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The co-regulation mechanism of transcription factors in the human gene regulatory network
Kim, Junil,Choi, Minsoo,Kim, Jeong-Rae,Jin, Hua,Kim, V. Narry,Cho, Kwang-Hyun Oxford University Press 2012 Nucleic acids research Vol.40 No.18
<P>The co-regulation of transcription factors (TFs) has been widely observed in various species. Why is such a co-regulation mechanism needed for transcriptional regulation? To answer this question, the following experiments and analyses were performed. First, examination of the human gene regulatory network (GRN) indicated that co-regulation was significantly enriched in the human GRN. Second, mathematical simulation of an artificial regulatory network showed that the co-regulation mechanism was related to the biphasic dose–response patterns of TFs. Third, the relationship between the co-regulation mechanism and the biphasic dose–response pattern was confirmed using microarray experiments examining different time points and different doses of the toxicant tetrachlorodibenzodioxin. Finally, two mathematical models were constructed to mimic highly co-regulated networks (HCNs) and little co-regulated networks (LCNs), and we found that HCNs were more robust to parameter perturbation than LCNs, whereas LCNs were faster in adaptation to environmental changes than HCNs.</P>
Oral Supplementation with Cocoa Extract Reduces UVB-Induced Wrinkles in Hairless Mouse Skin
Kim, Jong-Eun,Song, Dasom,Kim, Junil,Choi, Jina,Kim, Jong Rhan,Yoon, Hyun-Sun,Bae, Jung-Soo,Han, Mira,Lee, Sein,Hong, Ji Sun,Song, Dayoung,Kim, Seong-Jin,Son, Myoung-Jin,Choi, Sang-Woon,Chung, Jin Ho Elsevier 2016 The Journal of investigative dermatology Vol.136 No.5
<P>Cacao beans contain various bioactive phytochemicals that could modify the pathogeneses of certain diseases. Here, we report that oral administration of cacao powder (CP) attenuates UVB-induced skin wrinkling by the regulation of genes involved in dermal matrix production and maintenance. Transcriptome analysis revealed that 788 genes are down-or upregulated in the CP supplemented group, compared with the UVB-irradiated mouse skin controls. Among the differentially expressed genes, cathepsin G and serpin B6c play important roles in UVB-induced skin wrinkle formation. Gene regulatory network analysis also identified several candidate regulators responsible for the protective effects of CP supplementation against UVB-induced skin damage. CP also elicited antiwrinkle effects via inhibition of UVB-induced matrix metalloproteinases-1 expression in both the human skin equivalent model and human dermal fibroblasts. Inhibition of UVB-induced activator protein-1 via CP supplementation is likely to affect the expression of matrix metalloproteinases-1. CP supplementation also downregulates the expression of cathepsin G in human dermal fibroblasts. 5-(3',4'-Dihydroxyphenyl)-gamma-valerolactone, a major in vivo metabolite of CP, showed effects similar to CP supplementation. These results suggest that cacao extract may offer a protective effect against photoaging by inhibiting the breakdown of dermal matrix, which leads to an overall reduction in wrinkle formation.</P>
Kim, Junil,Kim, Tae-Geon,Jung, Sung Hoon,Kim, Jeong-Rae,Park, Taesung,Heslop-Harrison, Pat,Cho, Kwang-Hyun Oxford University Press 2008 Bioinformatics Vol.24 No.13
<P>MOTIVATION: Gene regulatory networks (GRNs) govern cellular differentiation processes and enable construction of multicellular organisms from single cells. Although such networks are complex, there must be evolutionary design principles that shape the network to its present form, gaining complexity from simple modules. RESULTS: To isolate particular design principles, we have computationally evolved random regulatory networks with a preference to result either in hysteresis (switching threshold depending on current state), or in multistationarity (having multiple steady states), two commonly observed dynamical features of GRNs related to differentiation processes. We have analyzed the resulting evolved networks and compared their structures and characteristics with real GRNs reported from experiments. Conclusion: We found that the artificially evolved networks have particular topologies and it was notable that these topologies share important features and similarities with the real GRNs, particularly in contrasting properties of positive and negative feedback loops. We conclude that the structures of real GRNs are consistent with selection to favor one or other of the dynamical features of multistationarity or hysteresis. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.</P>
Kim, Junil,Lee, Onyou,Mo, Young Kyu,Bang, Seungmin,Kang, Jong O,Lee, Hongseok,Nam, Seokho,Kang, Hyoungku The Korea Institute of Applied Superconductivity a 2015 한국초전도저온공학회논문지 Vol.17 No.3
A liquid nitrogen ($LN_2$) is usually used to be a coolant and insulant for a HTS coil system. HTS wires for a superconducting apparatus may be surrounded by gaseous nitrogen ($GN_2$) due to film boiling generated by a quench or voids occurred by electrical breakdown. The increased maximum electric field intensity at $GN_2$ may result in the degradation of dielectric strength of a HTS coil system. In this paper, a study on the dielectric characteristics of a composite insulation system composed of $LN_2$ and $GN_2$ is performed. A sphere-to-plane electrode system made with stainless steel is used to perform the experiments under AC and lightning impulse voltage condition. A sphere electrode is surrounded by $GN_2$ and a plane electrode is immersed into $LN_2$ to conduct dielectric experiments with a composite insulation system. The dielectric experiments are performed according to the level of $LN_2$ from the plane electrode to a sphere electrode. It is found that the dielectric characteristics of a composite insulation system are dependent on the level of $LN_2$ and the field utilization factor of an electrode system.
Fabrication Methods for Nanowire Tunnel FET with Locally Concentrated Silicon-germanium Channel
Junil Lee,Ryoongbin Lee,Sihyun Kim,Euyhwan Park,Hyun-Min Kim,Kitae Lee,Sangwan Kim,Byung-Gook Park 대한전자공학회 2019 Journal of semiconductor technology and science Vol.19 No.1
This paper proposes a method to fabricate tunnel field-effect transistors (TFETs) which have Silicon Germanium (SiGe) nanowire channel with graded Ge concentration on Silicon-on-insulator (SOI). To obtain the concentration-graded SiGe channel, Ge condensation method which is a kind of oxidation is adopted. The rectangular shape of the channel becomes a rounded nanowire through the Ge condensation process. The TFET with the concentration-graded SiGe channel can improve drive current due to a smaller band gap at the Gecondensed surface of the channel compared to Si or non-condensed SiGe channel TFETs. The electrical characteristics of the proposed TFET are verified by technology computer-aided design (TCAD) simulation.
Kim Junil,Lee Hyerim,Yi Sun-Ju,Kim Kyunghwan 생화학분자생물학회 2022 Experimental and molecular medicine Vol.54 No.-
Oxygen, which is necessary for sustaining energy metabolism, is consumed in many biochemical reactions in eukaryotes. When the oxygen supply is insufficient for maintaining multiple homeostatic states at the cellular level, cells are subjected to hypoxic stress. Hypoxia induces adaptive cellular responses mainly through hypoxia-inducible factors (HIFs), which are stabilized and modulate the transcription of various hypoxia-related genes. In addition, many epigenetic regulators, such as DNA methylation, histone modification, histone variants, and adenosine triphosphate-dependent chromatin remodeling factors, play key roles in gene expression. In particular, hypoxic stress influences the activity and gene expression of histone-modifying enzymes, which controls the posttranslational modification of HIFs and histones. This review covers how histone methylation and histone acetylation enzymes modify histone and nonhistone proteins under hypoxic conditions and surveys the impact of epigenetic modifications on gene expression. In addition, future directions in this area are discussed.