Molecular Dissection of the Cellular Reponse to Dengue Virus Infection

The immune response to viral infection involves a complexity of both innate and adaptive pathways at the cellular and the molecular level. There are many approaches to begin to define the pathways at work to control viral pathogenesis. The approach favored in this thesis was to conduct a broad screen of the innate immune response at the gene expression level of infected cells. The innate immune response is critical to the control of viral infections. Type I interferons (IFN), IFNα and IFNβ, are antiviral proteins that are an integral part of the innate immune response. Furthermore, by virtue of their effects on maturation and activation of antigen-presenting cells, IFNs are a pivotal link between the innate and adaptive immune systems. Most cell types produce type-I IFN when exposed to viruses. However, viruses have evolved multiple strategies to suppress IFN production or signaling. It is imperative to understand the virus-host interaction at the molecular level in order to identify as yet unknown mechanisms of the host antiviral response; these additional pathways may be useful in counteracting the viral suppression of IFN. Type-I IFNs regulate expression of at least five hundred genes, suggesting a complex network of signaling pathways. Depending on the cell type different proteins regulate the induction of IFN or the expression of IFN-inducible genes. Identification of proteins that induce selected IFN-inducible genes may provide synergistic activity with or may have an advantage over type-I IFN for anti-viral therapy in the future. Many diseases are untreatable if identified late in their progression. In resource-limited countries, many diseases are diagnosed clinically, which can lead to incorrect or delayed diagnosis and treatment. The identification of biomarkers of disease has the potential to guide the correct therapy in a timely fashion. The objective of this thesis was to identify novel anti-viral therapies and disease biomarkers for dengue virus (DENV) infection. DENV is a mosquito-borne positive-sense single-stranded RNA virus, which causes an estimated 50 million infections annually. Most DENV infections result in a febrile illness called Dengue fever (DF). Less frequently, infections cause Dengue hemorrhagic fever (DHF), a potentially fatal vascular leakage syndrome associated with the production of pro-inflammatory cytokines. At present patients infected with DENV can only be treated by intravenous fluid support to prevent hypovolemia and hypotensive shock. This treatment is less effective in severe cases if the diagnosis is delayed. Identification of therapeutics with both antiviral and immune-modulatory activity may lower patient mortality and reduce the burden of DENV on society. DENV infection is cleared in most individuals after a short period of viremia {Libraty, 2002 #2225}. Based on in vitro and mouse models, type-I and type-II IFN signaling pathways are thought to be critical in the regulation of DENV infection. Higher serum levels of type I and type II IFNs during acute DENV infection in patients lend support to the above hypothesis {Kurane, 1993 #2152; Libraty, 2002 #2225}. To understand the DENV-human host cell interaction at the molecular level, we performed global gene expression analysis on DENV-infected primary human cells using Affymetrix GeneChips (HG-U133A). We studied dendritic cells (DC), monocytes, B cells and human umbilical vein endothelial cells (HUVECs), all of which are known to be permissive to DENV infection. We first identified genes commonly regulated in multiple cell types in response to DENV infection; we hypothesized that understanding this common gene expression profile would identify signaling pathways involved in regulation of viral spread, activation of immune cells or induction of inflammation. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), one of the 23 common response genes, was identified as a key link between type I and type II interferon response genes. Pretreatment of cells with recombinant TRAIL (rTRAIL) inhibited DENV replication in monocytes, B cells, HUVECs and DCs. Using the DC infection model, we showed that this inhibition of viral replication was apoptosis-independent. Type-I IFN receptor (IFNR) blocking experiments showed that signaling through the type-I IFN receptor played an important role in the antiviral activity of exogenous rTRAIL. Furthermore, TRAIL also significantly reduced the expression of mRNA and protein of pro-inflammatory cytokines (TNFα, MIP-1β and IFNα) and chemokines (MCP-2, IP-10 and IL-6) in response to DENV infection. The data that TRAIL inhibits both viral replication and pro-inflammatory cytokine production suggest that TRAIL has therapeutic value in dengue. The endothelial cell is the site of pathology in DENV infection in vivo (vascular permeability and plasma leakage). To understand the direct effect of DENV infection on endothelial cells and its role in the induction of genes regulating vascular permeability, we compared gene expression in DENV-infected HUVECs to that of uninfected cells and cells infected with other RNA and DNA viruses, including flaviviruses (West Nile, yellow fever, and Japanese encephalitis viruses), bunyaviruses (Sin Nombre and Hantaan viruses), Epstein-Barr virus and vaccinia virus. Among the genes confirmed for their differential expression, ST2 (Interkeukin-1 receptor-like-1 protein-IL1RL1) and indoleamine 2,3-dioxygenase (IDO) were identified to be upregulated specifically in response to DENV infection. Higher serum soluble ST2 (sST2) levels were detected in DENV-infected patients than in patients with other febrile illnesses (OFI) at the end of the febrile stage and at defervescence (p=0.0088 and p=0.0004, respectively). In addition, patients with secondary DENV infections had higher serum sST2 levels compared with patients with primary DENV infections (p=0.047 at the last day of fever and p=0.030 at defervescence). Higher levels of IDO activity (pIn conclusion, global gene expression analysis identified novel proteins with promising characteristics for the treatment and/or diagnosis of DENV infection. Although further studies will be needed to validate the clinical utility of TRAIL, sST2, and IDO, these studies demonstrate the utility of this unbiased genomics approach to identify therapies to currently incurable diseases

MATHEMATICAL MODELING OF HEAT TREATING POWDER METALLURGY STEEL COMPONENTS

A mathematical model to predict the response of powder metallurgy steels to heat treatment is presentedand discussed. The model is based on modification of commercially available software that was originallydeveloped for wrought alloys so that it can account for the effect of porosity. An extensive database had to bedeveloped specifically for PM steels and includes porosity- and temperature-dependent phase transformationkinetics, and porosity- and temperature-dependent phase-specific mechanical, physical, and thermal properties.This extensive database has been developed for FL-4065 PM steel and has been used in the model to predictdimensional change, distortion, and type and quantity of metallurgical phases that develop in a typical PMcomponent upon heat treatment. The model predictions are compared to measured values and are found to be inexcellent agreement with them

A copper isotope investigation of methane cycling in Late Archaean sediments

This research was supported by NERC award NE/L002590/1 to the IAPETUS DTP, and by NERC Standard Grant NE/J023485/2 to A.L.Z. The initiation of Cu isotope analysis at the University of St Andrews was aided significantly by a Carnegie Trust Research Incentive Grant awarded to P.S.S.The rise of oxygenic photosynthesis arguably represents the most important evolutionary step in Earth history. Recent studies, however, suggest that Earth’s pre-oxidative atmosphere was also heavily influenced by biological feedbacks. Most notably, recent geochemical records propose the existence of a hydrocarbon haze which periodically formed in response to enhanced biospheric methane fluxes. Copper isotopes provide a potential proxy for biological methane cycling; Cu is a bioessential trace metal and a key element in the aerobic oxidation of methane to carbon dioxide (methanotrophy). In addition, Cu isotopes are fractionated during biological uptake. Here, we present a high-resolution Cu isotope record measured in a suite of shales and carbonates from core GKF01, through the ~2.6–2.5 Ga Campbellrand-Malmani carbonate platform. Our data show a 0.85‰ range in Cu isotope composition and a negative excursion that predates the onset of a haze event. We interpret this excursion as representing a period of enhanced aerobic methane oxidation before the onset of the Great Oxidation Event. This places valuable time constraints on the evolution of this metabolism and firmly establishing Cu isotopes as a biomarker in Late Archaean rocks.PostprintPeer reviewe

Repulsive Core of NN S-Wave Scattering in a Quark Model with a Condensed Vacuum

We work in a chiral invariant quark model, with a condensed vacuum, characterized by only one parameter. Bound state equations for the nucleon and Delta are solved in order to obtain an updated value of their radii and masses. Nucleon-nucleon S-Wave scattering is studied in the RGM framework both for isospin T=1 and T=0. The phase shifts are calculated and an equivalent local potential, which is consistent with K-N scattering, is derived. The result is a reasonable microscopic short range repulsion in the nucleon-nucleon interaction.Comment: 23 pages in latex revtex, 4 Postscript figure

Two-billion-year-old evaporites capture Earth's great oxidation

Funding sources: Simons Foundation (SCOL 339006 to C.L.B.), European Research Council (ERC Horizon 2020 grant 678812 to M.C.), Research Council of Norway (RCN Centres of Excellence funding scheme project 223259 to K.P. and A.L.), Estonian Science Agency (PUT696 to K.K., A.L., K.P., T.K.).Major changes in atmospheric and ocean chemistry occurred in the Paleoproterozoic Era (2.5–1.6 billion years ago). Increasing oxidation dramatically changed Earth’s surface, but few quantitative constraints exist on this important transition. This study describes the sedimentology, mineralogy, and geochemistry of a remarkably preserved two-billion-year-old and ~800 meter-thick evaporite succession from the Onega Basin in Russian Karelia. The deposit consists of a basal unit dominated by halite (~100 m) followed by anhydrite-magnesite (~500 m) and dolomite-magnesite (~200 m) dominated units. The evaporite minerals robustly constraint marine sulfate concentrations to at least 10 millimoles per kilogram of water, representing an oxidant reservoir equivalent to over 20% of the modern ocean-atmosphere oxidizing capacity. These results show that substantial amounts of surface oxidant accumulated during this critical transition in Earth’s oxygenation.PostprintPeer reviewe

Long- and medium-range components of the nuclear force in quark-model based calculations

Quark-model descriptions of the nucleon-nucleon interaction contain two main ingredients, a quark-exchange mechanism for the short-range repulsion and meson-exchanges for the medium- and long-range parts of the interaction. We point out the special role played by higher partial waves, and in particular the 1F3, as a very sensitive probe for the meson-exchange part employed in these interaction models. In particular, we show that the presently available models fail to provide a reasonable description of higher partial waves and indicate the reasons for this shortcoming.Comment: 19 pages, 7 figure

Differential expression of collectins in human placenta and role in inflammation during spontaneous Labor.

© 2014 Yadav et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Collectins, collagen-containing Ca2+ dependent C-type lectins and a class of secretory proteins including SP-A, SP-D and MBL, are integral to immunomodulation and innate immune defense. In the present study, we aimed to investigate their placental transcript synthesis, labor associated differential expression and localization at feto-maternal interface, and their functional implication in spontaneous labor. The study involved using feto-maternal interface (placental/decidual tissues) from two groups of healthy pregnant women at term (≥37 weeks of gestation), undergoing either elective C-section with no labor ('NLc' group, n = 5), or normal vaginal delivery with spontaneous labor ('SLv' group, n = 5). The immune function of SP-D, on term placental explants, was analyzed for cytokine profile using multiplexed cytokine array. SP-A, SP-D and MBL transcripts were observed in the term placenta. The 'SLv' group showed significant up-regulation of SP-D (p = 0.001), and down-regulation of SP-A (p = 0.005), transcripts and protein compared to the 'NLc' group. Significant increase in 43 kDa and 50 kDa SP-D forms in placental and decidual tissues was associated with the spontaneous labor (p<0.05). In addition, the MMP-9-cleaved form of SP-D (25 kDa) was significantly higher in the placentae of 'SLv' group compared to the 'NLc' group (p = 0.002). Labor associated cytokines IL-1α, IL-1β, IL-6, IL-8, IL-10, TNF-α and MCP-1 showed significant increase (p<0.05) in a dose dependent manner in the placental explants treated with nSP-D and rhSP-D. In conclusion, the study emphasizes that SP-A and SP-D proteins associate with the spontaneous labor and SP-D plausibly contributes to the pro-inflammatory immune milieu of feto-maternal tissues.Funding provided by BT/PR15227/BRB/10/906/2011) Department of Biotechnology (DBT), Government of India http://dbtindia.nic.in/index.asp (TM) and Indian Council of Medical Research (ICMR) Junior Research Fellowship (JRF)/Senior Research Fellowship (SRF), Government of India, www.icmr.nic.in (AKY)

Investigation of Immune Biomarkers Using Subcutaneous Model of M. tuberculosis Infection in BALB/c Mice: A Preliminary Report

Evaluation and screening of vaccines against tuberculosis depends on development of proper cost effective disease models along with identification of different immune markers that can be used as surrogate endpoints of protection in preclinical and clinical studies. The objective of the present study was therefore evaluation of subcutaneous model of M.tuberculosis infection along with investigation of different immune biomarkers of tuberculosis infection in BALB/c mice. Groups of mice were infected subcutaneously with two different doses : high (2×106 CFU) and low doses (2×102 CFU) of M.tuberculosis and immune markers including humoral and cellular markers were evaluated 30 days post M.tuberculosis infections. Based on results, we found that high dose of subcutaneous infection produced chronic disease with significant (p<0.001) production of immune markers of infection like IFNγ, heat shock antigens (65, 71) and antibody titres against panel of M.tuberculosis antigens (ESAT-6, CFP-10, Ag85B, 45kDa, GroES, Hsp-16) all of which correlated with high bacterial burden in lungs and spleen. To conclude high dose of subcutaneous infection produces chronic TB infection in mice and can be used as convenient alternative to aerosol models in resource limited settings. Moreover assessment of immune markers namely mycobacterial antigens and antibodies can provide us valuable insights on modulation of immune response post infection. However further investigations along with optimization of study protocols are needed to justify the outcome of present study and establish such markers as surrogate endpoints of vaccine protection in preclinical and clinical studies in futur

NN Core Interactions and Differential Cross Sections from One Gluon Exchange

We derive nonstrange baryon-baryon scattering amplitudes in the nonrelativistic quark model using the ``quark Born diagram" formalism. This approach describes the scattering as a single interaction, here the one-gluon-exchange (OGE) spin-spin term followed by constituent interchange, with external nonrelativistic baryon wavefunctions attached to the scattering diagrams to incorporate higher-twist wavefunction effects. The short-range repulsive core in the NN interaction has previously been attributed to this spin-spin interaction in the literature; we find that these perturbative constituent-interchange diagrams do indeed predict repulsive interactions in all I,S channels of the nucleon-nucleon system, and we compare our results for the equivalent short-range potentials to the core potentials found by other authors using nonperturbative methods. We also apply our perturbative techniques to the N$\Delta$ and $\Delta\Delta$ systems: Some $\Delta\Delta$ channels are found to have attractive core potentials and may accommodate ``molecular" bound states near threshold. Finally we use our Born formalism to calculate the NN differential cross section, which we compare with experimental results for unpolarised proton-proton elastic scattering. We find that several familiar features of the experimental differential cross section are reproduced by our Born-order result.Comment: 27 pages, figures available from the authors, revtex, CEBAF-TH-93-04, MIT-CTP-2187, ORNL-CCIP-93-0

Surfactant protein D inhibits HIV-1 infection of target cells via interference with gp120-CD4 interaction and modulates pro-inflammatory cytokine production

© 2014 Pandit et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Surfactant Protein SP-D, a member of the collectin family, is a pattern recognition protein, secreted by mucosal epithelial cells and has an important role in innate immunity against various pathogens. In this study, we confirm that native human SP-D and a recombinant fragment of human SP-D (rhSP-D) bind to gp120 of HIV-1 and significantly inhibit viral replication in vitro in a calcium and dose-dependent manner. We show, for the first time, that SP-D and rhSP-D act as potent inhibitors of HIV-1 entry in to target cells and block the interaction between CD4 and gp120 in a dose-dependent manner. The rhSP-D-mediated inhibition of viral replication was examined using three clinical isolates of HIV-1 and three target cells: Jurkat T cells, U937 monocytic cells and PBMCs. HIV-1 induced cytokine storm in the three target cells was significantly suppressed by rhSP-D. Phosphorylation of key kinases p38, Erk1/2 and AKT, which contribute to HIV-1 induced immune activation, was significantly reduced in vitro in the presence of rhSP-D. Notably, anti-HIV-1 activity of rhSP-D was retained in the presence of biological fluids such as cervico-vaginal lavage and seminal plasma. Our study illustrates the multi-faceted role of human SPD against HIV-1 and potential of rhSP-D for immunotherapy to inhibit viral entry and immune activation in acute HIV infection. © 2014 Pandit et al.The work (Project no. 2011-16850) was supported by Medical Innovation Fund of Indian Council of Medical Research, New Delhi, India (www.icmr.nic.in/)