Oscope.Author ContributionsConceived and designed the experiments: JHL JAF. Performed the experiments: JHL. Analyzed the data: JHL JAF. Contributed reagents/ materials/analysis tools: JHL JAF. Wrote the paper: JHL JAF.
The activation of the transcription factor NF-kB leads to a wide range of cellular responses including proliferation, apoptosis, and angiogenesis. More than 500 genes have been reported to be expressed upon activation of NF-kB including the immuneresponsive and NF-kB regulatory genes in addition to proliferation-, invasion/metastasis- and angiogenesis-promoting genes [1,2,3,4,5,6]. While NF-kB activation in normal cells is mostly transient, it is constitutively activated in malignant tumors and stimulates the growth of malignant cells [1,7,8]. Thus, the control of NF-kB activity is critical in cancer therapies. NF-kB is activated through two main pathways known as the classical (canonical) and the non-classical (non-canonical) pathways. In the classical pathway, NF-kB is activated by TNFa, 
IL1b, or bacterial products [3,4,7,9,10,11,12,13,14,15,16]. IL-1 stimulation results in the formation of a signaling complex composed of TRAF6, TAK1, and MEKK3 [17] which leads to the activation of TAK1 and MEKK3 [18]. IKK complex, which is a heterotrimer of IKKa, IKKb, and NEMO (IKKc) in the classical pathway, is recruited to the complex, and NEMO is ubiquitinated leading to the activation of IKK [19]. Activated IKK then phosphorylates IkBa in the NF-kB complex, which is a heterotrimer of IkBa, p50, and p65 (RelA) [20,21]. The phosphorylated IkBa is subsequently ubiquitinated and subjects to proteasomal degradation leading to the release of inhibition on NF-kB by IkBa [22]. Thus activatedNF-kB translocates to the nucleus, where it binds to the promoter or enhancer region of target genes. Interestingly, the concentration of nuclear NF-kB is known to Epigenetics oscillate by the application of TNFa. The analysis of a population of cells showed damped oscillation of nuclear NF-kB with a period of 1.5? hrs [17,23]. Damped oscillation of NF-kB was also reported in a single cell analysis with a period of 1? hrs using RelA fused to red fluorescent protein [24,25]. It has been reported that changes in the oscillation pattern of nuclear NF-kB led to changes in the gene expression pattern. Hoffmann et al. reported that shorter and longer applications of TNFa resulted in nonoscillating and oscillating nuclear NF-kB, respectively, and this difference led to the expression of quick and slow responsive genes [23]. It has also been reported that the change in the oscillation frequency, which was mimicked by changing the interval of pulsatile TNFa stimulation, resulted in different gene expression patterns [24]. Thus, it is thought that the oscillation pattern of nuclear NF-kB is important to the inhibitor selection of expressed genes [24,26,27]. According to experimental observations on the oscillation of nuclear NF-kB, nearly 40 computational models have been published. Among them, a model by Hoffmann et al. was the first to show the oscillation of nuclear NF-kB in computer simulation [23]. Their computational model included continuous activation of IKK, degradation of IkBa, shuttling of NF-kB3D Spatial Effect on Nuclear NF-kB Oscillationbetween the cytoplasm and nucleus, and NF-kB-dependent gene expression and protein synthesis of IkBa. Their simulations showed good agreement with experimental observations. After Hoffmann’s model, many models have been published showing.Oscope.Author ContributionsConceived and designed the experiments: JHL JAF. Performed the experiments: JHL. Analyzed the data: JHL JAF. Contributed reagents/ materials/analysis tools: JHL JAF. Wrote the paper: JHL JAF.
The activation of the transcription factor NF-kB leads to a wide range of cellular responses including proliferation, apoptosis, and angiogenesis. More than 500 genes have been reported to be expressed upon activation of NF-kB including the immuneresponsive and NF-kB regulatory genes in addition to proliferation-, invasion/metastasis- and angiogenesis-promoting genes [1,2,3,4,5,6]. While NF-kB activation in normal cells is mostly transient, it is constitutively activated in malignant tumors and stimulates the growth of malignant cells [1,7,8]. Thus, the control of NF-kB activity is critical in cancer therapies. NF-kB is activated through two main pathways known as the classical (canonical) and the non-classical (non-canonical) pathways. In the classical pathway, NF-kB is activated by TNFa, IL1b, or bacterial products [3,4,7,9,10,11,12,13,14,15,16]. IL-1 stimulation results in the formation of a signaling complex composed of TRAF6, TAK1, and MEKK3 [17] which leads to the activation of TAK1 and MEKK3 [18]. IKK complex, which is a heterotrimer of IKKa, IKKb, and NEMO (IKKc) in the classical pathway, is recruited to the complex, and NEMO is ubiquitinated leading to the activation of IKK [19]. Activated IKK then phosphorylates IkBa in the NF-kB complex, which is a heterotrimer of IkBa, p50, and p65 (RelA) [20,21]. The phosphorylated IkBa is subsequently ubiquitinated and subjects to proteasomal degradation leading to the release of inhibition on NF-kB by IkBa [22]. Thus activatedNF-kB translocates to the nucleus, where it binds to the promoter or enhancer region of target genes. Interestingly, the concentration of nuclear NF-kB is known to oscillate by the application of TNFa. The analysis of a population of cells showed damped oscillation of nuclear NF-kB with a period of 1.5? hrs [17,23]. Damped oscillation of NF-kB was also reported in a single cell analysis with a period of 1? hrs using RelA fused to red fluorescent protein [24,25]. It has 
been reported that changes in the oscillation pattern of nuclear NF-kB led to changes in the gene expression pattern. Hoffmann et al. reported that shorter and longer applications of TNFa resulted in nonoscillating and oscillating nuclear NF-kB, respectively, and this difference led to the expression of quick and slow responsive genes [23]. It has also been reported that the change in the oscillation frequency, which was mimicked by changing the interval of pulsatile TNFa stimulation, resulted in different gene expression patterns [24]. Thus, it is thought that the oscillation pattern of nuclear NF-kB is important to the selection of expressed genes [24,26,27]. According to experimental observations on the oscillation of nuclear NF-kB, nearly 40 computational models have been published. Among them, a model by Hoffmann et al. was the first to show the oscillation of nuclear NF-kB in computer simulation [23]. Their computational model included continuous activation of IKK, degradation of IkBa, shuttling of NF-kB3D Spatial Effect on Nuclear NF-kB Oscillationbetween the cytoplasm and nucleus, and NF-kB-dependent gene expression and protein synthesis of IkBa. Their simulations showed good agreement with experimental observations. After Hoffmann’s model, many models have been published showing.