounds, and many other organic compounds. These hydrocarbons are rapidly getting degraded by biosurfactant producing microorganisms. The present study deals with the isolation, purification, and characterization of biosurfactant producing microorganism from oil-contaminated soil. The ability of the microorganism producing biosurfactant was investigated by well diffusion method, drop collapse test, emulsification test, oil displacement activity, and blue agar plate method. The isolate obtained from the oil contaminated soil was identified as Bacillus subtilis. The identification was done by microscopic examinations and further characterization was done by Biochemical tests and 16SrRNA gene sequencing. Purification of the biosurfactant was performed by simple liquid-liquid extraction, and characterization of extracted biosurfactants was done using Fourier transform infrared spectroscopy (FTIR). The degradation of crude oil upon treatment with the partially purified biosurfactant was analyzed by FTIR spectroscopy and Gas-chromatography mass spectroscopy (GC-MS).

• Journal of Microbiology and Biotechnology
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• 제14권2호
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• pp.337-343
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• 2004

A bacterial strain concurrently producing extracellular chitosanase and chitinase was isolated from soil and identified as a member of the $\beta$-subgroup of Proteobacteria through its 16S rRNA analysis and some biochemical analyses. The newly discovered strain, named as KNU3, had 99% homology of its 16S rRNA sequence with chitinolytic $\beta$-Proteobacterium CTE108. Strain KNU3 produced 34 kDa of chitosanase in addition to two chitinases of 68 kDa and 30 kDa, respectively. The purified chitosanase protein (ChoK) showed activity toward soluble, colloidal, and glycol chitosan, but did not exhibit any activity toward colloidal chitin. The optimum pH and temperature of ChoK were 6.0 and $70^{\circ}C$, respectively. The chitosanase was stable in the pH 4.0 to 8.0 range at $70^{\circ}C$, while enzyme activity was relatively stable at below $45^{\circ}C$. MALDI-TOF MS and N-terminal amino acid sequence analyses indicated that ChoK protein is related to chitosanases from Matsuebacter sp. and Sphingobacterium multivorum. HPLC analysis of chitosan lysates revealed that glucosamine tetramers and hexamers were the major products of hydrolysis.

• 미생물학회지
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• 제35권2호
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• pp.121-127
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• 1999

염기서열 해독작업에서 각 핵산 단편을 조립하는 contig 구성문제에 활용이 가능한 computer program을 개발하였다. 본 프로그램은 국내에서 광범위하게 사용되고 있는 MS-Windows 운영체제의 개인용 컴퓨터에서 작동이 가능하며, GenBank, FASTA, ASCII 등과 같은 다양한 형태의 염기서열 자료를 입력할 수 있다. 두 단편에서 최대 유사도를 나타내는 부분을 정렬하는 작업에는 염기서열의 국부적 상동성을 계산하고 dynamic programming 알고리즘을 적용하는 방법을 이용하였다. 또한 사용하기 편리한 그래픽 방식의 인터페이스를 제공하여 초보자라도 손쉽게 조작할 수 있다는 장점을 갖는다. 본 프로그램의 성능을 검증하기 위하여 세균과 곰팡이로부터 해독된 16S rRNA 와 18S rRNA 유전자의 단편 염기서열을 재구성하는 작업에 프로그램을 사용하였을 때에 효율적인 작업이 가능하였다.

• 대한한의학방제학회지
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• 제28권3호
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• pp.255-269
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• 2020

Objectives : Hemistepta lyrata Bunge (Bunge) is a wild herb that has been used for managing fever and wound in Korean Traditional Medicine. The present study explored the effects of H. lyrata extract on liver X receptor (LXR) α-dependent lipogenic genes in hepatocyte-derived cells. Methods : After HepG2 cells or Huh7 cells were pre-treated with 1-10 ㎍/mL of H. lyrata extract or its fractionated extract for 0.5 h, the cells were subsequently exposed to LXR ligand for 6-24 h. Cell viability, LXR response element (LXRE)-driven luciferase activity, sterol regulatory element binding protein-response element (SREBP-RE)-driven luciferase activity, SREBP-1c expression, and mRNA levels of LXRα and its-dependent target genes were determined. In addition, LC-MS/MS analysis was conducted to explore major compounds in H. lyrata-chloroform fractionated extract #4 (HL-CF4). Results : Of various H. lyrata extracts tested, chloroform extract and its fractionated extract #4, HL-CF4, significantly decreased T0901317-mediated SREBP-1c expression. In addition, HL-CF4 significantly reduced LXRE atransactivation and LXRα mRNA expression without any cytotoxicity. Moreover, HL-CF4 prevented the SREBP-RE-driven luciferase activity and mRNA levels of fatty acid synthase and stearoyl-CoA desaturase-1 induced by T0901317. Results from LC-MS/MS analysis at positive/negative mode indicated that HL-CF4 contained several compounds showing m/z 197.1176 (C₁₁H₁₇O₃), 693.2913/227.1069 (C₃₈H₄₅O₁₂/C₁₅H₁₅O₂), 203.1797 (C₁₅H₂₃), 181.1225 (C₁₁H₁₇O₂), 591.2957 (C₃₅H₄₃O₈), 379.1040 (C₁₈H₁₉O₉), 409.1509 (C₂₀H₂₅O₉), 309.1348 (C₁₆H₂₁O₆), 391.1404 (C₂₀H₂₃O₈), and 669.2924/389.1248 (C₃₆H₄₅O₁₂/C₂₀H₂₁O₈). Conclusion : Based on its inhibition of the LXRα-dependent signaling pathway, H. lyrata chloroform extract and HL-CF4 have prophylactic potentials for managing non-alcoholic fatty liver.

• 분석과학
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• 제28권4호
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• pp.260-269
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• 2015

골관절염에 대한 참당귀 추출분말의 치료효과를 검토하고자 흰쥐의 monosodium iodoacetate(MIA)로 유발된 골관절염 부위에서 시료를 채취하여 염증관련 효소 및 염증성 cytokines의 발현에 대하여 참당귀 추출분말의 억제효능을 검토하였다. 고농도의 참당귀 추출분말 (50 μg/mL) 투여에서도 독성이 관찰되지 않았으며, 동일조건하에서 interleukin-1α (IL-1α)로 유발된 nitric oxide (NO)의 생성을 효과적으로 억제하였다. 특히, 관절연골 조직의 inducible nitric oxide synthase (iNOS) 및 cyclooxygenase-2(COX-2)의 발현을 농도 의존적으로 억제하였다. 따라서 참당귀 추출분말은 항염증 효능을 나타내는 농도에서 독성 없이 사용할 수 있으며, iNOS발현을 억제하여 방출되는 신호전달 물질인 NO의 생성을 억제하였다. 또한 참당귀 추출분말의 처리로 염증유발 부위에서 염증성 cytokines으로 알려진 tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β) 및 interleukin-6 (IL-6)의 발현이 억제됨을 확인하였다. 참당귀 추출분말의 항 염증효과는 TNF-α, IL-1β 및 IL-6의 혈중농도를 낮추어 염증부위뿐만 아니라 전체적으로 항염증효과를 나타내었다. 본 실험결과, 참당귀 추출분말의 투여는 MIA 또는 IL-1α로 유발되는 골관절염 동물모델에서 염증인자, 관련 효소의 발현 및 관련 신호전달 물질의 생성을 효과적으로 억제하여, 슬관절의 활액 내 glycosaminoglycan (GAG) 및 관절연골의 proteoglycan (PG)의 분해를 방지하여 골관절염의 발생을 억제할 것으로 추정되었다. 한편, 참당귀 추출분말의 주성분인 decursin은 혈중에서 2시간이내에 decursinol로 전환되어 8시간이상 LC-MS/MS로 검출되었다, 따라서 참당귀 추출분말에 의한 염증성 사이토카인 TNF-α, IL-1β 및 IL-6의 억제활성은 항염증활성이 큰 decursinol에 의한 것으로 추정된다.

• Asian-Australasian Journal of Animal Sciences
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• 제31권10호
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• pp.1581-1590
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• 2018

Objective: The aim of this study was to clone alternative splicing isoforms of pig myoneurin (MYNN), predict the structure and function of coding protein, and study temporal and spatial expression characteristics of each transcript. Methods: Alternative splice isoforms of MYNN were identified using RNA sequencing (RNA-seq) and cloning techniques. Quantitative real-time polymerase chain reaction (qPCR) was employed to detect expression patterns in 11 tissues of Large White (LW) and Mashen (MS) pigs, and to study developmental expression patterns in cerebellum (CE), stomach (ST), and longissimus dorsi (LD). Results: The results showed that MYNN had two alternatively spliced isoforms, MYNN-1 (GenBank accession number: KY470829) and MYNN-2 (GenBank accession number: KY670835). MYNN-1 coding sequence (CDS) is composed of 1,830 bp encoding 609 AA, whereas MYNN-2 CDS is composed of 1,746 bp encoding 581 AA. MYNN-2 was 84 bp less than MYNN-1 and lacked the sixth exon. MYNN-2 was found to have one $C_2H_2$ type zinc finger protein domain less than MYNN-1. Two variants were ubiquitously expressed in all pig tissues, and there were significant differences in expression of different tissues (p<0.05; p<0.01). The expression of MYNN-1 was significantly higher than that of MYNN-2 in almost tissues (p<0.05; p<0.01), which testified that MYNN-1 is the main variant. The expression of two isoforms decreased gradually with increase of age in ST and CE of MS pig, whereas increased gradually in LW pig. In LD, the expression of two isoforms increased first and then decreased with increase of age in MS pig, and decreased gradually in LW pig. Conclusion: Two transcripts of pig MYNN were successfully cloned and MYNN-1 was main variant. MYNN was highly expressed in ST, CE, and LD, and their expression was regular. We speculated that MYNN plays important roles in digestion/absorption and skeletal muscle growth, whereas the specific mechanisms require further elucidation.

• 약학회지
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• 제55권3호
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• pp.203-212
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• 2011

Adipocytes have been known to secrete a number of important proteins called adipokines with roles in energy metabolism, reproduction, cardiovascular function and immunity. In this study we have attempted to identify intensively secretory proteins from 3T3-L1 adipocytes. 3T3-L1 preadipocytes were differentiated into mature adipocytes and then the cells were left in serum-free medium. The supernatant was filtrated and dialyzed. Lyophilized secretome was fractionated by two different methods, 1-D SDS PAGE and RP-FPLC. The tryptic peptides from the gel slices and the FPLC fractions were analyzed by nanoLC/ESI-MS/MS. We identified a total of 303 identical proteins from two methods, 251 proteins from 1-D gel and 184 proteins from RP-FPLC. 86 of them were listed as a secretory protein Finally, we identified many known or unknown secreted proteins existed in the low level including adiponectin, angiotensinogen, bone morphogenetic protein-1 (BMP-1), macrophage migration inhibitory factor (MIF), insulin like growth factor-II (IGF-II), interleukin-6 (IL-6), follistatin-related protein-1, minecan, and resistin. The existence of some of secreted proteins has been confirmed in RNA level. This proteomic experiment is useful for the intensive screening of secretory proteins in many kinds of other cells.

• Applied Biological Chemistry
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• 제39권5호
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• pp.355-360
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• 1996

시험관내에서 합성한 오이모자이크 바이러스 RNA단편을 성공적으로 절단한 ribozyme (한국농화학회지 37: 56-63(1994))을 담배 식물체에 발현시켜 바이러스 저항성 식물체를 만들려고 하였다. 해당 ribozyme의 염기서열을 함유한 DNA 단편을 꽃양배추 바이러스 35S promoter와 nopaline 합성효소 terminator에 연결시키고 연결 부위 및 ribozyme의 염기서열을 확인하였다. 염기서열을 확인한 합성유전자를 Agrobacterium tumefaciens LBA4404에 합성유전자를 함유한 E. coli HB101을 E. coli HB101(pRK2073)를 helper로 Agrobacterium tumefaciens LBA4404와 함께 배양하는 tri-parental mating system을 이용하여 도입시켰다. Ribozyme 유전자를 함유한 Agrobacterium 세포를 담배잎 조각과 함께 배양한 후 항생제인 kanamycin을 함유한 MS 배지에서 자란 열개의 작은 식물체를 재분화하였다. 형질전환한 식물체내에 ribozyme 유전자가 존재하는지의 여부는 합성효소증폭반응(PCR)을 이용하였던바, 일곱개체가 예상된 570 염기쌍의 DNA 단편을 가지고 있었다. 이들 중 네 개체로부터 RNA을 분리하여 formamide를 함유한 agarose에서 전기영동한 후 35S-ribozyme-nos의 DNA 단편으로 Northern hybridization을 행하였던 바, 식물세포내의 nuclease에 의해 ribozyme RNA가 분해된 듯 감지 할 수 없었다. 따라서 ribozyme을 이용하여 바이러스 저항성 식물체를 얻으려면 nuclease에 의해 분해되지 않는 ribozyme이 필요할 것으로 사료된다.

• Parasites, Hosts and Diseases
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• 제55권6호
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• pp.601-606
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• 2017

Cystoisospora is responsible for morbidity in immunocompromised patients. PCR is sensitive for diagnosing Cystoisospora; however, it needs reevaluation for differential molecular diagnosis of cystoisosporiasis. We aimed at evaluating melting curve analysis (MCA) after real-time PCR (qPCR) in diagnosis and genotyping of Cystoisospora as an alternative to conventional PCR. We included 293 diarrheic stool samples of patients attending the Department of Clinical Oncology and Nuclear Medicine of Cairo University Hospitals, Egypt. Samples were subjected to microscopy, nested PCR (nPCR), and qPCR targeting the internal transcribed spacer 2 region (ITS2) of the ribosomal RNA (r RNA) gene followed by melting temperatures ($T_ms$) analysis and comparing the results to PCR-RFLP banding patterns. Using microscopy and ITS2-nPCR, 3.1% and 5.8% of cases were Cystoisospora positive, respectively, while 10.9% were positive using qPCR. Genotyping of Cystoisospora by qPCR-MCA revealed 2 genotypes. These genotypes matched with 2 distinct melting peaks with specified $T_ms$ at $85.8^{\circ}C$ and $88.6^{\circ}C$, which indicated genetic variation among Cystoisospora isolates in Egypt. Genotype II proved to be more prevalent (65.6%). HIV-related Kaposi sarcoma and leukemic patients harbored both genotypes with a tendency to genotype II. Genotype I was more prevalent in lymphomas and mammary gland tumors while colorectal and hepatocellular tumors harbored genotype II suggesting that this genotype might be responsible for the development of cystoisosporiasis in immunocompromised patients. Direct reliable identification and differentiation of Cystoisospora species could be established using $qPCR-T_ms$ analysis which is useful for rapid detection and screening of Cystoisospora genotypes principally in high risk groups.

• 환경생물
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• 제33권4호
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• pp.433-440
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• 2015

The Apostichopus japonicus is an important species in some Asia countries including Korea, China and Japan. The purpose of the present study was to investigate the differential gene expression of heat shock protein90 (Hsp90) and ferritin as a biomarker for the thermal stress during water temperature rising in the sea cucumber, A. japonicus. The A. japonicus (1.4 g) was cultured in incubator of separate temperature ($15^{\circ}C$, $20^{\circ}C$, $25^{\circ}C$ and $30^{\circ}C$) for each 0, 3, 6, 12, 24, 48 hours. The mRNA expression levels of Hsp90 and ferritin were examined using RT-PCR assay. Results showed that, the expression of Hsp90 mRNA was not significantly changed at $15^{\circ}C$. The expression of Hsp90 mRNA was significantly increased at high temperature such as $20^{\circ}C$ and $25^{\circ}C$. Furthermore, Hsp90 mRNA was early increased at $25^{\circ}C$ than $20^{\circ}C$. The ferritin mRNA was similar expression pattern with Hsp90. But, Hsp90 mRNA was more sensitive than ferritin mRNA at high thermal stress. These results indicate that Hsp90 and ferritin mRNAs were involved in the temperature changes response and may be play an important role in mediating the thermal stress in A. japonicas.