The immune modulation on innate immunity, from pathogen recognition to fungal clearance.

The human lung is not sterile but a complex environment with various microorganisms. Besides commensals in the lung, hundreds to thousands of individual microbiomes enter the lung every day but without causing the symptom. Host innate immunity plays an important role in maintaining homeostasis of the lung environment and as the first defense line against pathogens. Aspergillus fumigatus (A. fumigatus) is a saprophytic filamentous fungus that can cause human disease in immune compromised patients. However, with functional innate immunity, immune cells can quickly recognize pathogen associated molecular patterns (PAMPs) from A. fumigatus through pattern recognition receptors (PRRs). The activation of PRRs can activate innate immunity and facilitate inflammatory responses through cytokine and chemokine production. As the initiation of inflammation, the recruited innate immune cells can eliminate A. fumigatus through phagocytosis and kill them in the mature phagolysosome with ROS-dependent and independent mechanisms. In this dissertation, we will cover the regulation of antifungal immunity in two specific directions: (1) investigate the immune modulation on innate immunity in the post-viral environment and the cause of viral-fungal superinfection. (2) characterize a potential fungal binding receptor and examine its role in antifungal immunity. In the first project, we demonstrated a novel mechanism within specific cell types that can contribute to defective fungal clearance and lead to high mortality in Influenza A Virus- A. fumigatus superinfection. For the second part, we used our newly generated mutant mice line and biochemistry approach to study the potential role of fungal surface binding protein in host immunity. These results further demonstrate the importance of antifungal immunity and upstream immune modulation in preventing the initiation of invasive aspergillosis

J/psi absorption by nucleons in the meson-exchange model

We reinvestigate the $J/\psi$ dissociation processes induced by the reactions with nucleons, $J/\psi + N \to \bar{D}^{(*)} + \Lambda_c$, in the meson-exchange model. Main constraints used in this work are vector-meson dominance and charm vector-current conservation. We show that the cross section for $J/\psi + N \to \bar{D} + \Lambda_c$ can be larger than that for $J/\psi + N \to \bar{D}^{*} + \Lambda_c$ when these constraints are imposed. The dependence of the cross sections on the coupling constants is analyzed in detail, and the comparison with the recent quark-interchange model predictions is also made.Comment: 7 pages, 4 figures, REVTeX, a reference added, to appear in Phys. Rev.

Thermal Charm Production in Quark-Gluon Plasma at LHC

Charm production from the quark-gluon plasma created in the midrapidity of central heavy ion collisions at the Large Hadron Collider (LHC) is studied in the next-to-leading order in QCD. Using a schematic longitudinally boost-invariant and transversally expanding fire-cylinder model, we find that charm production could be appreciably enhanced at LHC as a result of the high temperature that is expected to be reached in the produced quark-gluon plasma. Sensitivities of our results to the number of charm quark pairs produced from initial hard scattering, the initial thermalization time and temperature of the quark-gluon plasma, and the charm quark mass are also studied.Comment: 8 pages, 9 figures; adding a figure and relevant discussion on the sensitivity of our results to the number of charm quark pairs produced from initial hard scattering. Version accepted for publication in PR

On (d,1)-total numbers of graphs

AbstractA (d,1)-total labelling of a graph G assigns integers to the vertices and edges of G such that adjacent vertices receive distinct labels, adjacent edges receive distinct labels, and a vertex and its incident edges receive labels that differ in absolute value by at least d. The span of a (d,1)-total labelling is the maximum difference between two labels. The (d,1)-total number, denoted λdT(G), is defined to be the least span among all (d,1)-total labellings of G. We prove new upper bounds for λdT(G), compute some λdT(Km,n) for complete bipartite graphs Km,n, and completely determine all λdT(Km,n) for d=1,2,3. We also propose a conjecture on an upper bound for λdT(G) in terms of the chromatic number and the chromatic index of G

Gene conversion limits divergence of mammalian TLR1 and TLR6

<p>Abstract</p> <p>Background</p> <p>Toll-like receptors (TLR) recognize pathogen-associated molecular patterns and are important mediators of the innate immune system. TLR1 and TLR6 are paralogs and located in tandem on the same chromosome in mammals. They form heterodimers with TLR2 and bind lipopeptide components of gram-positive and gram-negative bacterial cell walls. To identify conserved stretches in TLR1 and TLR6, that may be important for their function, we compared their protein sequences in nine mammalian species(<it>Homo sapiens</it>, <it>Pan troglodytes</it>, <it>Macaca mulatta</it>, <it>Mus musculus</it>, <it>Rattus norvegicus</it>; <it>Erinaceus europaeus</it>, <it>Bos Taurus</it>, <it>Sus scrofa </it>and <it>Canis familiaris</it>).</p> <p>Results</p> <p>The N-terminal sequences of the orthologous proteins showed greater similarity than corresponding paralog sequences. However, we identified a region of 300 amino acids towards the C-terminus of TLR1 and TLR6, where paralogs had a greater degree of sequence identity than orthologs. Preservation of DNA sequence identity of paralogs in this region was observed in all nine mammalian species investigated, and is due to independent gene conversion events. The regions having undergone gene conversion in each species are almost identical and encode the leucine-rich repeat motifs 16 to 19, the C-terminal cap motif, the transmembrane domain and most of the intracellular Toll/interleukin-1 receptor (TIR) domain.</p> <p>Conclusion</p> <p>Our results show that, for a specific conserved region, divergence of TLR1 and TLR6 is limited by gene conversion, most likely because of the need for co-evolution with multiple intracellular and extracellular binding partners. Thus, gene conversion provides a mechanism for limiting the divergence of functional regions of protein paralogs, while allowing other domains to evolve diversified functions.</p

Simulation and design of nonlinear material structures for energy and biomedical devices

The project's main objective is the development of mathematical models and solutions of the models for simulation and design of some modern nonlinear material structures for energy and biomedical devices. One of the challenges in modeling the structural behavior of the materials is that they cannot be modeled accurately by the theory of linear elasticity or common linearization theory even at small strains for not having a well-defined yield stress point

Experimental study of seismo-acoustic frequency and flow velocity of debris flow

Seismo-acoustic wave radiated from debris flows motion is one of the main properties used for its monitoring and detection. Understanding the Seismo-acoustic wave using geophone recordings may give us great insight into the physical process of debris flows such as flow velocity and flow rate. To connect the seismo acoustic observation to the debris flows motion, vibration signal recorded from fixed geophones were analysed. In this study, a small-scale granular flow of volume 0.2 m3 consisting of material with average particle diameter 3.34 mm was simulated in a hydraulic flume with cross section of 0.5 m X 0.5 m through granular bed to simulate the debris flow. A series of three-axis geophones were buried along channel bed to record the vibrations produced by granular flows. The discrete Fourier transform was used to decompose vibrations into frequency spectrum and the weighted non-linear least square regression was adopted to isolate the dominant frequency functions and peak frequency. Meanwhile, the physical parameters including front profile, surface velocity, flow depth and discharge were tracked through video recordings and were compared with respect to isolated peak frequency. Assuming the radiated peak frequency in the moving granular flow is within 20-50 Hz and normally distributed, the isolated peak frequency shift in the fixed geophone location was analysed with the tracked flow parameters. Results shows that the peak frequency shift seems to have a non-linear relation with the surface velocity