Transcriptional regulation in eukaryotic ribosomal protein genes

AbstractUnderstanding ribosomal protein gene regulation provides a good avenue for understanding gene regulatory networks. Even after 5 decades of research on ribosomal protein gene regulation, little is known about how higher eukaryotic ribosomal protein genes are coordinately regulated at the transcriptional level. However, a few recent papers shed some light on this complicated problem

A new measurement of sequence conservation

<p>Abstract</p> <p>Background</p> <p>Understanding sequence conservation is important for the study of sequence evolution and for the identification of functional regions of the genome. Current studies often measure sequence conservation based on every position in contiguous regions. Therefore, a large number of functional regions that contain conserved segments separated by relatively long divergent segments are ignored. Our goal in this paper is to define a new measurement of sequence conservation such that both contiguously conserved regions and discontiguously conserved regions can be detected based on this new measurement. Here and in the following, conserved regions are those regions that share similarity higher than a pre-specified similarity threshold with their homologous regions in other species. That is, conserved regions are good candidates of functional regions and may not be always functional. Moreover, conserved regions may contain long and divergent segments.</p> <p>Results</p> <p>To identify both discontiguously and contiguously conserved regions, we proposed a new measurement of sequence conservation, which measures sequence similarity based only on the conserved segments within the regions. By defining conserved segments using the local alignment tool CHAOS, under the new measurement, we analyzed the conservation of 1642 experimentally verified human functional non-coding regions in the mouse genome. We found that the conservation in at least 11% of these functional regions could be missed by the current conservation analysis methods. We also found that 72% of the mouse homologous regions identified based on the new measurement are more similar to the human functional sequences than the aligned mouse sequences from the UCSC genome browser. We further compared BLAST and discontiguous MegaBLAST with our method. We found that our method picks up many more conserved segments than BLAST and discontiguous MegaBLAST in these regions.</p> <p>Conclusions</p> <p>It is critical to have a new measurement of sequence conservation that is based only on the conserved segments in one region. Such a new measurement can aid the identification of better local "orthologous" regions. It will also shed light on the identification of new types of conserved functional regions in vertebrate genomes <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>.</p

Identification of Three Required Positive Cis-Regulated Inputs of the Sea Urchin Pigment Cell Gene Polyketide Synthase 1

Sea urchin pigment cells are single cells of mesodermal origin embedded in the aboral ectoderm. Strongylocentrotus purpuratus polyketide synthase 1 (Sp-PKS1) is required for the biosynthesis of the echinochrome pigment. Evidence suggests that pigment cells are immune cells. In order to reconstruct the gene regulatory network of pigment cells a bottom-up approach combined with comparative genomics has been used in this study. We compared the cis-regulatory regions of five pigment cell genes, Sp-Pks1, flavin monooxygenase 1, 2, and 3 (Sp-Fmo) and sulfotransferase (Sp-Sult), across three different species, Strongylocentrotus purpuratus, Mesocentrotus franciscanus, and Strongylocentrotus fragilis. The computational tool used was multiple expectation maximization motif elicitation analysis. Thirty cis-regulatory motif candidates were identified, three of which were considered for further analysis. The functionality of these motifs was tested by injecting embryos with a -2KbPks-Gfp DNA construct having one of the three motifs mutagenized. All three motifs resulted to be functional cis-regulatory sequences. Specifically, they contained DNA-binding sites for transcriptional activators of Sp-Pks1

Study of drug release behaviour from HPMC matrix tablets and EC coated matrix reservoir system

Master'sMASTER OF SCIENCE (PHARMACY

Low-Latency Strategies for Service Migration in Fog Computing Enabled Cellular Networks

This chapter presents a fog computing enabled cellular network (FeCN), in which the high user-mobility feature brings critical challenges for service continuity under stringent service requirements. Service migration is promising to fulfill the service continuity during mobility. However, service migration cannot be completed immediately and may lead to situations where the user-experience degrades. For this, a quality-of-service aware service migration strategy is proposed. The method is based on existing handover procedures with newly introduced distributed fog computing resource management scheme to minimize the potential negative effects induced by service migration. The performance of the proposed schemes is evaluated by a case study, where realistic vehicular mobility pattern in the metropolitan network of Luxembourg is used. Results show that low end-to-end latency for vehicular communication can be achieved. During service migration, both the traffic generated by migration and the other traffic (e.g., control information, video) are transmitted via mobile backhaul networks. To balance the performance of the two kinds of traffic, a delay-aware bandwidth slicing scheme is proposed. Simulation results show that, with the proposed method, migration data can be transmitted successfully within a required time threshold, while the latency and jitter for nonmigration traffic with different priorities can be reduced significantly

Semi-Supervised Self-Taught Deep Learning for Finger Bones Segmentation

Segmentation stands at the forefront of many high-level vision tasks. In this study, we focus on segmenting finger bones within a newly introduced semi-supervised self-taught deep learning framework which consists of a student network and a stand-alone teacher module. The whole system is boosted in a life-long learning manner wherein each step the teacher module provides a refinement for the student network to learn with newly unlabeled data. Experimental results demonstrate the superiority of the proposed method over conventional supervised deep learning methods.Comment: IEEE BHI 2019 accepte

Osthole induces G2/M arrest and apoptosis in lung cancer A549 cells by modulating PI3K/Akt pathway

<p>Abstract</p> <p>Background</p> <p>To explore the effects of Osthole on the proliferation, cell cycle and apoptosis of human lung cancer A549 cells.</p> <p>Methods</p> <p>Human lung cancer A549 cells were treated with Osthole at different concentrations. Cell proliferation was measured using the MTT assay. Cell cycle was evaluated using DNA flow cytometry analysis. Induction of apoptosis was determined by flow cytometry and fluorescent microscopy. The expressions of Cyclin B1, p-Cdc2, Bcl-2, Bax, t-Akt and p-Akt were evaluated by Western blotting.</p> <p>Results</p> <p>Osthole inhibited the growth of human lung cancer A549 cells by inducing G2/M arrest and apoptosis. Western blotting demonstrated that Osthole down-regulated the expressions of Cyclin B1, p-Cdc2 and Bcl-2 and up-regulated the expressions of Bax in A549 cells. Inhibition of PI3K/Akt signaling pathway was also observed after treating A549 cells with Osthole.</p> <p>Conclusions</p> <p>Our findings suggest that Osthole may have a therapeutic application in the treatment of human lung cancer.</p

Spatial Organization in Proteinaceous Membrane‐Stabilized Coacervate Protocells

As a model protocell, the membrane-free coacervate microdroplet is widely utilized in functional studies to provide insights into the physicochemical properties of the cell and to engineer cytomimetic soft technologies; however, the lack of a discrete membrane contributes to its instability and limits further application. Herein, a strategy is developed to fabricate a hybrid protocell based on the self-assembly of a proteinaceous membrane at the surface of coacervate microdroplets driven by a combination of electrostatic adhesion and steric/hydrophilic surface buoyancy. The semipermeable proteinaceous membrane can enhance coacervate stability obviously without compromising sequestration behavior. Significantly, such hybrid protocells demonstrate spatial organization whereby various functional enzymes can be located in discrete regions, which facilitates an on/off modulation for a cascade enzymatic reaction along with enhanced chemical communication between subpopulations

An advanced general dominant eigenvalue method of accelerating successive substitution during flash calculation for compositional reservoir model

The efficiency and accuracy of phase equilibrium calculations are essential in compositional reservoir models. Usually, a significant part of the computational effort in compositional reservoir simulations is spent on phase equilibrium calculations. The nonlinear nature of phase equilibrium calculations requires an iterative solution procedure. Although the successive substitution method (SSM) is robust and simple to implement, it suffers from slow convergence, especially near the critical point of the mixture. The general dominant eigenvalue method (GDEM) has been widely used to accelerate SSM, but its stability and efficiency deteriorate as the temperature and pressure approach the critical point. This paper proposes a modified form of GDEM to improve its performance in the near-critical region. The modifications have two aspects. First, the liquid phase fraction in the mixture is added as a variable when performing GDEM acceleration, improving both stability and efficiency. The second modification is a post-calibration step imposed to replace the conventional criterion, which is applied before triggering GDEM. With the help of the post-calibration step, the stability of the modified GDEM is ensured, and more importantly, the calculation efficiency can be improved. Numerical tests of three hydrocarbon mixtures, including different numbers of components, show that the stability of the modified GDEM is almost the same as SSM and that its calculation efficiency is much higher than SSM and the conventional GDEM.Cited as: Wang, X., Wei, D., Wang, X., Zhao, X., Li, J., Noetinger, B. An advanced general dominant eigenvalue method of accelerating successive substitution during flash calculation for compositional reservoir model. Advances in Geo-Energy Research, 2022, 6(3): 241-251. https://doi.org/10.46690/ager.2022.03.0