Efficiency of Xist-mediated silencing on autosomes is linked to chromosomal domain organisation

BACKGROUND: X chromosome inactivation, the mechanism used by mammals to equalise dosage of X-linked genes in XX females relative to XY males, is triggered by chromosome-wide localisation of a cis-acting non-coding RNA, Xist. The mechanism of Xist RNA spreading and Xist-dependent silencing is poorly understood. A large body of evidence indicates that silencing is more efficient on the X chromosome than on autosomes, leading to the idea that the X chromosome has acquired sequences that facilitate propagation of silencing. LINE-1 (L1) repeats are relatively enriched on the X chromosome and have been proposed as candidates for these sequences. To determine the requirements for efficient silencing we have analysed the relationship of chromosome features, including L1 repeats, and the extent of silencing in cell lines carrying inducible Xist transgenes located on one of three different autosomes. RESULTS: Our results show that the organisation of the chromosome into large gene-rich and L1-rich domains is a key determinant of silencing efficiency. Specifically genes located in large gene-rich domains with low L1 density are relatively resistant to Xist-mediated silencing whereas genes located in gene-poor domains with high L1 density are silenced more efficiently. These effects are observed shortly after induction of Xist RNA expression, suggesting that chromosomal domain organisation influences establishment rather than long-term maintenance of silencing. The X chromosome and some autosomes have only small gene-rich L1-depleted domains and we suggest that this could confer the capacity for relatively efficient chromosome-wide silencing. CONCLUSIONS: This study provides insight into the requirements for efficient Xist mediated silencing and specifically identifies organisation of the chromosome into gene-rich L1-depleted and gene-poor L1-dense domains as a major influence on the ability of Xist-mediated silencing to be propagated in a continuous manner in cis

Semantic analysis of field sports video using a petri-net of audio-visual concepts

The most common approach to automatic summarisation and highlight detection in sports video is to train an automatic classifier to detect semantic highlights based on occurrences of low-level features such as action replays, excited commentators or changes in a scoreboard. We propose an alternative approach based on the detection of perception concepts (PCs) and the construction of Petri-Nets which can be used for both semantic description and event detection within sports videos. Low-level algorithms for the detection of perception concepts using visual, aural and motion characteristics are proposed, and a series of Petri-Nets composed of perception concepts is formally defined to describe video content. We call this a Perception Concept Network-Petri Net (PCN-PN) model. Using PCN-PNs, personalized high-level semantic descriptions of video highlights can be facilitated and queries on high-level semantics can be achieved. A particular strength of this framework is that we can easily build semantic detectors based on PCN-PNs to search within sports videos and locate interesting events. Experimental results based on recorded sports video data across three types of sports games (soccer, basketball and rugby), and each from multiple broadcasters, are used to illustrate the potential of this framework

Fatty-acid uptake in prostate cancer cells using dynamic microfluidic raman technology

It is known that intake of dietary fatty acid (FA) is strongly correlated with prostate cancer progression but is highly dependent on the type of FAs. High levels of palmitic acid (PA) or arachidonic acid (AA) can stimulate the progression of cancer. In this study, a unique experimental set-up consisting of a Raman microscope, coupled with a commercial shear-flow microfluidic system is used to monitor fatty acid uptake by prostate cancer (PC-3) cells in real-time at the single cell level. Uptake of deuterated PA, deuterated AA, and the omega-3 fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were monitored using this new system, while complementary flow cytometry experiments using Nile red staining, were also conducted for the validation of the cellular lipid uptake. Using this novel experimental system, we show that DHA and EPA have inhibitory effects on the uptake of PA and AA by PC-3 cells

The Use of Gamma-ray Bursts as Direction and Time Markers in SETI Strategies

When transmitting a signal over a large distance it is more efficient to send a brief beamed signal than a continuous omni-directional transmission but this requires that the receiver knows where and when to look for the transmission. For SETI, the use of various natural phenomena has previously been suggested to achieve the desired synchronization. Here it is proposed that gamma-ray bursts may well the best ``synchronizers'' of all currently known phenomena due to their large intrinsic luminosities, high occurrence rate, isotropic sky distribution, large distance from the Galaxy, short duration, and easy detectability. For targeted searches, precise positions for gamma-ray bursts are required together with precise distance measurements to a target star. The required burst position determinations are now starting to be obtained, aided in large part by the discovery of optical afterglows. Good distance measurements are currently available from Hipparcos and even better measurements should be provided by spacecraft now being developed. For non-targeted searches, positional accuracies simply better than a detector's field of view may suffice but the time delay between the detection of a gamma-ray burst and the reception of the transmitted signal cannot be predicted in an obvious way.Comment: 8 pages, accepted for publication in PAS

Reversible Metal-Semiconductor Transition of ssDNA-Decorated Single-Walled Carbon Nanotubes

A field effect transistor (FET) measurement of a SWNT shows a transition from a metallic one to a p-type semiconductor after helical wrapping of DNA. Water is found to be critical to activate this metal-semiconductor transition in the SWNT-ssDNA hybrid. Raman spectroscopy confirms the same change in electrical behavior. According to our ab initio calculations, a band gap can open up in a metallic SWNT with wrapped ssDNA in the presence of water molecules due to charge transfer.Comment: 13 pages, 6 figure

Observation of generalized synchronization of chaos in a driven chaotic system

We report on the experimental observation of the generalized synchronization of chaos in a real physical system. We show that under a nonlinear resonant interaction, the chaotic dynamics of a single mode laser can become functionally related to that of a chaotic driving signal and furthermore as the coupling strength is further increased, the chaotic dynamics of the laser approaches that of the driving signal.Tang, D. Dykstra, R. ; Hamilton, M. ; Heckenberg, N

An architecture for IEEE 802.16 MAC scheduler design

Copyright © 2007 IEEEThe scheduling algorithm for IEEE 802.16 broadband wireless access system has been left open in the standard. In this paper, we consider three criteria that we have identified as important criteria for an 802.16 scheduler: Service Type differentiation, dynamic sub-frame partition and Subscriber Station differentiation. We investigate the scheduler design from a general perspective, based on these three criteria