• KSBB Journal
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• 제25권5호
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• pp.490-496
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• 2010

미생물은 지구상에 약 $5\;{\times}\;10^{30}$ 정도의 개체가 존재하며, 350~550 Pg (1Pg = 1015g)의 탄소, 85~130 Pg의 질소, 9~14 Pg의 인 등, 지구상의 어떠한 생물 종보다 거대한 양의 원소를 포함하고 있다. 또한 이러한 미생물과 생태계를 구성하는 다른 유기체나 무기물과의 관계가 지속적으로 밝혀지고 있다. 이러한 연구들의 기본적인 목표는 상호작용에 중요한 인자들의 규명 (대표적으로 유전자)하는 것이기 때문에, 염색체에 존재하는 true ORF의 검색과 확인은 가장 중요한 기본 수단이 된다. 그러나 다양한 미생물로 구성된 환경 유전체는 기존 정보로 검색 가능한 비율을 정확하게 유추할 수 없기에 많은 어려움이 있다. 이렇게 경계가 불분명한 자료의 검색을 위해서는 보다 많은 정보를 필요 (training이나 space를 규정하기 위한 보다 많은 유전자 서열)로 하며, 다른 검색 방법이나 기법들이 추가적으로 개발되어야 할 것이다. 이러한 방법의 대안으로써, 미생물의 유전자간 서열에 존재하는 전사/번역인자의 보존성에 근거한 검색방법은 개량 여하에 따라 광범위한 적용 범위를 지닐 것이다. 현 수준에서도 조합 탐색, 즉 기존의 방법과 혼용하거나 기존의 방법을 보완하는 과정으로 충분한 가치를 지니고 있다. 이러한 추정은, 기존의 ORF 중심의 발굴 결과와 전혀 일치되지 않는 경우에서부터 90% 이상 일치하는 등의 결과로서 확인하였다. 일치 되지 않는 많은 경우가 BLASTing으로 검색되지 않는 새로운 ORF를 포함하기 때문이다.

• Journal of Genetic Medicine
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• 제6권1호
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• pp.1-7
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• 2009

프로모터 CpG island 과메틸화와 히스톤 변경으로 대변되는 후성유전적 변화는 거의 모든 종류의 암에서 발견되는 중요한 발암기전이다. 인간유전자의 60-70% 가량이 프로모터에 CpG islands를 가지고 있으며, 이 유전자들 중 일부가 과메틸화됨으로써 해당유전자의 발현이 차단되고, 종양억제기능이 소실되어 종양세포의 성장을 촉진하게 된다. 암에는 프로모터 CpG island 과메틸화라는 국소적 변화 이외에, 유전체 전반에 걸친 탈메틸화를 동시에 보이는 경우가 대부분인데, 이러한 유전체 저메틸화는 염색체 불안정성과 밀접한 연관관계가 있다. 국소적 과메틸화와 전반적인 저메틸화라는 이러한 상반된 DNA 메틸화 변화는 암세포뿐만 아니라 그 전단계 병변인 이 형성 병변에서도 관찰된다. 프로모터CpG island 과메틸화는 유전자 발현억제 기전으로서의 중요성뿐만 아니라 종양표지자로서의 중요성이 부각되고 있다. 즉, 정상세포에서는 관찰되지 않으면서 암세포에서만 관찰되는 프로모터 CpG island 과메틸화는 암세포의 바이오마커로서의 가치가 있으며, 이를 이용하여 체액에서 암을 진단하려는 시도들이 이루어지고, 이를 활용한 암의 분자진단방법이 개발되고 있다. 또한 이러한 DNA 메틸화는 암환자의 예후 판정이나 항암치료제의 감수성 결정 등에 활용되고 있다. 본 원고에서는 인체 암세포에서의 DNA 메틸화 변화에 관하여 소개하고자 한다.

• Asian Pacific Journal of Cancer Prevention
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• 제13권8호
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• pp.4113-4117
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• 2012

Breast cancer is a prevalent heterogeneous malignant disease. Gene expression profiling by DNA microarray can classify breast tumors into five different molecular subtypes: luminal A, luminal B, HER-2, basal and normal-like which have differing prognosis. Recently it has been shown that immunohistochemistry (IHC) markers including estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (Her2), can divide tumors to main subtypes: luminal A (ER+; PR+/-; HER-2-), luminal B (ER+;PR+/-; HER-2+), basal-like (ER-;PR-;HER2-) and Her2+ (ER-; PR-; HER-2+). Some subtypes such as basal-like subtype have been characterized by poor prognosis and reduced overall survival. Due to the importance of the ER signaling pathway in mammary cell proliferation; it appears that epigenetic changes in the $ER{\alpha}$ gene as a central component of this pathway, may contribute to prognostic prediction. Thus this study aimed to clarify the correlation of different IHC-based subtypes of breast tumors with $ER{\alpha}$ methylation in Iranian breast cancer patients. For this purpose one hundred fresh breast tumors obtained by surgical resection underwent DNA extraction for assessment of their ER methylation status by methylation specific PCR (MSP). These tumors were classified into main subtypes according to IHC markers and data were collected on pathological features of the patients. $ER{\alpha}$ methylation was found in 25 of 28 (89.3%) basal tumors, 21 of 24 (87.5%) Her2+ tumors, 18 of 34 (52.9%) luminal A tumors and 7 of 14 (50%) luminal B tumors. A strong correlation was found between $ER{\alpha}$ methylation and poor prognosis tumor subtypes (basal and Her2+) in patients (P<0.001). Our findings show that $ER{\alpha}$ methylation is correlated with poor prognosis subtypes of breast tumors in Iranian patients and may play an important role in pathogenesis of the more aggressive breast tumors.

• Membrane and Water Treatment
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• 제7권3호
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• pp.175-191
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• 2016

In this work, oil-in-water emulsions (O/W) were prepared successfully by membrane emulsification with $0.5{\mu}m$ pore size membrane. Sunflower oil was emulsified in aqueous Tween80 solution with a simple crossflow apparatus equipped with ceramic tube membrane. In order to increase the shear-stress near the membrane wall, a helical-shaped reducer was installed within the lumen side of the tube membrane. This method allows the reduction of continuous phase flow and the increase of dispersed phase flux, for cost effective production. Results were compared with the conventional cross-flow membrane emulsification method. Monodisperse O/W emulsions were obtained using tubular membrane with droplet size in the range $3.3-4.6{\mu}m$ corresponded to the membrane pore diameter of $0.5{\mu}m$. The final aim of this study is to obtain O/W emulsions by simple membrane emulsification method without reducer and compare the results obtained by membrane equipped with helix shaped reducer. To indicate the results statistical methods, $3^p$ type full factorial experimental designs were evaluated, using software called STATISTICA. For prediction of the flux, droplet size and PDI a mathematical model was set up which can describe well the dependent variables in the studied range, namely the run of the flux and the mean droplet diameter and the effects of operating parameters. The results suggested that polynomial model is adequate for representation of selected responses.

• Journal of Microbiology and Biotechnology
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• 제31권10호
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• pp.1358-1365
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• 2021

To clarify the role of long intergenic nonprotein-coding RNA 1232 (LINC01232) in the progression of gastric cancer and the potential mechanism, we analyzed the expression of LINC01232 in TCGA database using the GEPIA online tool, and the LINC01232 level in gastric cancer cell lines was detected by quantitative real time-polymerase chain reaction (qRT-PCR) as well. Cell proliferation assay, colony formation assay, transwell assay and tumor formation experiment in nude mice were conducted to observe the biological behavior changes of gastric cancer cells through the influence of LINC01232 knockdown. LncATLAS database and subcellular isolation assay were used for subcellular distribution of LINC01232 in gastric cancer cells. The interaction among LINC01232, zeste homolog 2 (EZH2) and kruppel-like factor 2 (KLF2) was clarified by RNA-protein interaction prediction (RPISeq), RNA immunoprecipitation (RIP), qRT-PCR and chromatin immunoprecipitation (ChIP) assay. Rescue experiments were further conducted to elucidate the biological function of LINC01232/KLF2 axis in the progression of gastric cancer. LINC01232 was upregulated in stomach adenocarcinoma (STAD) tissues and gastric cancer lines. LINC01232 knockdown inhibited the proliferative capacities of gastric cancer cells in vitro, and impaired in vivo tumorigenicity. LINC01232 was mainly distributed in the cell nucleus where it epigenetically repressed KLF2 expression via binding to the enhancer of EZH2, which was capable of binding to promoter regions of KLF2 to induce histone H3 lysine 27 trimethylation (H3K27me3). LINC01232 exerts oncogenic activities in gastric cancer via inhibition of KLF2, and therefore, the knockdown of KLF2 could reverse the regulatory effect of LINC01232 in the proliferative ability of gastric cancer cells.

• Genomics & Informatics
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• 제20권2호
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• pp.19.1-19.15
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• 2022

Alfalfa (Medicago sativa) is an important food and feed crop which rich in mineral sources. The WUSCHEL-related homeobox (WOX) gene family plays important roles in plant development and identification of putative gene families, their structure, and potential functions is a primary step for not only understanding the genetic mechanisms behind various biological process but also for genetic improvement. A variety of computational tools, including MAFFT, HMMER, hidden Markov models, Pfam, SMART, MEGA, ProtTest, BLASTn, and BRAD, among others, were used. We identified 34 MsWOX genes based on a systematic analysis of the alfalfa plant genome spread in eight chromosomes. This is an expansion of the gene family which we attribute to observed chromosomal duplications. Sequence alignment analysis revealed 61 conserved proteins containing a homeodomain. Phylogenetic study sung reveal five evolutionary clades with 15 motif distributions. Gene structure analysis reveals various exon, intron, and untranslated structures which are consistent in genes from similar clades. Functional analysis prediction of promoter regions reveals various transcription binding sites containing key growth, development, and stress-responsive transcription factor families such as MYB, ERF, AP2, and NAC which are spread across the genes. Most of the genes are predicted to be in the nucleus. Also, there are duplication events in some genes which explain the expansion of the family. The present research provides a clue on the potential roles of MsWOX family genes that will be useful for further understanding their functional roles in alfalfa plants.

• Journal of Microbiology
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• 제44권1호
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• pp.64-71
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• 2006

To investigate the effects of the nucleotide sequences in Shine-Dalgarno (SD) and the spacer region (SD-ATG) on bovine growth hormone (bGH) gene expression, the expression vectors under the control of the T7 promoter (pT7-7 vector) were constructed using bGH derivatives (bGH1 & bGH14) which have different 5'-coding regions and were induced in E. coli BL21 (DE3). Oligonucleotides containing random SD sequences and a spacer region were chemically synthesized and the distance between the SD region and the initiation codon were fixed to nine bases in length. The oligonucleotides were annealed and fused to the bGH1 and bGH14 cDNA, respectively. When the bGH gene was induced with IPTG in E. coli BL21(DE3), some clones containing only bGH14 cDNA produced considerable levels of bGH in the range of $6.9\%\;to\;8.5\%$ of total cell proteins by SDS-PAGE and Western blot. Otherwise, the bGH was not detected in any clones with bGH1 cDNA. Accordingly, the nucleotide sequences of SD and the spacer region affect on bGH expression indicates that the sequences sufficiently destabilize the mRNA secondary structure of the bGH14 gene. When the free energy was calculated from the transcription initiation site to the +51 nucleotide of bGH cDNA using a program of nucleic acid folding and hybridization prediction, the constructs with values below -26.3 kcal/mole (toward minus direction) were not expressed. The constructs with the original sequence of bGH cDNA also did not show any expression, regardless of the free energy values. Thus, the disruption of the mRNA secondary structure may be a major factor regulating bGH expression in the translation initiation process. Accordingly, the first stem-loop among two secondary structures present in the 5'-end region of the bGH gene should be disrupted for the effective expression of bGH.

• Investigative Magnetic Resonance Imaging
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• 제22권3호
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• pp.158-167
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• 2018

Purpose: To investigate the surgical, perfusion, and molecular characteristics of glioblastomas which influence long-term survival after treatment, and to explore the association between MR perfusion parameters and the presence of MGMT methylation and 1p/19q deletions. Materials and Methods: This retrospective study was approved by our institutional review board. A total 43 patients were included, all with pathologic diagnosis of glioblastoma with known MGMT methylation and 1p/19q deletion statuses. We divided these patients into long-term (${\geq}60\;months$, n = 7) and short-term (< 60 months, n = 36) survivors, then compared surgical extent, molecular status, and rCBV parameters between the two groups using Fisher's exact test or Mann-Whitney test. The rCBV parameters were analyzed according to the presence of MGMT methylation and 1p/19q deletions. We investigated the relationship between the mean rCBV and overall survival using linear correlation. Multivariable linear regression was performed in order to find the variables related to overall survival. Results: Long-term survivors (100% [7 of 7]) demonstrated a greater percentage of gross total or near total resection than short-term survivors (54.5% [18 of 33]). A higher prevalence of 1p/19q deletions was also noted among the long-term survivors (42.9% [3 of 7]) than the short-term survivors (0.0% [0 of 36]). The rCBV parameters did not differ between the long-term and short-term survivors. The rCBV values were marginally lower in patients with MGMT methylation and 1p/19q deletions. Despite no correlation found between overall survival and rCBV in the whole group, the short-term survivor group showed negative correlation ($R^2=0.181$, P = 0.025). Multivariable linear regression revealed that surgical extent and 1p/19q deletions, but not rCBV values, were associated with prolonged overall survival. Conclusion: While preoperative rCBV and 1p/19q deletion status are related to each other, only surgical extent and the presence of 1p/19q deletion in GBM patients may predict long-term survival.

• Korean Journal of Radiology
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• 제21권6호
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• pp.707-716
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• 2020

Objective: To evaluate pharmacokinetic variables from contrast-enhancing lesions (CELs) and non-enhancing T2 high signal intensity lesions (NE-T2HSILs) on dynamic contrast-enhanced (DCE) magnetic resonance (MR) imaging for predicting progression-free survival (PFS) in glioblastoma (GBM) patients. Materials and Methods: Sixty-four GBM patients who had undergone preoperative DCE MR imaging and received standard treatment were retrospectively included. We analyzed the pharmacokinetic variables of the volume transfer constant (Ktrans) and volume fraction of extravascular extracellular space within the CEL and NE-T2HSIL of the entire tumor. Univariate and multivariate Cox regression analyses were performed using preoperative clinical characteristics, pharmacokinetic variables of DCE MR imaging, and postoperative molecular biomarkers to predict PFS. Results: The increased mean Ktrans of the CEL, increased 95th percentile Ktrans of the CELs, and absence of methylated O⁶-methylguanine-DNA methyltransferase promoter were relevant adverse variables for PFS in the univariate analysis (p = 0.041, p = 0.032, and p = 0.083, respectively). The Kaplan-Meier survival curves demonstrated that PFS was significantly shorter in patients with a mean Ktrans of the CEL > 0.068 and 95th percentile Ktrans of the CEL > 0.223 (log-rank p = 0.038 and p = 0.041, respectively). However, only mean Ktrans of the CEL was significantly associated with PFS (p = 0.024; hazard ratio, 553.08; 95% confidence interval, 2.27-134756.74) in the multivariate Cox proportional hazard analysis. None of the pharmacokinetic variables from NE-T2HSILs were significantly related to PFS. Conclusion: Among the pharmacokinetic variables extracted from CELs and NE-T2HSILs on preoperative DCE MR imaging, the mean Ktrans of CELs exhibits potential as a useful imaging predictor of PFS in GBM patients.

• 생명과학회지
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• 제18권8호
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• pp.1132-1139
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• 2008

CpG island는 유전자의 발현 기작과 많은 관련이 있다. 포유동물 유전자의 약 $30{\sim}60$% 정도의 프로모터와 엑손부위에 CpG island가 존재 한다. 최근의 연구 결과에 따르면 CpG island의 과메틸화는 주요 암 억제유전자들을 불활성화 시켜 암을 일으키는 주요 요인이 되는 것으로 밝혀졌다. CpG island의 과메틸화는 거의 모든 암 종류에서 발견되고 있다. 따라서 CpG island를 검색하는 프로그램은 매우 중요한 의미를 갖는다. 그래서 D. Takai 와 P. A. Jones 등이 2002년 검증한 CpG island 정의 기준을 이용하여 윈도우 기반의 소프트웨어 프로그램인 CpGi를 개발하였다. CpGi는 Visual C++ 6.0로 구현하였으며, 입력서열 양식은 FASTA 포맷을 허용하도록 구성하였다. CpGi의 검색 성능을 평가하기 위해 2개의 인간 Contig, 즉, AP00524 (22번 염색체)와 NT_029490.3 (21번 염색체) 등을 대상으로 기존의 다른 CpG island 검색 프로그램인 Emboss-CpGPlot 및 CpG Island Searcher 등과 검색결과를 비교 분석하였다. CpGi에 의한 검색 결과는 다른 두 프로그램에 비해 같거나 오히려 보다 정확한 검색 결과를 보여주었다. CpGi는 사용자 친화적인 윈도우 인터페이스로 구현되어 있어 사용자가 프로그램을 구동하고 이용하기 매우 쉽고, 분석결과에 대한 이해도 용이하다. 본 프로그램은 사용자가 지정한 파라미터 값들(%GC, Obs (CpG)/Exp (CpG), 분석 윈도우 크기, 스텝크기, Gap 허용치, #CG)에 의해 CpG island의 위치를 결정하고, G+C%와 CpG island의 위치를 시각적으로 보여준다. 결과적으로, CpGi는 CpG island 관련 실험 연구자들뿐만 아니라 대용량 서열 분석 및 주석 작업을 위해 매우 유용한 도구로 활용될 수 있을 것이다.