BPSL1626 : Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design Against Burkholderia pseudomallei

Due to significant advances in computational biology, protein prediction, together with antigen and epitope design, have rapidly moved from conventional methods, based on experimental approaches, to in silico-based bioinformatics methods. In this context, we report a reverse vaccinology study that identified a panel of 104 candidate antigens from the Gram-negative bacterial pathogen Burkholderia pseudomallei, which is responsible for the disease melioidosis. B. pseudomallei can cause fatal sepsis in endemic populations in the tropical regions of the world and treatment with antibiotics is mostly ineffective. With the aim of identifying potential vaccine candidates, we report the experimental validation of predicted antigen and type I fimbrial subunit, BPSL1626, which we show is able to recognize and bind human antibodies from the sera of Burkholderia infected patients and to stimulate T-lymphocytes in vitro. The prerequisite for a melioidosis vaccine, in fact, is that both antibody- and cell-mediated immune responses must be triggered. In order to reveal potential antigenic regions of the protein that may aid immunogen re-design, we also report the crystal structure of BPSL1626 at 1.9 angstrom resolution on which structure-based epitope predictions were based. Overall, our data suggest that BPSL1626 and three epitope regions here-identified can represent viable candidates as potential antigenic molecules

Channel Assignment with Separation for Interference Avoidance in Wireless Networks

Given an integer $\sigma > 1$, a vector $(\delta_1, \delta_2, \ldots, \delta_{\sigma-1})$ of nonnegative integers, and an undirected graph $G=(V,E)$, an $L(\delta_1, \delta_2, \ldots,\delta_{\sigma-1})$-coloring of $G$ is a function $f$ from the vertex set $V$ to a set of nonnegative integers such that $| f(u) -f(v) | \ge \delta_i$, if $d(u,v) = i, \ 1 \le i \le \sigma-1, \$ where $d(u,v)$ is the distance (i.e. the minimum number of edges) between the vertices $u$ and $v$. An optimal $L(\delta_1, \delta_2, \ldots,\delta_{\sigma-1})$-coloring for $G$ is one using the smallest range $\lambda$ of integers over all such colorings. This problem has relevant application in channel assignment for interference avoidance in wireless networks, where channels (i.e. colors) assigned to interfering stations (i.e. vertices) at distance $i$ must be at least $\delta_i$ apart, while the same channel can be reused in vertices whose distance is at least $\sigma$. In particular, two versions of the coloring problem -- $L(2,1,1)$, and $L(\delta_1, 1, \ldots,1)$ -- are considered. Since these versions of the problem are $NP$-hard for general graphs, efficient algorithms for finding optimal colorings are provided for specific graphs modeling realistic wireless networks including rings, bidimensional grids, and cellular grids

From crystal structure to in silico epitope discovery in the Burkholderia pseudomallei flagellar hook-associated protein FlgK

Melioidosis, caused by the Gram-negative bacterium Burkholderia pseudomallei, is a potentially fatal infection that is endemic in Southeast Asia and Northern Australia that is poorly controlled by antibiotics. Research efforts to identify antigenic components for a melioidosis vaccine have led to the identification of several proteins, including subunits forming the flagella that mediate bacterial motility, host colonization, and virulence. This study focuses on the B. pseudomallei flagellar hook-associated protein (FlgKBp), and provides the first insights into the 3D structure of FlgK proteins as targets for structure-based antigen engineering. The FlgKBp crystal structure (presented here at 1.8-\uc5 resolution) reveals a multidomain fold, comprising two small \u3b2-domains protruding from a large elongated \u3b1-helical bundle core. The evident structural similarity to flagellin, the flagellar filament subunit protein, suggests that, depending on the bacterial species, flagellar hook-associated proteins are likely to show a conserved, elongated \u3b1-helical bundle scaffold coupled to a variable number of smaller domains. Furthermore, we present immune serum recognition data confirming, in agreement with previous findings, that recovered melioidosis patients produce elevated levels of antibodies against FlgKBp, in comparison with seronegative and seropositive healthy subjects. Moreover, we show that FlgKBp has cytotoxic effects on cultured murine macrophages, suggesting an important role in bacterial pathogenesis. Finally, computational epitope prediction methods applied to the FlgKBp crystal structure, coupled with in vitro mapping, allowed us to predict three antigenic regions that locate to discrete protein domains. Taken together, our results point to FlgKBp as a candidate for the design and production of epitope-containing subunits/domains as potential vaccine components