YY1 is autoregulated through its own DNA-binding sites

<p>Abstract</p> <p>Background</p> <p>The transcription factor Yin Yang 1 (YY1) is a ubiquitously expressed, multifunctional protein that controls a large number of genes and biological processes in vertebrates. As a general transcription factor, the proper levels of YY1 protein need to be maintained for the normal function of cells and organisms. However, the mechanism for the YY1 homeostasis is currently unknown.</p> <p>Results</p> <p>The current study reports that the YY1 gene locus of all vertebrates contains a cluster of its own DNA-binding sites within the 1^stintron. The intact structure of these DNA-binding sites is absolutely necessary for transcriptional activity of the YY1 promoter. In an inducible cell line system that over-expresses an exogenous YY1 gene, the overall increased levels of YY1 protein caused a reduction in transcription levels of the endogenous YY1 gene. Reversion to the normal levels of YY1 protein restored the transcriptional levels of the endogenous YY1 to normal levels. This homeostatic response was also mediated through its cluster of YY1 binding sites.</p> <p>Conclusion</p> <p>Taken together, the transcriptional level of YY1 is self-regulated through its internal DNA-binding sites. This study identifies YY1 as the first known autoregulating transcription factor in mammalian genomes.</p

Identification of an antisense transcript to ZIM2 in the primate lineage

In this study, we identified an antisense transcript to ZIM2 (zinc finger imprinted gene 2) in the human, called ZIM2as. Sequence analysis of the 110 kb region spanned by this transcript revealed a cluster of tandemly repeated sequence in the human, orangutan, and chimpanzee as well as a loss of approximately 70 kb from the corresponding region in the rhesus. The homologous region in most mammals contains a cluster of olfactory receptor (OLFR) genes, but this gene cluster has been lost from the primate lineage. Expression analyses confirmed that ZIM2as is expressed in the human brain and testis. Two CpG islands near the promoter region of ZIM2as showed different methylation patterns in these three species. The CpG island distal to ZIM2as showed an allele-specific DNA methylation pattern in the human testis, while the CpG island proximal to the ZIM2as promoter showed a mosaic methylation pattern in the chimpanzee. The methylation status of several nearby zinc finger genes was unchanged among the primates tested. Overall, this study reports the presence of a previously unreported primate-specific antisense transcript in the PEG3 imprinted domain, suggesting that the formation of this transcript may coincide with the loss of the OLFR cluster

Two evolutionarily conserved sequence elements for Peg3/Usp29 transcription

<p>Abstract</p> <p>Background</p> <p>Two evolutionarily Conserved Sequence Elements, CSE1 and CSE2 (YY1 binding sites), are found within the 3.8-kb CpG island surrounding the bidirectional promoter of two imprinted genes, <it>Peg3 </it>(Paternally expressed gene 3) and <it>Usp29 </it>(Ubiquitin-specific protease 29). This CpG island is a likely ICR (Imprinting Control Region) that controls transcription of the 500-kb genomic region of the <it>Peg3 </it>imprinted domain.</p> <p>Results</p> <p>The current study investigated the functional roles of CSE1 and CSE2 in the transcriptional control of the two genes, <it>Peg3 </it>and <it>Usp29</it>, using cell line-based promoter assays. The mutation of 6 YY1 binding sites (CSE2) reduced the transcriptional activity of the bidirectional promoter in the <it>Peg3 </it>direction in an orientation-dependent manner, suggesting an activator role for CSE2 (YY1 binding sites). However, the activity in the <it>Usp29 </it>direction was not detectable regardless of the presence/absence of YY1 binding sites. In contrast, mutation of CSE1 increased the transcriptional activity of the promoter in both the <it>Peg3 </it>and <it>Usp29 </it>directions, suggesting a potential repressor role for CSE1. The observed repression by CSE1 was also orientation-dependent. Serial mutational analyses further narrowed down two separate 6-bp-long regions within the 42-bp-long CSE1 which are individually responsible for the repression of <it>Peg3 </it>and <it>Usp29</it>.</p> <p>Conclusion</p> <p>CSE2 (YY1 binding sites) functions as an activator for <it>Peg3 </it>transcription, while CSE1 acts as a repressor for the transcription of both <it>Peg3 </it>and <it>Usp29</it>.</p

Imprinting control region (ICR) of the Peg3 domain

The imprinting and transcription of the 500 kb genomic region surrounding the mouse Peg3 is predicted to be regulated by the Peg3-differentially methylated region (DMR). In the current study, this prediction was tested using a mutant mouse line lacking this potential imprinting control region (ICR). At the organismal level, paternal and maternal transmission of this knockout (KO) allele caused either reduced or increased growth rates in the mouse, respectively. In terms of the imprinting control, the paternal transmission of the KO allele resulted in bi-allelic expression of the normally maternally expressed Zim2, whereas the maternal transmission switched the transcriptionally dominant allele for Zfp264 (paternal to maternal). However, the allele-specific DNA methylation patterns of the DMRs of Peg3, Zim2 and Zim3 were not affected in the mice that inherited the KO allele either paternally or maternally. In terms of the transcriptional control, the paternal transmission caused a dramatic down-regulation in Peg3 expression, but overall up-regulation in the other nearby imprinted genes. Taken together, deletion of the Peg3-DMR caused global changes in the imprinting and transcription of the Peg3 domain, confirming that the Peg3-DMR is an ICR for this imprinted domain. © The Author 2012. Published by Oxford University Press. All rights reserved

Perspective and Potential of Smart Optical Materials

The increasing requirements of hyperspectral imaging optics, electro/photo-chromic materials, negative refractive index metamaterial optics, and miniaturized optical components from microscale to quantum-scale optics have all contributed to new features and advancements in optics technology. Development of multifunctional capable optics has pushed the boundaries of optics into new fields that require new disciplines and materials to maximize the potential benefits. The purpose of this study is to understand and show the fundamental materials and fabrication technology for field-controlled spectrally active optics (referred to as smart optics) that are essential for future industrial, scientific, military, and space applications, such as membrane optics, light detection and ranging (LIDAR) filters, windows for sensors and probes, telescopes, spectroscopes, cameras, light valves, light switches, and flat-panel displays. The proposed smart optics are based on the Stark and Zeeman effects in materials tailored with quantum dot arrays and thin films made from readily polarizable materials via ferroelectricity or ferromagnetism. Bound excitonic states of organic crystals are also capable of optical adaptability, tunability, and reconfigurability. To show the benefits of smart optics, this paper reviews spectral characteristics of smart optical materials and device technology. Experiments testing the quantum-confined Stark effect, arising from rare earth element doping effects in semiconductors, and applied electric field effects on spectral and refractive index are discussed. Other bulk and dopant materials were also discovered to have the same aspect of shifts in spectrum and refractive index. Other efforts focus on materials for creating field-controlled spectrally smart active optics (FCSAO) on a selected spectral range. Surface plasmon polariton transmission of light through apertures is also discussed, along with potential applications. New breakthroughs in micro scale multiple zone plate optics as a micro convex lens are reviewed, along with the newly discovered pseudo-focal point not predicted with conventional optics modeling. Micron-sized solid state beam scanner chips for laser waveguides are reviewed as well

Yoga Training Improves Metabolic Parameters in Obese Boys

Yoga has been known to have stimulatory or inhibitory effects on the metabolic parameters and to be uncomplicated therapy for obesity. The purpose of the present study was to test the effect of an 8-week of yoga-asana training on body composition, lipid profile, and insulin resistance (IR) in obese adolescent boys. Twenty volunteers with body mass index (BMI) greater than the 95th percentile were randomly assigned to yoga (age 14.7±0.5 years, n=10) and control groups (age 14.6±1.0 years, n=10). The yoga group performed exercises three times per week at 40~60% of heart-rate reserve (HRR) for 8 weeks. IR was determined with the homeostasis model assessment of insulin resistance (HOMA-IR). After yoga training, body weight, BMI, fat mass (FM), and body fat % (BF %) were significantly decreased, and fat-free mass and basal metabolic rate were significantly increased than baseline values. FM and BF % were significantly improved in the yoga group compared with the control group (p\u3c0.05). Total cholesterol (TC) was significantly decreased in the yoga group (p\u3c0.01). HDL-cholesterol was decreased in both groups (p\u3c0.05). No significant changes were observed between or within groups for triglycerides, LDL-cholesterol, glucose, insulin, and HOMA-IR. Our findings show that an 8-week of yoga training improves body composition and TC levels in obese adolescent boys, suggesting that yoga training may be effective in controlling some metabolic syndrome factors in obese adolescent boys

Traveltime calculations from frequency-domain downward-continuation algorithms

We present a new, fast 3D traveltime calculation algorithm that employs existing frequency-domain waveequation downward-continuation software. By modifying such software to solve for a few complex (rather than real) frequencies, we are able to calculate not only the first arrival and the approximately most energetic traveltimes at each depth point but also their corresponding amplitudes.We compute traveltimes by either taking the logarithm of displacements obtained by the oneway wave equation at a frequency or calculating derivatives of displacements numerically. Amplitudes are estimated from absolute value of the displacement at a frequency. By using the one-way downgoing wave equation, we also circumvent generating traveltimes corresponding to near-surface upcoming head waves not often needed in migration.We compare the traveltimes computed by our algorithm with those obtained by picking the most energetic arrivals from finite-difference solutions of the one-way wave equation, and show that our traveltime calculation method yields traveltimes comparable to solutions of the one-way wave equation. We illustrate the accuracy of our traveltime algorithm by migrating the 2D IFP Marmousi and the 3D SEG/EAGE salt models.This work was financially supported by National Laboratory Project of Ministry of Science and Technology, Brain Korea 21 project of theKorea Ministry of Education, and grant No. R03- 2000-000-00003-0 from the Basic Research Program of the Korea Science & Engineering Foundation

Contention-Aware Adaptive Data Rate for Throughput Optimization in LoRaWAN

In Long Range Wide Area Network (LoRaWAN), the data rate of the devices can be adjusted to optimize the throughput by changing the spreading factor. However, the adaptive data rate has to be carefully utilized because the collision probability, which directly affects the throughput, is changed according to the use of spreading factors. Namely, the greater the number of devices using the same spreading factor, the greater the probability of collision, resulting in a decrease of total throughput. Nevertheless, in the current system, the only criteria to determine the data rate to be adjusted is a link quality. Therefore, contention-aware adaptive data rate should be designed for the throughput optimization. Here, the number of devices which can use a specific data rate is restricted, and accordingly the optimization problem can be regarded as constrained optimization. To find an optimal solution, we adopt the gradient projection method. By adjusting the data rate based on the retrieved set of optimal data rate, the system performance can be significantly improved. The numerical results demonstrate that the proposed method outperforms the comparisons regardless of the number of devices and is close to the theoretical upper bound of throughput

Impact of MAC Delay on AUV Localization: Underwater Localization Based on Hyperbolic Frequency Modulation Signal

Medium Access Control (MAC) delay which occurs between the anchor node’s transmissions is one of the error sources in underwater localization. In particular, in AUV localization, the MAC delay significantly degrades the ranging accuracy. The Cramer-Rao Low Bound (CRLB) definition theoretically proves that the MAC delay significantly degrades the localization performance. This paper proposes underwater localization combined with multiple access technology to decouple the localization performance from the MAC delay. Towards this goal, we adopt hyperbolic frequency modulation (HFM) signal that provides multiplexing based on its good property, high-temporal correlation. Owing to the multiplexing ability of the HFM signal, the anchor nodes can transmit packets without MAC delay, i.e., simultaneous transmission is possible. In addition, the simulation results show that the simultaneous transmission is not an optional communication scheme, but essential for the localization of mobile object in underwater

Contention-Aware Adaptive Data Rate for Throughput Optimization in LoRaWAN

In Long Range Wide Area Network (LoRaWAN), the data rate of the devices can be adjusted to optimize the throughput by changing the spreading factor. However, the adaptive data rate has to be carefully utilized because the collision probability, which directly affects the throughput, is changed according to the use of spreading factors. Namely, the greater the number of devices using the same spreading factor, the greater the probability of collision, resulting in a decrease of total throughput. Nevertheless, in the current system, the only criteria to determine the data rate to be adjusted is a link quality. Therefore, contention-aware adaptive data rate should be designed for the throughput optimization. Here, the number of devices which can use a specific data rate is restricted, and accordingly the optimization problem can be regarded as constrained optimization. To find an optimal solution, we adopt the gradient projection method. By adjusting the data rate based on the retrieved set of optimal data rate, the system performance can be significantly improved. The numerical results demonstrate that the proposed method outperforms the comparisons regardless of the number of devices and is close to the theoretical upper bound of throughput