Quantitative Proteomic Approach Reveals Altered Metabolic Pathways in Response to the Inhibition of Lysine Deacetylases in A549 Cells under Normoxia and Hypoxia

Growing evidence is showing that acetylation plays an essential role in cancer, but studies on the impact of KDAC inhibition (KDACi) on the metabolic profile are still in their infancy. Here, we analyzed, by using an iTRAQ-based quantitative proteomics approach, the changes in the proteome of KRAS-mutated non-small cell lung cancer (NSCLC) A549 cells in response to trichostatin-A (TSA) and nicotinamide (NAM) under normoxia and hypoxia. Part of this response was further validated by molecular and biochemical analyses and correlated with the proliferation rates, apoptotic cell death, and activation of ROS scavenging mechanisms in opposition to the ROS production. Despite the differences among the KDAC inhibitors, up-regulation of glycolysis, TCA cycle, oxidative phosphorylation and fatty acid synthesis emerged as a common metabolic response underlying KDACi. We also observed that some of the KDACi effects at metabolic levels are enhanced under hypoxia. Furthermore, we used a drug repositioning machine learning approach to list candidate metabolic therapeutic agents for KRAS mutated NSCLC. Together, these results allow us to better understand the metabolic regulations underlying KDACi in NSCLC, taking into account the microenvironment of tumors related to hypoxia, and bring new insights for the future rational design of new therapies.     

Local residence time,residence revolution,and residence volume distributions in twin‐screw extruders

This work was aimed at studying the overall, partial, and local residence time distributions (RTD); overall, partial and local residence revolution distributions (RRD) and overall, partial and local residence volume distributions (RVD) in a co‐rotating twin screw extruder, on the one hand; and establishing the relationships among them, on the other hand. Emphasis was placed on the effects of the type and geometry of mixing elements (a gear block and various types of kneading elements differing in staggering angle) and process parameters on the RTD, RRD and RVD. The overall and partial RTD were directly measured in‐line during the extrusion process and the local ones were calculated by deconvolution based on a statistical theory. The local RTD allowed comparing the mixing performance of mixing elements. Also it was confirmed both experimentally and theoretically that specific throughput, defined as a ratio of throughput (Q) over screw speed (N), controlled all the above three types of residence distributions, be they local, partial or overall. The RRD and RVD do not provide more information on an extrusion process than the corresponding RTD. Rather they are different ways of representing the same phenomena. POLYM. ENG. SCI., 48:19–28, 2008. © 2007 Society of Plastics Engineers     

JaTS: a fully portable seismic tomography software based on Fresnel wavepaths and a probabilistic reconstruction approach

JaTS, a Java 2D seismic tomography software, is presented. It implements original algorithms achieving optimal accuracy with reasonable computing costs. A second-order Fast Marching Method (FMM) is used for solving the eikonal equation, therefore enabling a fast and robust computation of seismic traveltimes between sources and receivers. The wavepaths are materialized by Fresnel volumes rather than by conventional rays. This approach accounts for complex velocity models and has the advantage of considering the effects of the wave frequency in the velocity model resolution. The model is computed by a Simultaneous Iterative Reconstruction Technique (SIRT) which has been reformulated to integrate Fresnel wavepaths by using a probabilistic approach. In addition, various utilities are implemented, such as a tapering filter, used to decrease artifact effects occurring in the vicinity of the sources and receivers. The software also offers the possibility of reconstructing the velocity field on a grid larger than the one used for the wave propagation computation. This contributes to stabilize the estimated values. All of the seismic processing tools have been integrated with a user-friendly graphical interface. JaTS represents a tightly integrated tool suite that supports the entire process of importing the SG2 field records, first-break picking, forward modeling and velocity-field computing across multiple platforms.     

Development of Covalent Chitosan-Polyethylenimine Derivatives as Gene Delivery Vehicle: Synthesis,Characterization, and Evaluation

There is an increasing interest in cationic polymers as important constituents of non-viral gene delivery vectors. In the present study, we developed a versatile synthetic route for the production of covalent polymeric conjugates consisting of water-soluble depolymerized chitosan (dCS; M_W 6–9 kDa) and low molecular weight polyethylenimine (PEI; 2.5 kDa linear, 1.8 kDa branched). dCS-PEI derivatives were evaluated based on their physicochemical properties, including purity, covalent bonding, solubility in aqueous media, ability for DNA condensation, and colloidal stability of the resulting polyplexes. They were complexed with non-integrating DNA vectors coding for reporter genes by simple admixing and assessed in vitro using liver-derived HuH-7 cells for their transfection efficiency and cytotoxicity. Using a rational screening cascade, a lead compound was selected (dCS-Suc-LPEI-14) displaying the best balance of biocompatibility, cytotoxicity, and transfection efficiency. Scale-up and in vivo evaluation in wild-type mice allowed for a direct comparison with a commercially available non-viral delivery vector (in vivo-jetPEI). Hepatic expression of the reporter gene luciferase resulted in liver-specific bioluminescence, upon intrabiliary infusion of the chitosan-based polyplexes, which exceeded the signal of the in vivo jetPEI reference formulation by a factor of 10. We conclude that the novel chitosan-derivative dCS-Suc-LPEI-14 shows promise and potential as an efficient polymeric conjugate for non-viral in vivo gene therapy.     

Cardiac Oxidative Signaling and Physiological Hypertrophy in the Na/K-ATPase α1s/sα2s/s Mouse Model of High Affinity for Cardiotonic Steroids

The Na/K-ATPase is the specific receptor for cardiotonic steroids (CTS) such as ouabain and digoxin. At pharmacological concentrations used in the treatment of cardiac conditions, CTS inhibit the ion-pumping function of Na/K-ATPase. At much lower concentrations, in the range of those reported for endogenous CTS in the blood, they stimulate hypertrophic growth of cultured cardiac myocytes through initiation of a Na/K-ATPase-mediated and reactive oxygen species (ROS)-dependent signaling. To examine a possible effect of endogenous concentrations of CTS on cardiac structure and function in vivo, we compared mice expressing the naturally resistant Na/K-ATPase α1 and age-matched mice genetically engineered to express a mutated Na/K-ATPase α1 with high affinity for CTS. In this model, total cardiac Na/K-ATPase activity, α1, α2, and β1 protein content remained unchanged, and the cardiac Na/K-ATPase dose–response curve to ouabain shifted to the left as expected. In males aged 3–6 months, increased α1 sensitivity to CTS resulted in a significant increase in cardiac carbonylated protein content, suggesting that ROS production was elevated. A moderate but significant increase of about 15% of the heart-weight-to-tibia-length ratio accompanied by an increase in the myocyte cross-sectional area was detected. Echocardiographic analyses did not reveal any change in cardiac function, and there was no fibrosis or re-expression of the fetal gene program. RNA sequencing analysis indicated that pathways related to energy metabolism were upregulated, while those related to extracellular matrix organization were downregulated. Consistent with a functional role of the latter, an angiotensin-II challenge that triggered fibrosis in the α1^r/rα2^s/s mouse failed to do so in the α1^s/sα2^s/s. Taken together, these results are indicative of a link between circulating CTS, Na/K-ATPase α1, ROS, and physiological cardiac hypertrophy in mice under baseline laboratory conditions.     

Mixing of a self-assembled supramolecular polymer and a covalent polymer in organic solutions

We report on a neutron scattering study of the molecular structure of a self-assembled supramolecular polymer composed of a bicopper complex within a solution of a covalent polymer (atactic polystyrene/trans-decalin). The study is achieved by putting two binary phases in contact and allowing for diffusion of both components in either phase. It is shown that the one-dimensional bicopper filaments are compatible to a high extent with the atactic polymer. These results are discussed in the light of a recently devised encapsulation process of the bicopper filaments within the fibrils of a physical network of isotactic polystyrene.     

Reactive Robust Routing: Anomaly Localization and Routing Reconfiguration for Dynamic Networks

This paper presents a novel approach to deal with dynamic and highly uncertain traffic in dynamic network scenarios. The Reactive Robust Routing (RRR) approach is introduced, a combination of proactive and reactive techniques to improve network efficiency and robustness, simplifying network operation. RRR optimizes routing for normal-operation traffic, using a time-varying extension of the already established Robust Routing technique that outperforms the stable approach. To deal with anomalous and unexpected traffic variations, RRR uses a fast anomaly detection and localization algorithm that rapidly detects and localizes abrupt changes in traffic flows, permitting an accurate routing adaptation. This algorithm presents well-established optimality properties in terms of detection/localization rates and localization delay, which allows for generalization of results, independently of particular evaluations. The algorithm is based on a novel parsimonious model for traffic demands which allows for detection of anomalies using easily available aggregated-traffic measurements, reducing the overheads of data collection.     

Dealing with midair collisions in dense collective aerial systems

The idea of creating collective aerial systems is appealing because several rather simple flying vehicles could join forces to cover a large area in little time in applications such as monitoring, mapping, search and rescue, or airborne communication relays. In most of these scenarios, a fleet of cooperating vehicles is dispatched to a confined airspace area and requested to fly close to a nominal altitude. Moreover, depending on the task each vehicle is assigned to, individual flight trajectories in this essentially two‐dimensional space may interfere, resulting in disastrous collisions. This paper begins by introducing a probabilistic model to predict the rate of midair collisions that would occur if nothing is done to prevent them. In a second step, a control strategy for midair collision avoidance is proposed, which is interesting because it requires only local communication and information about flight altitudes. The proposed strategy is systematically analyzed in theory and simulation as well as in experiments with five physical aerial vehicles. A significant reduction in collision rates can be achieved. Statistically, values close to zero are possible when the swarm's density is below an application‐dependent threshold. Such low collision rates warrant an acceptable level of confidence in collision‐free operation of a physical swarm. © 2011 Wiley Periodicals, Inc.     

Students’ performance and satisfaction with Web vs. paper-based practice quizzes and lecture notes

The use of computers to deliver course-related materials is rapidly expanding in most universities. Yet the effects of computer vs. printed delivery modes on students’ performance and motivation are not yet fully known. We compared the impacts of Web vs. paper to deliver practice quizzes that require information search in lecture notes. Hundred and twenty two undergraduate students used either a web site or printed documents to answer 18 mathematics questions during a tutored session. A revised Web site was designed based on ergonomic criteria, to test the hypothesis that improved usability would decrease time spent on the task, the number of pages consulted, and students’ perceived cognitive load. The group working with printed documents had the highest performance. Furthermore, students perceived the paper materials as less effortful to read, and expressed preference for printing lecture notes and questions. However, students appreciated having a Web site available. No differences were found between the two sites. We conclude that Web delivery imposed higher perceived cognitive load due to the need to read lengthy documents. We suggest possible ways to improve Web-based practice materials, such as simultaneous display of questions and lecture notes.