• Genomics & Informatics
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• 제16권4호
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• pp.37.1-37.3
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• 2018

Gene-gene interaction is a key factor for explaining missing heritability. Many methods have been proposed to identify gene-gene interactions. Multifactor dimensionality reduction (MDR) is a well-known method for the detection of gene-gene interactions by reduction from genotypes of single-nucleotide polymorphism combinations to a binary variable with a value of high risk or low risk. This method has been widely expanded to own a specific objective. Among those expansions, fuzzy-MDR uses the fuzzy set theory for the membership of high risk or low risk and increases the detection rates of gene-gene interactions. Fuzzy-MDR is expanded by a maximum likelihood estimator as a new membership function in empirical fuzzy MDR (EFMDR). However, EFMDR is relatively slow, because it is implemented by R script language. Therefore, in this study, we implemented EFMDR using RCPP ($c^{{+}{+}}$ package) for faster executions. Our implementation for faster EFMDR, called EMMDR-Fast, is about 800 times faster than EFMDR written by R script only.

• 생명과학회지
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• 제22권8호
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• pp.1009-1017
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• 2012

Rodobacter sphaeroides에서 orf282 유전자는 cbb3 terminal oxidase를 암호화하는 ccoNOQP 오페론과 혐기적 활성자인 FnrL을 암호화하는 fnrL 유전자 사이에 있으며, 아직은 기능이 잘 알려지지 않았다. orf282 유전자의 기능을 알기 위해 우리는 orf282의 일부를 삭제함으로써 유전자를 붕괴시켜 orf282-minus mutant를 제조하였다. 두개의 FnrL 결합 부위가 orf282의 upstream에 존재한다는 것이 밝혀져 있으며, orf282 유전자가 FnrL에 의해 양성적으로 조절된다는 것이 증명되었다. orf282 유전자는 B875와 B800-850 spectral complexes의 형성과 관련이 없다. orf282 mutant에서의 cbb3 oxidase 활성을 wild type와 비교해보면 orf282 유전자가 ccoNOQP 오페론의 조절과 cbb3 cytochrome c oxidase의 생합성과 무관하다는 것을 알 수 있다. orf282 mutant의 구조 유전자인 nifH와 조절유전자인 nifA의 프로모터 활성이 증가한 것은 orf282 유전자 산물이 nifH와 nifA의 발현에서 음성적 effector로 작용한다는 것을 시사한다.

• Journal of mucopolysaccharidosis and rare diseases
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• 제2권2호
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• pp.38-40
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• 2016

Prader-Willi syndrome (PWS) is a rare genetic disorder often caused by a deletion of the chromosome 15q11-q13 region inherited from the father or by maternal disomy 15. Growth hormone deficiency with short stature, hypogonadism, cognitive and behavioral problems, analgesia, decreased gastric motility and decreased ability to vomit with hyperphagia are common in PWS leading to severe obesity in early childhood, if not controlled. The goal of this study is to investigate the effects of recombinant human GH (rhGH, henceforth designated GH) on the gene expression related to cognitive function in the brain of PWS mouse model (Snord116del). GH restored the mRNA expression level of several genes in the cerebellum. These data suggest the effect of GH on the expression of cognitive function related genes in cerebellum may provide a mechanism for the GH-induced brain function in PWS patients.

• Journal of Microbiology and Biotechnology
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• 제14권2호
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• pp.390-394
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• 2004

The genetically modified glyphosate-tolerant soybean contains the following introduced DNA sequences: the EPSPS (5-enol-pyruvylshikimate-3-phosphate synthase) gene from Agrobacterium sp. strain CP4, the 35S promoter from the cauliflower mosaic virus, and the NOS terminator from Agrobacterium tumefaciens. In the present study, detection of these introduced DNAs was performed by amplification using the polymerase chain reaction (PCR). A multiplex PCR method was also applied to prevent false positive results. When primers for 35S promoter, nos3', CTP(chloroplast transit peptide), and CP4 EPSPS (EPSPS from Agrobacterium sp. CP4) were used, positive results were obtained in PCR reactions using DNA from genetically modified glyphosate-tolerant soybeans. There were no false positive results when using DNA from non-genetically modified soybeans. The CP4 EPSPS gene was detected when less than 125 pg glyphosate-tolerant soybean DNA was amplified. Lectin Lel and psb A were amplified from both non-genetically modified and genetically modified glyphosate-tolerant soybean DNA. Multiplex PCR was performed using different primer sets for actin Sacl, 35S promoter and CP4 EPSPS. The actin gene was detectable in both non-genetically modified and glyphosate-tolerant soybeans as a constant endogenous gene. Target DNAs for the 35S promoter, and CP4 EPSPS were detected in samples containing 0.01-0.1% glyphosate-tolerant soybean, although there were variations depending on primers by multiplex PCR. Soybean seeds from five plants of non-genetically modified soybean were co-cultivated for six months with those of genetically modified soybean, and they were analyzed by PCR. As a result, they were not positive for 35S promoter, nos3' or CP4 EPSPS. Therefore, these results suggest there was no natural crossing of genes between glyphosate-tolerant and non-genetically modified soybean during co-cultivation, which indicates that gene transfer between these plants is unlikely to occur in nature.

• Asian-Australasian Journal of Animal Sciences
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• 제21권5호
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• pp.745-753
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• 2008

Gene-manipulated mice were discovered for the first time about a quarter century ago. Since then, numerous sophisticated technologies have been developed and applied to answer key questions about the fundamental roles of the genes of interest. Functional genomics can be characterized into gain-of-function and loss-of-function, which are called transgenic and knock-out studies, respectively. To make transgenic mice, the most widely used technique is the microinjection of transgene-containing vectors into the embryonic pronucleus. However, there are critical drawbacks: namely position effects, integration of unknown copies of a foreign gene, and instability of the foreign DNA within the host genome. To overcome these problems, the ROSA26 locus was used for the knock-in site of a transgene. Usage of this locus is discussed for the gain of function study as well as for several brilliant approaches such as conditional/inducible transgenic system, reproducible/inducible knockdown system, specific cell ablation by Cre-mediated expression of DTA, Cre-ERTM mice as a useful tool for temporal gene regulation, MORE mice as a germ line delete and site specific recombinase system. Techniques to make null mutant mice include complicated steps: vector design and construction, colony selection of embryonic stem (ES) cells, production of chimera mice, confirmation of germ line transmission, and so forth. It is tedious and labor intensive work and difficult to approach. Thus, it is not readily accessible by most researchers. In order to overcome such limitations, technical breakthroughs such as reporter knock-in and gene knock-out system, production of homozygous mutant ES cells from a single targeting vector, and production of mutant mice from tetraploid embryos are developed. With these upcoming progresses, it is important to consider how we could develop these systems further and expand to other animal models such as pigs and monkeys that have more physiological similarities to humans.

• Molecules and Cells
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• 제38권1호
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• pp.75-80
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• 2015

Osteoclasts are unique cells responsible for the resorption of bone matrix. MicroRNAs (miRNAs) are involved in the regulation of a wide range of physiological processes. Here, we examined the role of miR-26a in RANKL-induced osteoclastogenesis. The expression of miR-26a was upregulated by RANKL at the late stage of osteoclastogenesis. Ectopic expression of an miR-26a mimic in osteoclast precursor cells attenuated osteoclast formation, actin-ring formation, and bone resorption by suppressing the expression of connective tissue growth factor/CCN family 2 (CTGF/CCN2), which can promote osteoclast formation via upregulation of dendritic cell-specific transmembrane protein (DC-STAMP). On the other hand, overexpression of miR-26a inhibitor enhanced RANKL-induced osteoclast formation and function as well as CTGF expression. In addition, the inhibitory effect of miR-26a on osteoclast formation and function was prevented by treatment with recombinant CTGF. Collectively, our results suggest that miR-26a modulates osteoclast formation and function through the regulation of CTGF.

• 생물정신의학
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• 제25권4호
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• pp.101-109
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• 2018

Objectives According to previous studies, the Chromogranin B (CHGB) gene could be an important candidate gene for schizophrenia which is located on chromosome 20p12.3. Some studies have linked the polymorphism in CHGB gene with the risk of schizophrenia. Meanwhile, smooth pursuit eye movement (SPEM) abnormality has been regarded as one of the most consistent endophenotype of schizophrenia. In this study, we investigated the association between the polymorphisms in CHGB gene and SPEM abnormality in Korean patients with schizophrenia. Methods We measured SPEM function in 24 Korean patients with schizophrenia (16 male, 8 female) and they were divided according to SPEM function into two groups, good and poor SPEM function groups. We also investigated genotypes of polymorphisms in CHGB gene in each group. A logistic regression analysis was performed to find the association between SPEM abnormality and the number of polymorphism. Results The natural logarithm value of signal/noise ratio (Ln S/N ratio) of good SPEM function group was $4.19{\pm}0.19$ and that of poor SPEM function group was $3.17{\pm}0.65$. In total, 15 single nucleotide polymorphisms of CHGB were identified and the genotypes were divided into C/C, C/R, and R/R. Statistical analysis revealed that two genetic variants (rs16991480, rs76791154) were associated with SPEM abnormality in schizophrenia (p = 0.004). Conclusions Despite the limitations including a small number of samples and lack of functional study, our results suggest that genetic variants of CHGB may be associated with SPEM abnormality and provide useful preliminary information for further study.nwhile, smooth pursuit eye movement (SPEM) abnormality has been regarded as one of the most consistent endophenotype of schizophrenia. In this study, we investigated the association between the polymorphisms in CHGB gene and SPEM abnormality in Korean patients with schizophrenia. MethodsZZWe measured SPEM function in 24 Korean patients with schizophrenia (16 male, 8 female) and they were divided according to SPEM function into two groups, good and poor SPEM function groups. We also investigated genotypes of polymorphisms in CHGB gene in each group. A logistic regression analysis was performed to find the association between SPEM abnormality and the number of polymorphism. ResultsZZThe natural logarithm value of signal/noise ratio (Ln S/N ratio) of good SPEM function group was $4.19{\pm}0.19$ and that of poor SPEM function group was $3.17{\pm}0.65$. In total, 15 single nucleotide polymorphisms of CHGB were identified and the genotypes were divided into C/C, C/R, and R/R. Statistical analysis revealed that two genetic variants (rs16991480, rs76791154) were associated with SPEM abnormality in schizophrenia (p = 0.004). ConclusionsZZDespite the limitations including a small number of samples and lack of functional study, our results suggest that genetic variants of CHGB may be associated with SPEM abnormality and provide useful preliminary information for further study.

• 한국축산식품학회:학술대회논문집
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• 한국축산식품학회 1997년도 제18차 정기총회 및 학술발표회
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• pp.7-9
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• 1997

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVI)
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• pp.336-336
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• 2005

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVI)
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• pp.335-335
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• 2005