• Animal cells and systems
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• 제16권6호
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• pp.488-497
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• 2012

A DNA barcode based on 648 bp of cytochrome c oxidase I (COI) gene aims to build species-specific libraries for animal groups. However, it is hard to recover full-length (648 bp) barcode gene from environmental fecal samples due to DNA degradation. In this study, we designed a new primer set (K_Bird), which amplifies a 226 bp fragment targeted an inner position of full-length COI barcode based on 102 species of Korean birds to improve amplification success, and we attempted to identify bird species from 39 avian fecal samples collected during 4 months from Jinan, South Korea. Simultaneously, we conducted a dietary analysis using a universal DNA mini-barcode (Uni_Minibar) from same fecal samples. In silico analysis on newly designed mini-barcode represented that genetic distances were 0.5% in species and 9.1% in genera. Intraspecific variations of 149 species out of 174 species (86%) between Korea and North America were within the threshold (5.3% threshold in this study). From environmental fecal samples collected in Jinan, we identified seven avian species, which have high similarity (99-100%) with registered COI sequences in GenBank. Eight kinds of prey species, such as moth, spider, fly, and dragonfly, were identified in dietary analysis. We suppose that our strategy applying mini-barcode for environmental fecal samples, might be a useful and convenient tool for species identification and dietary analysis for birds.

• Journal of Microbiology and Biotechnology
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• 제23권3호
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• pp.297-303
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• 2013

Phylogenetic analysis of the groEL1 and xynB1 gene sequences from Sorangium cellulosum strains isolated in Korea previously revealed the existence of at least 5 subgroups (A-E). In the present study, we used sequence analysis of polymerase chain reaction-amplified biosynthetic genes of strains from the 5 subgroups to indicate correlations between S. cellulosum subgroups and their secondary metabolic gene categories. We detected putative biosynthetic genes for disorazol, epothilone, ambruticin, and soraphen in group A, group C, group D, and group E strains, respectively. With the exception of KYC3204, culture extracts from group A, group B, and group C strains exhibited no noticeable antimicrobial inhibitory activities. By contrast, culture extracts from group D strains inhibited the growth of Candida albicans, whereas culture extracts from group E strains inhibited the growth of C. albicans and Staphylococcus aureus. High performance liquid chromatography analysis of the culture extracts from the strains of each subgroup revealed unique peak patterns. Our findings indicate the existence of at least 5 subgroups of S. cellulosum strains, each of which has the potential to produce a unique set of secondary metabolites.

• Journal of Microbiology and Biotechnology
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• 제23권4호
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• pp.555-559
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• 2013

Vibrio cholerae O1 and O139 are the major serotypes associated with illness, and some V. cholera non-O1 and non-O139 isolates produce cholera toxin. The present study describes a quantitative polymerase chain reaction (qPCR) assay for the species-specific detection and quantitation of V. cholera using a primer pair based on an outer membrane lipoprotein lolB gene for the amplification of a 195 bp DNA fragment. The qPCR primer set for the accurate diagnosis of V. cholera was developed from publically available genome sequences. This quantitative PCR-based method will potentially simplify and facilitate the diagnosis of this pathogen and guide disease management.

• ETRI Journal
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• 제41권3호
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• pp.358-370
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• 2019

The main aim of this study is to select the optimal set of genes from microarray cancer datasets that contribute to the prediction of specific cancer types. This study proposes the enhancement of the feature selection filter algorithm based on Joe's normalized mutual information and its use for gene selection. The proposed algorithm is implemented and evaluated on seven benchmark microarray cancer datasets, namely, central nervous system, leukemia (binary), leukemia (3 class), leukemia (4 class), lymphoma, mixed lineage leukemia, and small round blue cell tumor, using five well-known classifiers, including the naive Bayes, radial basis function network, instance-based classifier, decision-based table, and decision tree. An average increase in the prediction accuracy of 5.1% is observed on all seven datasets averaged over all five classifiers. The average reduction in training time is 2.86 seconds. The performance of the proposed method is also compared with those of three other popular mutual information-based feature selection filters, namely, information gain, gain ratio, and symmetric uncertainty. The results are impressive when all five classifiers are used on all the datasets.

• BMB Reports
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• 제52권2호
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• pp.139-144
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• 2019

Breast cancer (BRC) is the most invasive cancer in women. Although the survival rate of BRC is gradually increasing due to improved screening systems, development of novel therapeutic targets for inhibition of BRC proliferation, metastasis and recurrence have been constantly needed. Thus, in this study, we identified overexpression of SETDB1 (SET Domain Bifurcated 1), a histone methyltransferase, in RNA-seq data of BRC derived from TCGA portal. In Gene Ontology (GO) analysis, cell migration-related GO terms were enriched, and we confirmed down-regulation of cell migration/invasion and alteration of EMT /MET markers after knockdown of SETDB1. Moreover, gene network analysis showed that SMAD7 expression is regulated by SETDB1 levels, indicating that up-regulation of SMAD7 by SETDB1 knockdown inhibited BRC metastasis. Therefore, development of SETDB1 inhibitors and functional studies may help develop more effective clinical guidelines for BRC treatment.

• 한국작물학회지
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• 제5권1호
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• pp.57-64
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• 1969

1. 단백질: 오페이크-2 옥수수에서 비록 적은 단백질함량이 분석되었지만 정상적인 옥수수와 오페이크-2 옥수수 사이에 있어서 유의적인 상관관계는 없었다. 2. 라이신: 라이신 함량역시 품종에 따라 다르며 오페이크-2 옥수수에 있어서의 라이신 함량은 품종간에 큰 차이가 없었다. 정상적인 옥수수와 오페이크-2 옥수수 사이에 있어서 라이신 함량간에는 유의적인 상관관계가 없었다. 3. 분리비율: 오페이크-2 옥수수는 열성단일 인자로서 대개 나타났다. 표현형에 있어서는 사용한 품종에 따라 다르게 나타났다. 오페이크-2 옥수수는 이병성이 약한 듯 하였으며 종실중이 가벼웠다. 4. 오페이크-2 인자와 후라워리-2 인자는 대립유전인자가 아니다. 5. 배우자적 불화합성과 웅성 불임이 오페이크 교배 조합에서 나타났다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.191-191
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• 2017

Hydroxy fatty acid (HFA) is an important industrial resource that known to be extracted from seeds of Castor or Lesquerella. However, mass production of HFA from those crops are difficult because of their behavior or life cycle. In this study, we applied HFA synthesis related gene FAH12, RcPDAT1, RcLPCAT, RcDGAT2, and RcPDCT on bioenergy crop Camelina sativa. Furthermore, we determined NaCl or cold stress tolerance changes of transgenic Camelina. RcFAH12, RcPDAT1, RcLPCAT, RcDGAT2, and RcPDCT genes were cloned into multigene expression vector which is engineered with seed specific promoter of FAE1 or Napin. Combination of HFA genes multi-expression vector constructs were divided into Set3 (RcFAH12, RcPDAT1-2, RcLPCAT), Set4 (RcFAH12, RcDGAT2, RCPDAT1-2, RcLPCAT), and Set5 (RcFAH12, RcDGAT2, RCPDAT1-2, RcLPCAT, RcPDCT). Transgenic HFA synthesis Camelina plants were generated using agrobacterium-mediated vacuum infiltration system. Results of fatty acid composition of T1 transgenic Camelina seeds analyzed by GC-MS showed 9.5, 9.0, and 13.6 % of HFA contents in Set3#6, Set4#8, and Set5#10, respectively. Therefore, seeds of T2 generation were harvest from Set5#10 which is shown highest HFA contents, and, 17.7, 8.1 and 10.5 % of HFA contents were determined in Set5#10-5, Set5#10-8, and Set#10-10, respectively. However, 7.7% of C18:2 and 22.3 % of C18:3 among unsaturated fatty acids were decreased in Set5#10-5 than WT. Meanwhile, we confirmed abiotic stress responses in T2 transgenic Camelina Set5#10-5 and Set5#10-10 under 0, 100, 150, and 200 mM NaCl or 25, 15, and $10^{\circ}C$ temperature for 5 weeks. Both Set5#10-5 and Set5#10-10 showed lower growth in height than WT in control and NaCl condition. Growth of leaf length and width were similar in WT and Set5#10-10 but lower in Set5#10-5 under NaCl stress. Number of opened flowers showed that both transgenic Camelina were lower than WT under normal condition. But, WT and Set5#10-10 showed similar opened flower number in 100 and 200 mM NaCl. In cold stress, 15 and $10^{\circ}C$ treatment for 5 weeks did not showed significant changes in between WT and both transgenic lines even they showed different growth rate in control condition. Taken together, growth and development are delayed by expression of exogenous HFA related genes in transgenic lines but relative abiotic stress sensitivity is similar with WT. In conclusion, reduced C18:2 or C18:3 fatty acid composition of seed by HFA synthesis is resulted from lack of resource supplement for development at seedling stage but it is not affect NaCl and cold stress tolerance.

• Asian Pacific Journal of Cancer Prevention
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• 제13권11호
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• pp.5433-5438
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• 2012

Background: Hepatocellular carcinoma (HCC) is a common and aggressive malignancy. Despite of the improvements in its treatment, HCC prognosis remains poor due to its recurrence after resection. This study provides complete genetic profile for Egyptian HCC. Genome-wide analyses were performed to identify the predictive signatures. Patients and Methods: Liver tissue was collected from 31 patients with diagnosis of HCC and gene expression levels in the tumours and their adjacent non-neoplastic tissues samples were studied by analyzing changes by microarray then correlate these with the clinico-pathological parameters. Genes were validated in an independent set by qPCR. The genomic profile was associated with genetic disorders and cancer focused on gene expression, cell cycle and cell death. Molecular profile analysis revealed cell cycle progression and arrest at G2/M, but progression to mitosis; unregulated DNA damage check-points, and apoptosis. Result: Nine hundred fifty eight transcripts out of the 25,000 studied cDNAs were differentially expressed; 503 were up-regulated and 455 were down-regulated. A total of 19 pathways were up-regulated through 27 genes and 13 pathways were down-regulated through 19 genes. Thirty-seven genes showed significant differences in their expression between HCC cases with high and low Alpha Feto Protein ($AFP{\geq}600$ IU/ml). The validation for the microarray was done by real time PCR assay in which PPP3CA, ATG-5, BACE genes showed down-regulation and ABCG2, RXRA, ELOVL2, CXR3 genes showed up-regulation. cDNA microarrays showed that among the major upregulated genes in HCC are sets. Conclusion: The identified genes could provide a panel of new diagnostic and prognostic aids for HCC.

• BMB Reports
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• 제50권11호
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• pp.590-595
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• 2017

High-mobility group box-1 (HMGB-1) is expressed in almost all cells, and its dysregulated expression correlates with inflammatory diseases, ischemia, and cancer. Some of these conditions accompany HMGB-1-mediated abnormal angiogenesis. Thus far, the mechanism of HMGB-1-induced angiogenesis remains largely unknown. In this study, we performed time-dependent DNA microarray analysis of endothelial cells (ECs) after HMGB-1 or VEGF treatment. The pathway analysis of each gene set upregulated by HMGB-1 or VEGF showed that most HMGB-1-induced angiogenic pathways were also activated by VEGF, although the activation time and gene sets belonging to the pathways differed. In addition, HMGB-1 upregulated some VEGFR signaling-related angiogenic factors including EGR1 and, importantly, novel angiogenic factors, such as ABL2, CEACAM1, KIT, and VIPR1, which are reported to independently promote angiogenesis under physiological and pathological conditions. Our findings suggest that HMGB-1 independently induces angiogenesis by activating HMGB-1-specific angiogenic factors and also functions as an accelerator for VEGF-mediated conventional angiogenesis.

• 한국작물학회지
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• 제30권2호
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• pp.131-139
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• 1985

이모작재배에 적합한 극조숙 양질 다수성 소맥품종육성을 위하여 등수기간에 관여하는 유전자 작용에 대한 연구는 매우 중요하다. 추파성품종 Yam-hill과 Hyslop, 춘파성품종 Red Bobs와 Siete Cellos를 사용하여 4 $\times$ 4 complete diallel crosses F$_1$, F$_2$, BC$_1$ 및 BC$_2$를 작성, Jinks-Hay-man model를 이용하여 등숙기간에 관여하는 유전자 작용을 분석하였다. 본 시험은 오레곤 주립대학교에서 실시되었다. 그 결과의 개요는 다음과 같다. 전등숙기간인 출수에서 생리적 성숙기까지의 기간과 출수에서 개화까지의 기간에서 maternal effect 가 인정되지 않았으며 비대립유전자간 상호작용도 발현되지 않았다. 개화에서 생리적 성숙기까지의 기간에서는 비대립유전자간에 상호작용이 인정되었다. 춘파성 품종인 Red Bobs와 Siete Cellos는 전등숙기간과 출수에서 개화까지의 기간을 지배하는 우성유전자들을 가지고 있었으며 짧은 쪽에 비하여 긴쪽이 우성으로 발현되고 있었다. 대조적으로 추파성 품종인 Yamhill 과 Hyslop은 개화에서 생리적 성숙기까지의 기간을 지배하는 우성유전자들을 가지고 있었으며 긴쪽이 우성으로 작용하고 있었다. 그리고 이 유전자들은 문배친들간에 독립적으로 분포되어 있었다.