Even the Easiest(?) Graph Coloring Problem Is Not Easy in Streaming!

We study a graph coloring problem that is otherwise easy in the RAM model but becomes quite non-trivial in the one-pass streaming model. In contrast to previous graph coloring problems in streaming that try to find an assignment of colors to vertices, our main work is on estimating the number of conflicting or monochromatic edges given a coloring function that is streaming along with the graph; we call the problem Conflict-Est. The coloring function on a vertex can be read or accessed only when the vertex is revealed in the stream. If we need the color on a vertex that has streamed past, then that color, along with its vertex, has to be stored explicitly. We provide algorithms for a graph that is streaming in different variants of the vertex arrival in one-pass streaming model, viz. the Vertex Arrival (VA), Vertex Arrival With Degree Oracle (VAdeg), Vertex Arrival in Random Order (VArand) models, with special focus on the random order model. We also provide matching lower bounds for most of the cases. The mainstay of our work is in showing that the properties of a random order stream can be exploited to design efficient streaming algorithms for estimating the number of monochromatic edges. We have also obtained a lower bound, though not matching the upper bound, for the random order model. Among all the three models vis-a-vis this problem, we can show a clear separation of power in favor of the VArand model

Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein

RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host

Elucidating the molecular mechanisms of oxidative damage in viral hepatitis

Virale Hepatitis zählt zu den häufigsten Todesursachen, die durch Lebererkrankungen verursacht werden. Sie zeichnet sich durch eine komplexe Pathogenese aus, die sowohl durch Mechanismen des Immunsystems als auch durch Veränderungen in der zellulären und gewebsspezifischen Homöostase ausgelöst wird und letzten Endes zu einem schweren Leberschaden führt. Die durch das Virus ausgelöste Immunpathologie wird in erster Linie durch Zellpopulationen und Botenstoffe ausgelöst, die ein natürlicher Bestandteil der antiviralen Immunantwort sind. Eine Veränderung in der Homöostase entsteht durch Ungleichgewichte im physiologischen Zustand der beteiligten Zellen. Beispielsweise kann das intrazelluläre Redox-Gleichgewicht verändert werden, was zu einer erhöhtem oxidativen Stress führen kann. Es wurde gezeigt, dass solch oxidativer Stress ein wichtigen Parameter ist, der zur Pathologie einer viralen Hepatitis beiträgt. Trotz dieser Erkenntnis sind die molekularen Mechanismen, die zu einer Zunahme an oxidativem Stress während einer viralen Infektion führen, sowie die Rolle der anti-oxidativen Schutzmechanismen des Wirtes, beispielsweise den Superoxid-Dismutasen (SODs), bisher wenig verstanden. In dieser Arbeit zeigen wir einen bisher nicht beschriebenen Mechanismus, wie Typ I Interferon (IFN-I), welches ein Botenstoff des angeborenen Immunsystems ist, zu oxidativem Leberschaden führen kann. Wir haben außerdem das anti-oxidative Enzym Superoxid-Dismutase 1 (SOD1) als den essentiellen Wirtsfaktor identifiziert, der die Leber während einer viralen Infektion vor oxidativem Stress schützt. Nach einer viralen Infektion der Leber haben wir beobachtet, dass dies zu einer Herunterregulation von SOD1 führt. Sod1-/- Mäuse zeigten nach einer viralen Infektion erhöhte Entzündungsreaktionen und erhöhten Leberschaden. Dieser konnte durch Behandlung der Mäuse mit einem Antioxidans rückgängig gemacht werden. Die Behandlung von Wildtyp-Mäusen mit IFN-I verringerte die Expression von SOD1 in der Leber und führte in nichtinfizierten Sod1-/- und Wildtyp-Mäusen zu einem oxidativen Leberschaden. Zusätzlich hat eine Blockade der IFN-I-Signalwege dazu geführt, dass sowohl Wildtyp- als auch Sod1-/- Mäuse nach viraler Infektion vor Leberschaden geschützt waren. Aus den Ergebnissen dieser Arbeit leitet sich ein neues Konzept einer vom angeborenen Immunsystem-induzierten Immunpathologie ab, welches IFN-I-Signalwege auf neuartige Weise mit der Redox-Homöostase und Gewebeschaden in der Leber in Zusammenhang bringt.Viral hepatitis is a primary cause of mortality due to liver diseases worldwide. It manifests with a complex pathogenesis that involves immune-related events and altered cellular and tissue homeostasis, both of which eventually drive liver damage. The immunological response of the host to the viral infection involves various cellular populations and mediators. The altered cellular homeostasis, on the other hand, refers to disruptions in the physiological state of the cell. This includes, for example, an imbalance in the cellular redox state, a consequence of which would be oxidative stress. One of the important factors implicated in the pathology of viral hepatitis is oxidative stress. However, there are several aspects till date that are not clearly understood, for example, what molecular mechanisms are responsible for initiating oxidative stress and what roles do the host anti-oxidative systems such as superoxide dismutases (SODs) play in protecting the host from liver damage. We describe a new concept of how type I interferon (IFN-I), a branch of the innate immune system induces oxidative stress and subsequently liver damage. We further identified the key antioxidant enzyme superoxide dismutase 1 (SOD1) as an essential host factor that prevented oxidative stress and hepatitis. Upon viral infection of the liver, we observed dysregulation of redox pathways, which included downregulation of SOD1. Sod1-/- mice suffered from exacerbated hepatitis compared to wild type mice post viral infection, which was ameliorated upon administration of antioxidant. Type I interferon (IFN-I) downregulated Sod1 in wild type mice on a transcriptional level and was sufficient to cause oxidative damage in the livers of Sod1-/- and wild type mice in the absence of infection. Moreover, both WT and Sod1-/- mice were protected against virus-induced hepatitis upon blocking IFN-I signaling. These results provide a new concept of innate immunity-driven immunopathology, connecting IFN-I signaling with redox homeostasis and tissue damage.submitted by Anannya BhattacharyaZusammenfassung in deutscher SpracheAbweichender Titel laut Übersetzung der Verfasserin/des VerfassersMedizinische Universität Wien, Dissertation, 2016OeBB(VLID)171449

Reactivity of polyaminocarboxylatoruthenium(III) complexes with serine and their protease inhibition

Reaction of [Ru(edta)(H2O)]� (edta4�¼ethylenediaminetetraacetate), [Ru(pdta)(H2O)]� (pdta4�¼propylenediaminetetraacetate) and [Ru(hedtra)(H2O)] (hedtra3�¼N-hydroxyethylethylenediaminetriacetate) with S-serine (Ser) was studied spectrophotometrically and kinetically. Serine protease inhibition studies were performed with the three complexes using the serine protease enzymes chymotrypsin and subtilisin with azoalbumin as substrate. Results are discussed in terms of the reactivity of the Ru-pac (pac¼polyaminopolycarboxylates) complexes with serine. The order of protease inhibition efficacy of the Ru-pac complexes is [Ru(pdta)(H2O)]�>[Ru(edta)(H2O)]��[Ru(hedtra)(H2O)], in good agreement with the observed reactivity of Ru-pac complexes with serin

Interferon inducible GBPs restrict Burkholderia thailandensis motility induced cell-cell fusion.

Innate immunity responds to pathogens by producing alarm signals and activating pathways that make host cells inhospitable for pathogen replication. The intracellular bacterium Burkholderia thailandensis invades the cytosol, hijacks host actin, and induces cell fusion to spread to adjacent cells, forming multinucleated giant cells (MNGCs) which promote bacterial replication. We show that type I interferon (IFN) restricts macrophage MNGC formation during B. thailandensis infection. Guanylate-binding proteins (GBPs) expressed downstream of type I IFN were required to restrict MNGC formation through inhibition of bacterial Arp2/3-dependent actin motility during infection. GTPase activity and the CAAX prenylation domain were required for GBP2 recruitment to B. thailandensis, which restricted bacterial actin polymerization required for MNGC formation. Consistent with the effects in in vitro macrophages, Gbp2-/-, Gbp5-/-, GbpChr3-KO mice were more susceptible to intranasal infection with B. thailandensis than wildtype mice. Our findings reveal that IFN and GBPs play a critical role in restricting cell-cell fusion and bacteria-induced pathology during infection

The lipid-sensor TREM2 aggravates disease in a model of LCMV-induced hepatitis

textabstractLipid metabolism is increasingly being appreciated to affect immunoregulation, inflammation and pathology. In this study we found that mice infected with lymphocytic choriomeningitis virus (LCMV) exhibit global perturbations of circulating serum lipids. Mice lacking the lipid-sensing surface receptor triggering receptor expressed on myeloid cells 2 (Trem2 -/-) were protected from LCMV-induced hepatitis and showed improved virus control despite comparable virus-specific T cell responses. Non-hematopoietic expression of TREM2 was found to be responsible for aggravated hepatitis, indicating a novel role for TREM2 in the non-myeloid compartment. These results suggest a link between virus-perturbed lipids and TREM2 that modulates liver pathogenesis upon viral infection. Targeted interventions of this immunoregulatory axis may ameliorate tissue pathology in hepatitis

Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein

<div><p>RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected <i>Trim21</i>^-/- mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host.</p></div

Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein

<div><p>RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected <i>Trim21</i>^-/- mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host.</p></div

Functional screening for L protein interactors involved in LCMV life cycle.

<p>(<b>A</b>) Two independently generated HeLa S3 CRISPR-Cas9 targeted cell pools per gene of interest for 5 genes were infected in triplicate wells with LCMV Cl13 WT at a MOI of 0.01 and viral loads were measured at 36 hours post infection by focus forming assay. The obtained data were normalized to the non-target control and log2 transformed. (<b>B</b>) Two HeLa S3 CRISPR-Cas9 TRIM21-targeted cell pools were reconstituted either with TRIM21-expressing plasmid or with non-target control and 36 hour post transfection were infected in triplicate wells with LCMV Cl13 WT at a MOI of 0.01. Viral loads were measured at 36 hours post infection by focus forming assay. The obtained data were normalized to the non-target control and log2 transformed. (<b>C</b>-<b>D</b>) C57BL/6 and <i>Trim21</i>^-/- mice were infected with 2x10⁶ FFU of the indicated viruses. Viral titers were determined in (<b>C</b>) blood at indicated time points and in (<b>D</b>) organs at 21 days post infection. The data shown in (<b>C</b>) is representative of two similar experiments. Each symbol and bar represents the mean ± SEM of three to five mice. Statistical significance was calculated by unpaired t-test (<b>A, B, D</b>) or by Two-way ANOVA (<b>C</b>). Significant p values were indicated as follows: ns—non significant, * p≤0.05, ** p≤0.01, *** p≤0.001, **** p≤0.0001.</p

Viral RNA-dependent RNA-polymerases target host proteome by common and virus-specific strategies.

<p><b>(A)</b> Integrated interactome of viral RdRp targets. Host proteins interacting with viral RdRps are highlighted in blue, the rest of the human proteome—in grey. <b>(B)</b> Largest connected component (LCC) analyses for global RdRps and LCMV only datasets. <b>(C)</b> Functional protein modules targeted by RdRps based on the community detection method. <b>(D)</b> Heat map representing virus-specific targeting of protein functional modules.</p