An Integrated Routing and Rate Adaptation Framework for Multi-rate Multi-hop Wireless Networks

International audienceIn this paper, we propose a new integrated framework for joint routing and rate adaptation in multi-rate multi-hop wireless networks. Unlike many previous efforts, our framework considers several factors that affect end-to-end performance. Among these factors, the framework takes into account the effect of the relative positions of the links on a path when choosing the rates of operation and the importance of avoiding congested areas. The key element of our framework is a new comprehensive path metric that we call ETM (for expected transmission cost in multi-rate wireless networks). We analytically derive the ETM metric. We show that the ETM metric can be used to determine the best end-to-end path with a greedy routing approach. We also show that the metric can be used to dynamically select the best transmission rate for each link on the path via a dynamic programming approach. We implement the ETM-framework on an indoor wireless mesh network and compare its performance with that of frameworks based on the popular ETT and the recently proposed ETOP metrics. Our experiments demonstrate that the ETM-framework can yield throughput improvements of up to 253 and 368 % as compared with the ETT and ETOP frameworks

The Effect of Transposable Element Insertions on Gene Expression Evolution in Rodents

Background:Many genomes contain a substantial number of transposable elements (TEs), a few of which are known to be involved in regulating gene expression. However, recent observations suggest that TEs may have played a very important role in the evolution of gene expression because many conserved non-genic sequences, some of which are know to be involved in gene regulation, resemble TEs. Results:Here we investigate whether new TE insertions affect gene expression profiles by testing whether gene expression divergence between mouse and rat is correlated to the numbers of new transposable elements inserted near genes. We show that expression divergence is significantly correlated to the number of new LTR and SINE elements, but not to the numbers of LINEs. We also show that expression divergence is not significantly correlated to the numbers of ancestral TEs in most cases, which suggests that the correlations between expression divergence and the numbers of new TEs are causal in nature. We quantify the effect and estimate that TE insertion has accounted for ~20% (95% confidence interval: 12% to 26%) of all expression profile divergence in rodents. Conclusions:We conclude that TE insertions may have had a major impact on the evolution of gene expression levels in rodents

Algorithms for locating extremely conserved elements in multiple sequence alignments

<p>Abstract</p> <p>Background</p> <p>In 2004, Bejerano <it>et al</it>. announced the startling discovery of hundreds of "ultraconserved elements", long genomic sequences perfectly conserved across human, mouse, and rat. Their announcement stimulated a flurry of subsequent research.</p> <p>Results</p> <p>We generalize the notion of ultraconserved element in a natural way from extraordinary human-rodent conservation to extraordinary conservation over an arbitrary set of species. We call these "Extremely Conserved Elements". There is a linear time algorithm to find all such Extremely Conserved Elements in any multiple sequence alignment, provided that the conservation is required to be across all the aligned species. For the general case of conservation across an arbitrary subset of the aligned species, we show that the question of whether there exists an Extremely Conserved Element is <it>NP</it>-complete. We illustrate the linear time algorithm by cataloguing all 177 Extremely Conserved Elements in the currently available 44-vertebrate whole-genome alignment, and point out some of the characteristics of these elements.</p> <p>Conclusions</p> <p>The <it>NP</it>-completeness in the case of conservation across an arbitrary subset of the aligned species implies that it is unlikely an efficient algorithm exists for this general case. Despite this fact, for the interesting case of conservation across all or most of the aligned species, our algorithm is efficient enough to be practical. The 177 Extremely Conserved Elements that we catalog demonstrate many of the characteristics of the original ultraconserved elements of Bejerano <it>et al</it>.</p

An integrated priority-based cell attenuation model for dynamic cell sizing

A new, robust integrated priority-based cell attenuation model for dynamic cell sizing is proposed and simulated using real mobile traffic data.The proposed model is an integration of two main components; the modified virtual community – parallel genetic algorithm (VC-PGA) cell priority selection module and the evolving fuzzy neural network (EFuNN) mobile traffic prediction module.The VC-PGA module controls the number of cell attenuations by ordering the priority for the attenuation of all cells based on the level of mobile level of mobile traffic within each cell.The EFuNN module predicts the traffic volume of a particular cell by extracting and inserting meaningful rules through incremental, supervised real-time learning.The EFuNN module is placed in each cell and the output, the predicted mobile traffic volume of the particular cell, is sent to local and virtual community servers in the VC-PGA module.The VC-PGA module then assigns priorities for the size attenuation of all cells within the network, based on the predicted mobile traffic levels from the EFuNN module at each cell.The performance of the proposed module was evaluated on five adjacent cells in Selangor, Malaysia. Real-time predicted mobile traffic from the EFuNN structure was used to control the size of all the cells.Results obtained demonstrate the robustness of the integrated module in recognizing the temporal pattern of the mobile traffic and dynamically controlling the cell size in order to reduce the number of calls dropped

Novel insights into host-fungal pathogen interactions derived from live-cell imaging

Acknowledgments The authors acknowledge funding from the Wellcome Trust (080088, 086827, 075470 and 099215) including a Wellcome Trust Strategic Award for Medical Mycology and Fungal Immunology 097377 and FP7-2007–2013 grant agreement HEALTH-F2-2010-260338–ALLFUN to NARG.Peer reviewedPublisher PD

Noninvasive Monitoring of Placenta-Specific Transgene Expression by Bioluminescence Imaging

BACKGROUND: Placental dysfunction underlies numerous complications of pregnancy. A major obstacle to understanding the roles of potential mediators of placental pathology has been the absence of suitable methods for tissue-specific gene manipulation and sensitive assays for studying gene functions in the placentas of intact animals. We describe a sensitive and noninvasive method of repetitively tracking placenta-specific gene expression throughout pregnancy using lentivirus-mediated transduction of optical reporter genes in mouse blastocysts. METHODOLOGY/PRINCIPAL FINDINGS: Zona-free blastocysts were incubated with lentivirus expressing firefly luciferase (Fluc) and Tomato fluorescent fusion protein for trophectoderm-specific infection and transplanted into day 3 pseudopregnant recipients (GD3). Animals were examined for Fluc expression by live bioluminescence imaging (BLI) at different points during pregnancy, and the placentas were examined for tomato expression in different cell types on GD18. In another set of experiments, blastocysts with maximum photon fluxes in the range of 2.0E+4 to 6.0E+4 p/s/cm(2)/sr were transferred. Fluc expression was detectable in all surrogate dams by day 5 of pregnancy by live imaging, and the signal increased dramatically thereafter each day until GD12, reaching a peak at GD16 and maintaining that level through GD18. All of the placentas, but none of the fetuses, analyzed on GD18 by BLI showed different degrees of Fluc expression. However, only placentas of dams transferred with selected blastocysts showed uniform photon distribution with no significant variability of photon intensity among placentas of the same litter. Tomato expression in the placentas was limited to only trophoblast cell lineages. CONCLUSIONS/SIGNIFICANCE: These results, for the first time, demonstrate the feasibility of selecting lentivirally-transduced blastocysts for uniform gene expression in all placentas of the same litter and early detection and quantitative analysis of gene expression throughout pregnancy by live BLI. This method may be useful for a wide range of applications involving trophoblast-specific gene manipulations in utero

CASZ1b, the Short Isoform of CASZ1 Gene, Coexpresses with CASZ1a during Neurogenesis and Suppresses Neuroblastoma Cell Growth

In Drosophila, the CASZ1 (castor) gene encodes a zinc finger transcription factor and is a neural fate-determination gene. In mammals, the CASZ1 gene encodes two major isoforms, CASZ1a with 11 zinc fingers and CASZ1b with 5 zinc fingers. CASZ1b is more evolutionally conserved since it is the only homologue found in drosophila and Xenopus. Our previous study showed that full length CASZ1 (CASZ1a) functions to suppress growth in neuroblastoma tumor. However, the function of CASZ1b isoform in mammals is unknown. In this study, realtime PCR analyses indicate that mouse CASZ1b (mCASZ1b) is dynamically expressed during neurogenesis. CASZ1b and CASZ1a co-exist in all the neuronal tissues but exhibit distinct expression patterns spatially and temporally during brain development. CASZ1b and CASZ1a expression is coordinately upregulated by the differentiation agent Retinoic Acid, as well as agents that modify the epigenome in neural crest derived neuroblastoma cell lines. In contrast CASZ1b is down regulated while CASZ1a is upregulated by agents that raise intracellular cAMP levels. CASZ1b and CASZ1a have no synergistic or antagonistic activities on the regulation of their target NGFR gene transcription. Specific restoration of CASZ1b in NB cells suppresses tumor growth in vitro and in vivo. Consistent with its function role, we find that low CASZ1b expression is significantly associated with decreased survival probability of neuroblastoma patients (p<0.02). This study indicates that although their mechanisms of regulation may be distinct, both CASZ1b and CASZ1a have largely redundant but critical roles in suppressing tumor cell growth

Association of a functional microsatellite within intron 1 of the BMP5 gene with susceptibility to osteoarthritis

<p>Abstract</p> <p>Background</p> <p>In a previous study carried out by our group, the genotyping of 36 microsatellite markers from within a narrow interval of chromosome 6p12.3-q13 generated evidence for linkage and for association to female hip osteoarthritis (OA), with the most compelling association found for a marker within intron 1 of the bone morphogenetic protein 5 gene (<it>BMP5</it>). In this study, we aimed to further categorize the association of variants within intron 1 of <it>BMP5 </it>with OA through an expanded genetic association study of the intron and subsequent functional analysis of associated polymorphisms.</p> <p>Methods</p> <p>We genotyped 18 common polymorphisms including 8 microsatellites and 9 single nucleotide polymorphisms (SNPs) and 1 insertion/deletion (INDEL) from within highly conserved regions between human and mouse within intron 1 of <it>BMP5</it>. These markers were then tested for association to OA by a two-stage approach in which the polymorphisms were initially genotyped in a case-control cohort comprising 361 individuals with associated polymorphisms (<it>P </it>≤ 0.05) then genotyped in a second case-control cohort comprising 1185 individuals.</p> <p>Results</p> <p>Two <it>BMP5 </it>intron 1 polymorphisms demonstrated association in the combined case-control cohort of 1546 individuals (765 cases and 781 controls): microsatellite D6S1276 (<it>P </it>= 0.018) and SNP rs921126 (<it>P </it>= 0.013). Functional analyses in osteoblastic, chondrocytic, and adipocytic cell lines indicated that allelic variants of D6S1276 have significant effects on the transcriptional activity of the <it>BMP5 </it>promoter <it>in vitro</it>.</p> <p>Conclusion</p> <p>Variability in gene expression of <it>BMP5 </it>may be an important contributor to OA genetic susceptibility.</p