Predicting Axonal Response to Molecular Gradients with a Computational Model of Filopodial Dynamics

Axons are often guided to their targets in the developing nervous system by attractive or repulsive molecular concentration gradients. We propose a computational model for gradient sensing and directed movement of the growth cone mediated by filopodia. We show that relatively simple mechanisms are sufficient to generate realistic rajectories for both the short-term response of axons to steep gradients and the long-term response of axons to shallow gradients. The model makes testable predictions for axonal response to attractive and repulsive gradients of different concentrations and steepness, the size of the intracellular amplification of the gradient signal, and the differences in intracellular signaling required for repulsive versus attractive turning

A Novel Sequence-Based Antigenic Distance Measure for H1N1, with Application to Vaccine Effectiveness and the Selection of Vaccine Strains

H1N1 influenza causes substantial seasonal illness and was the subtype of the 2009 influenza pandemic. Precise measures of antigenic distance between the vaccine and circulating virus strains help researchers design influenza vaccines with high vaccine effectiveness. We here introduce a sequence-based method to predict vaccine effectiveness in humans. Historical epidemiological data show that this sequence-based method is as predictive of vaccine effectiveness as hemagglutination inhibition (HI) assay data from ferret animal model studies. Interestingly, the expected vaccine effectiveness is greater against H1N1 than H3N2, suggesting a stronger immune response against H1N1 than H3N2. The evolution rate of hemagglutinin in H1N1 is also shown to be greater than that in H3N2, presumably due to greater immune selection pressure.Comment: 26 pages, 7 figures, 2 tables, supplemen

The epitope regions of H1-subtype influenza A, with application to vaccine efficacy

The recent emergence of H1N1 (swine flu) illustrates the ability of the influenza virus to create antigens new to the human immune system, even within a given hemagglutinin and neuraminidase subtype. This new H1N1 strain is sufficiently distinct, for example, from the A/Brisbane/59/2007 (H1N1)-like virus strain of influenza in the 2008/09 Northern hemisphere vaccine that protection is not expected to be substantial. The human immune system responds primarily to the five epitope regions of the hemagglutinin protein. By determining the fraction of amino acids that differ between a vaccine strain and a viral challenge strain in the dominant epitope regions, a measure of antigenic distance that correlates with epidemiological studies of H3 influenza A vaccine efficacy in humans with R2 = 0.81 is derived. This measure of antigenic distance is called pepitope. The relation between vaccine efficacy and pepitope is given by E = 0.47 – 2.47 × pepitope. We here identify the epitope regions of H1 hemagglutinin, so that vaccine efficacy may be reliably estimated for H1N1 influenza A

Exploring the Pathogenic and Drug Resistance Mechanisms of Staphylococcus aureus

We have previously identified σS, an ECF sigma factor that is important in the virulence and stress response of S. aureus. Transcriptional profiling of sigS revealed that it is differentially regulated in a variety of laboratory and clinical strains of S. aureus, suggesting that there exists a regulatory network that modulates its expression. In order to identify direct regulators of sigS expression, we performed a biotin pull down assay in tandem with mass spectrometry. We identified CymR as a direct regulator and observed that sigS expression is increased in cells lacking cymR. In addition, transposon mutagenesis was performed to identify regulators of sigS expression. We identified insertions in genes that are transcriptional regulators, and elements involved in amino acid biosynthesis and DNA replication, recombination and repair as influencing sigS expression. Finally, methyl nitro-nitrosoguanidine mutagenesis in conjunction with whole genome sequencing was employed and revealed mutations in the lactose repressor, lacR, and the membrane sensor histidine kinase, kdpD, as negatively effecting sigS expression. EMSAs revealed that LacR is an indirect regulator of sigS expression, while the response regulator KdpE is a direct repressor. These results indicate that a complex regulatory network is in place for sigS that modulates its expression. In a continuation of studies on σS regulation, we next explored interplay with the products of genes conserved within the sigS locus. We determined that this region is conserved amongst all the sequenced staphylococci, and includes four genes: SAUSA300_1721 (a conserved hypothetical protein), as well as sigS, ecfX, and ecfY. In order to investigate the relationship between EcfX and σS we performed protein pull down assays and observed that these two protein interact. Further to this, transcriptional analysis of sigS in an ecfX mutant reveal that expression of sigS is decreased, indicating that it is an activator. Architectural analysis of the sigS locus via RNAseq revealed that the majority of transcription in this region comes from ecfY, a gene that is downstream and divergent to sigS. We demonstrate that inactivation of ecfY leads to a significant increase in sigS expression, and that ecfY null strains are more resistant to DNA damaging agents such as UV, H2O2, MMS, and ethidium bromide, which we have previously demonstrated that a sigS mutant is highly sensitive to. Our studies also revealed that an ecfY null strain is better able to survive intracellularly following phagocytosis by RAW 264.7 cell and demonstrates increased survival in whole-human blood, which is again opposed to that previously observed for sigS deficient strains. Because the ecfY null strain overexpresses sigS, we investigated the regulon of this sigma factor using this mutant in conjunction with RNAseq analysis. We identified that genes putatively under the control of σS are involved in DNA damage and repair, virulence, amino acid starvation and nucleic acid biosynthesis. Collectively, our results indicate that σS is regulated via a unique mechanism: positively through an apparent need for an activator protein (EcfX) and negatively via RNA-RNA interaction (the 3’ UTR of ecfY). We suggest that the evidence presented here greatly adds not only to our understanding of the regulatory circuits extant within S. aureus, but also to alternative sigma factor biology in general. Finally, we evaluated the efficacy of a novel library of quinazoline-based compounds against a highly drug resistant strain of S. aureus. We performed structure activity and structure property relationship assays in order to identify lead compounds. These methods lead to the identification of N2,N4-disubstituted quinazoline-2,4-diamines that had low minimum inhibitory concentrations, along with favorable physiochemical properties. Evaluation of their biological activity demonstrated limited potential for resistance of to our quinazoline based compounds, low toxicity to human epithelial cells, and strong efficacy in vivo. Taken together, our findings support the use of quinazoline derivatives as potential new antimicrobials against multidrug resistant S. aureus

Coal-water slurry atomization characteristics

The overall objective of this work was to fully characterize the CWS fuel sprays of a medium-speed diesel engine injection system. Specifically, the spray plume penetration as a function of time was determined for a positive-displacement fuel injection system. The penetration was determined as a function of orifice diameter, coal loading, gas density in the engine, and fuel line pressure. Preliminary droplet information also was obtained. The results of this study will assist CWS engine development by providing much needed insight about the fuel spray. In addition, the results will aid the development and use of CWS engine cycle simulations which require information on the fuel spray characteristics

Coal-water slurry spray characteristics of a positive displacement fuel injection system

Experiments have been completed to characterized coal-water slurry sprays from a modified positive displacement fuel injection system of a diesel engine. The injection system includes an injection jerk pump driven by an electric motor, a specially designed diaphragm to separate the abrasive coal from the pump, and a single-hole fuel nozzle. The sprays were injected into a pressurized chamber equipped with windows. High speed movies and instantaneous fuel line pressures were obtained. For injection pressures of order 30 MPa or higher, the sprays were similar for coal-water slurry, diesel fuel and water. The time until the center core of the spray broke-up (break-up time) was determined from both the movies and from a model using the fuel line pressures. Results from these two independent procedures were in good agreement. For the base conditions, the break-up time was 0.58 and 0.50 ms for coal-water slurry and diesel fuel, respectively. The break-up times increased with increasing nozzle orifice size and with decreasing chamber density. The break-up time was not a function of coal loading for coal loadings up to 53%. Cone angles of the sprays were dependent on the operating conditions and fluid, as well as on the time and location of the measurement. For one set of cases studied, the time-averaged cone angle was 15.9{degree} and 16.3{degree} for coal-water slurry and diesel fuel, respectively

Signatures of the disk-jet coupling in the Broad-line Radio Quasar 4C+74.26

Here we explore the disk-jet connection in the broad-line radio quasar 4C+74.26, utilizing the results of the multiwavelength monitoring of the source. The target is unique in that its radiative output at radio wavelengths is dominated by a moderately-beamed nuclear jet, at optical frequencies by the accretion disk, and in the hard X-ray range by the disk corona. Our analysis reveals a correlation (local and global significance of 96\% and 98\%, respectively) between the optical and radio bands, with the disk lagging behind the jet by $250 \pm 42$ days. We discuss the possible explanation for this, speculating that the observed disk and the jet flux changes are generated by magnetic fluctuations originating within the innermost parts of a truncated disk, and that the lag is related to a delayed radiative response of the disk when compared with the propagation timescale of magnetic perturbations along relativistic outflow. This scenario is supported by the re-analysis of the NuSTAR data, modelled in terms of a relativistic reflection from the disk illuminated by the coronal emission, which returns the inner disk radius $R_{\rm in}/R_{\rm ISCO} =35^{+40}_{-16}$. We discuss the global energetics in the system, arguing that while the accretion proceeds at the Eddington rate, with the accretion-related bolometric luminosity $L_{\rm bol} \sim 9 \times 10^{46}$ erg s$^{-1}$ $\sim 0.2 L_{\rm Edd}$, the jet total kinetic energy $L_\textrm{j} \sim 4 \times 10^{44}$ erg s$^{-1}$, inferred from the dynamical modelling of the giant radio lobes in the source, constitutes only a small fraction of the available accretion power.Comment: 9 pages and 6 figures, ApJ accepte

Micronized-coal-water slurry sprays from a diesel engine positive displacement fuel injection system

Experiments have been conducted to characterize the sprays from a modified positive displacement fuel injection system for a diesel engine. Diesel fuel water and three concentrations of micronized-coal-water slurry were used in these experiments. The injection system includes an injection jerk pump driven by an electric motor, a specially designed diaphragm to separate the abrasive coal slurry fuel from the pump, and a single-hole fuel nozzle. The sprays were injected into a pressurized chamber equipped with windows. High speed movies and still photographs of the sprays were obtained. In addition, instaneous fuel line pressures and needle lifts were obtained. Data were acquired as a function of fluid, nozzle orifice diameter, rack setting and chamber conditions. The high speed movies were used to determine spray penetration and spray growth

Programming of embryonic development

Assisted reproductive techniques (ART) and parental nutritional status have profound effects on embryonic/fetal and placental development, which are probably mediated via “programming” of gene expression, as reflected by changes in their epigenetic landscape. Such epigenetic changes may underlie programming of growth, development, and function of fetal organs later in pregnancy and the offspring postnatally, and potentially lead to long-term changes in organ structure and function in the offspring as adults. This latter concept has been termed developmental origins of health and disease (DOHaD), or simply developmental programming, which has emerged as a major health issue in animals and humans because it is associated with an increased risk of non-communicable diseases in the offspring, including metabolic, behavioral, and reproductive dysfunction. In this review, we will briefly introduce the concept of developmental programming and its relationship to epigenetics. We will then discuss evidence that ART and periconceptual maternal and paternal nutrition may lead to epigenetic alterations very early in pregnancy, and how each pregnancy experiences developmental programming based on signals received by and from the dam. Lastly, we will discuss current research on strategies designed to overcome or minimize the negative consequences or, conversely, to maximize the positive aspects of developmental programming