Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions

This work was supported in part by the European Union, Area NMP.2013.1.1–2: Self-assembly of naturally occurring nanosystems: CellulosomePlus Project number: 604530, and by the EU Seventh Framework Programme (FP7 2007–2013) under the WallTraC project (Grant Agreement no 263916), and BioStruct-X (grant agreement no 283570). This paper reflects the author’s views only. The European Community is not liable for any use that may be made of the information contained herein. CMGAF is also supported by Fundação para a Ciência e a Tecnologia (Lisbon, Portugal) through grants PTDC/BIA-PRO/103980/2008 and EXPL/BIA-MIC/1176/2012. EAB is also funded by a grant (No. 1349/13) from the Israel Science Foundation (ISF), Jerusalem, Israel and by a grant (No. 2013284) from the U.S.-Israel Binational Science Foundation (BSF). E.A.B. is the incumbent of The Maynard I. and Elaine Wishner Chair of Bio-organic Chemistry.Peer reviewedPublisher PD

USP18-Based Negative Feedback Control Is Induced by Type I and Type III Interferons and Specifically Inactivates Interferon α Response

Type I interferons (IFN) are cytokines that are rapidly secreted upon microbial infections and regulate all aspects of the immune response. In humans 15 type I IFN subtypes exist, of which IFN α2 and IFN β are used in the clinic for treatment of different pathologies. IFN α2 and IFN β are non redundant in their expression and in their potency to exert specific bioactivities. The more recently identified type III IFNs (3 IFN λ or IL-28/IL-29) bind an unrelated cell-type restricted receptor. Downstream of these two receptor complexes is a shared Jak/Stat pathway. Several mechanisms that contribute to the shut down of the IFN-induced signaling have been described at the molecular level. In particular, it has long been known that type I IFN induces the establishment of a desensitized state. In this work we asked how the IFN-induced desensitization integrates into the network built by the multiple type I IFN subtypes and type III IFNs. We show that priming of cells with either type I IFN or type III IFN interferes with the cell's ability to further respond to all IFN α subtypes. Importantly, primed cells are differentially desensitized in that they retain sensitivity to IFN β. We show that USP18 is necessary and sufficient to induce differential desensitization, by impairing the formation of functional binding sites for IFN α2. Our data highlight a new type of differential between IFNs α and IFN β and underline a cross-talk between type I and type III IFN. This cross-talk could shed light on the reported genetic variation in the IFN λ loci, which has been associated with persistence of hepatitis C virus and patient's response to IFN α2 therapy

A duality theory of bilattices

Abstract. Recent studies of the algebraic properties of bilattices have provided insight into their internal strucutres, and have led to practical results, especially in reducing the computational complexity of bilattice-based multivalued logic programs. In this paper the representation theorem for interlaced bilattices without negation found i

XPath containment in the presence of disjunction, DTDs, and variables

Abstract. XPath is a simple language for navigating an XML tree and returning a set of answer nodes. The focus in this paper is on the complexity of the containment problem for various fragments of XPath. In addition to the basic operations (child, descendant, filter, and wildcard), we consider disjunction, DTDs and variables. W.r.t. variables we study two semantics: (1) the value of variables is given by an outer context; (2) the value of variables is defined existentially. We establish an almost complete classification of the complexity of the containment problem w.r.t. these fragments.

An Infinite Automaton Characterization of Double Exponential Time

Infinite-state automata are a new invention: they are automata that have an infinite number of states represented by words, transitions defined using rewriting, and with sets of initial and final states. Infinite-state automata have gained recent interest due to a remarkable result by Morvan and Stirling, which shows that automata with transitions defined using rational rewriting precisely capture context-sensitive (NLinSpace) languages. In this paper, we show that infinite automata defined using a form of multi-stack rewriting precisely defines double exponential time (more precisely, 2ETime, the class of problems solvable in 22O(n) time). The salient aspect of this characterization is that the automata have no ostensible limits on time nor space, and neither direction of containment with respect to 2ETime is obvious. In this sense, the result captures the complexity class qualitatively, by restricting the power of rewriting