• Journal of Microbiology and Biotechnology
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• 제26권8호
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• pp.1375-1382
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• 2016

The extremely halophilic archaeon Halobacterium noricense is a member of the genus Halobacterium. Strain CBA1132 (= KCCM 43183, JCM 31150) was isolated from solar salt. The genome of strain CBA1132 assembled with 4 contigs, including three rRNA genes, 44 tRNA genes, and 3,208 open reading frames. Strain CBA1132 had nine putative CRISPRs and the genome contained genes encoding metal resistance determinants: copper-translocating P-type ATPase (CtpA), arsenical pump-driving ATPase (ArsA), arsenate reductase (ArsC), and arsenical resistance operon repressor (ArsR). Strain CBA1132 was related to Halobacterium noricense, with 99.2% 16S rRNA gene sequence similarity. Based on the comparative genomic analysis, strain CBA1132 has distinctly evolved; moreover, essential genes related to nitrogen metabolism were only detected in the genome of strain CBA1132 among the reported genomes in the genus Halobacterium. This genome sequence of Halobacterium noricense CBA1132 may be of use in future molecular biological studies.

• Reproductive and Developmental Biology
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• 제33권1호
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• pp.41-48
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• 2009

Placenta is the main nutrition source for the fetus during pregnancy. Thus, it has a pivotal function in the pregnant process. Many functions of the placenta have been elucidated. An abnormal placenta is associated with a high rate of pregnancy failure in somatic cloned bovine. Differentially expressed genes (DEGs) were examined in a comparison between normal and cloned bovine placenta using annealing control primer (ACP)-based GeneFishing PCR. Using 120 ACPs, nearly 80 genes were identified and the fragments of 42 DEGs were sequenced. 38 of these genes were known genes and four were unknown. To determine the DEGs result, six target clones expressing on one-side of a normal and a clone placenta were selected. Through an analysis of the target genes using the real-time PCR, the expressing pattern was found to be somewhat different from the DEGs. Additionally, several genes appeared with the same expression pattern. Taken together, this suggests that the target genes would be essential for research into what influences the placental formative mechanisms during fetal development.

• BMB Reports
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• 제49권4호
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• pp.199-200
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• 2016

Gene regulation in the brain is essential for long-term plasticity and memory formation. Despite this established notion, the quantitative translational map in the brain during memory formation has not been reported. To systematically probe the changes in protein synthesis during memory formation, our recent study exploited ribosome profiling using the mouse hippocampal tissues at multiple time points after a learning event. Analysis of the resulting database revealed novel types of gene regulation after learning. First, the translation of a group of genes was rapidly suppressed without change in mRNA levels. At later time points, the expression of another group of genes was downregulated through reduction in mRNA levels. This reduction was predicted to be downstream of inhibition of ESR1 (Estrogen Receptor 1) signaling. Overexpressing Nrsn1, one of the genes whose translation was suppressed, or activating ESR1 by injecting an agonist interfered with memory formation, suggesting the functional importance of these findings. Moreover, the translation of genes encoding the translational machineries was found to be suppressed, among other genes in the mouse hippocampus. Together, this unbiased approach has revealed previously unidentified characteristics of gene regulation in the brain and highlighted the importance of repressive controls.

• Animal cells and systems
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• 제7권3호
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• pp.173-186
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• 2003

The transition metal cadmium is a serious occupational and environmental toxin. To inhibit cadmium-induced damage, cells respond by increasing the expression of genes that encode stress-responsive proteins. The metal-regulatory transcription factor 1 (MTF-1) is a key regulator of heavy-metal induced transcription of metallothionein-I and II and other genes in mammals and other metazoans. Transcriptional activation of genes by MTF-1 is mediated through binding to metal-responsive elements in the target gene promoters. Phosphorylation of MTF-1 plays a critical role in the cadmium-inducible transcriptional activation of metallothionein and other responses. Studies using inhibitors indicate that multiple kinases and signal transduction cascades, including those mediated by protein kinase C, tyrosine kinase and casein kinase II, are essential for cadmium-mediated transcriptional activation. In addition, calcium signaling is also involved in regulating metal-activated transcription. In several species, cadmium induces heat shock genes. Recently much progress has been made in elucidating the cellular machinery that regulates this metal-inducible gene expression. This review summarizes these recent advances in understanding the role of some known cadmium-responsive genes and the molecular mechanisms that activate metal-responsive transcription factor, MTF-1.

• 한국미생물·생명공학회지
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• 제21권2호
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• pp.181-186
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• 1993

The functions of n-alkane inducible genes, ALI1 and POX18Cm isolated from Canida maltosa were investigated, using it's distruptants. As a result, it is suggested that ALI1 is essential for n-alkane assimilation in C. mltosa and it regulates genes related to assimilation of n-alkane (ALI1, P450alk POX18Cm) at transcriptional level. Nuclear localization experiments indicated that ALI1 was located and functioned in the nucleus. POX18Cm is considered as a peroxisomal nonspecific lipid transfer protein gene related to n-alkane assimilation in C. maltosa also regulated by ALI1. But it had no significant effect on n-alkane assimilation in C. maltosa.

• Clinical and Experimental Reproductive Medicine
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• 제41권2호
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• pp.47-61
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• 2014

Stored maternal factors in oocytes regulate oocyte differentiation into embryos during early embryonic development. Before zygotic gene activation (ZGA), these early embryos are mainly dependent on maternal factors for survival, such as macromolecules and subcellular organelles in oocytes. The genes encoding these essential maternal products are referred to as maternal effect genes (MEGs). MEGs accumulate maternal factors during oogenesis and enable ZGA, progression of early embryo development, and the initial establishment of embryonic cell lineages. Disruption of MEGs results in defective embryogenesis. Despite their important functions, only a few mammalian MEGs have been identified. In this review we summarize the roles of known MEGs in mouse fertility, with a particular emphasis on oocytes and early embryonic development. An increased knowledge of the working mechanism of MEGs could ultimately provide a means to regulate oocyte maturation and subsequent early embryonic development.

• BMB Reports
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• 제31권5호
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• pp.475-483
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• 1998

Many antibiotics contain partially deoxygenated sugar components that are usually essential for biological activity, affinity, structural stability, and solubility of antibiotics. Gene probes of the biosynthetic genes related with the deoxysugar were obtained from PCR. Primers were designed from the conserved peptide sequences of the known dTDP-D-glucose 4,6-dehydratases, which are the key step enzymes in the biosynthesis of deoxysugar. The primers were applied to amplify parts of dehydratase genes to 27 actinomycetes that produce the metabolites containing deoxysugar as structural constituents. About 180 and 340 bp DNA fragments from all of the actinomycetes were produced by PCR and analyzed by Southern blot and DNA sequencing. The PCR products were used as gene probes to clone the biosynthetic gene clusters for the antibiotic mithramycin, rubradirin, spectinomycin, and elaiophyrin. This method should allow for detecting of the biosynthetic gene clusters of a vast array of secondary metabolites isolated from actinomycetes because of the widespread existence of deoxysugar constituents in secondary metabolites.

• Bioinformatics and Biosystems
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• 제2권1호
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• pp.12-16
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• 2007

DNA repair means a collection of processes that a cell identifies and corrects damage to genome sequence. The DNA repair processes are important because a genome would not be able to maintain its essential cellular functions without the processes. In this research, we make some gene regulatory networks of DNA repair in S. cerevisiae to know how each gene interacts with others. Two approaches are adapted to make the networks; Bayesian Network and ARACNE. After construction of gene regulatory networks based on the two approaches, the two networks are compared to each other to predict which genes have important roles in the DNA repair processes by finding conserved interactions and looking for hubs. In addition, each interaction between genes in the networks is validated with interaction information in S. cerevisiae genome database to support the meaning of predicted interactions in the networks.

• Journal of Microbiology
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• 제40권2호
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• pp.173-177
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• 2002

In order to identify Yawowia lipolytica genes induced by serum, cDNA representational difference analysis was performed using a PCR-select CDNA subtraction method. One of the genes cloned from the subtraction was a gene (YIMBFl) homologous to Saccharomyces cerevisiae MBF1 encoding the coactivator multiprotein bridging factor 1. Disruption of YIMBFl revealed that the gene was net essential for viability, and the Ylmbf△ strain did not show any distinct phenotypic change on solid serum medium. In liquid medium, however. a difference was found in the ability to maintain hyphae induced by serum. This result suggests that the YIMbf1 protein may mediate transcriptional activation of certain genes involved in the hypha fonmation of Y. lipolytica.

• BMB Reports
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• 제52권10호
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• pp.577-588
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• 2019

DNA methylation at CpG sites is an essential epigenetic mark that regulates gene expression during mammalian development and diseases. Methylome refers to the entire set of methylation modifications present in the whole genome. Over the last several years, an increasing number of reports on brain DNA methylome reported the association between aberrant methylation and the abnormalities in the expression of critical genes known to have critical roles during aging and neurodegenerative diseases. Consequently, the role of methylation in understanding neurodegenerative diseases has been under focus. This review outlines the current knowledge of the human brain DNA methylomes during aging and neurodegenerative diseases. We describe the differentially methylated genes from fetal stage to old age and their biological functions. Additionally, we summarize the key aspects and methylated genes identified from brain methylome studies on neurodegenerative diseases. The brain methylome studies could provide a basis for studying the functional aspects of neurodegenerative diseases.