The POLIPO Security Framework

Systems of systems are dynamic coalitions of distributed, autonomous and heterogeneous systems that collaborate to achieve a common goal. While offering several advantages in terms of scalability and flexibility, the systems of systems paradigm has a significant impact on systems interoperability and on the security requirements of the collaborating systems. In this chapter we introduce POLIPO, a security framework that protects the information exchanged among the systems in a system of systems, while preserving systems’ autonomy and interoperability. Information is protected from unauthorized access and improper modification by combining context-aware access control with trust management. Autonomy and interoperability are enabled by the use of ontology-based services. More precisely, each authority may refer to different ontologies to define the semantics of the terms used in the security policy of the system it governs and to describe domain knowledge and context information. A semantic alignment technique is then employed to map concepts from different ontologies and align the systems’ vocabularies. We demonstrate the applicability of our solution with a prototype implementation of the framework for a scenario in the maritime safety and security domain

A Genetically Hard-Wired Metabolic Transcriptome in Plasmodium falciparum Fails to Mount Protective Responses to Lethal Antifolates

Genome sequences of Plasmodium falciparum allow for global analysis of drug responses to antimalarial agents. It was of interest to learn how DNA microarrays may be used to study drug action in malaria parasites. In one large, tightly controlled study involving 123 microarray hybridizations between cDNA from isogenic drug-sensitive and drug-resistant parasites, a lethal antifolate (WR99210) failed to over-produce RNA for the genetically proven principal target, dihydrofolate reductase-thymidylate synthase (DHFR-TS). This transcriptional rigidity carried over to metabolically related RNA encoding folate and pyrimidine biosynthesis, as well as to the rest of the parasite genome. No genes were reproducibly up-regulated by more than 2-fold until 24 h after initial drug exposure, even though clonal viability decreased by 50% within 6 h. We predicted and showed that while the parasites do not mount protective transcriptional responses to antifolates in real time, P. falciparum cells transfected with human DHFR gene, and adapted to long-term WR99210 exposure, adjusted the hard-wired transcriptome itself to thrive in the presence of the drug. A system-wide incapacity for changing RNA levels in response to specific metabolic perturbations may contribute to selective vulnerabilities of Plasmodium falciparum to lethal antimetabolites. In addition, such regulation affects how DNA microarrays are used to understand the mode of action of antimetabolites

A Major Role for the Plasmodium falciparum ApiAP2 Protein PfSIP2 in Chromosome End Biology

The heterochromatic environment and physical clustering of chromosome ends at the nuclear periphery provide a functional and structural framework for antigenic variation and evolution of subtelomeric virulence gene families in the malaria parasite Plasmodium falciparum. While recent studies assigned important roles for reversible histone modifications, silent information regulator 2 and heterochromatin protein 1 (PfHP1) in epigenetic control of variegated expression, factors involved in the recruitment and organization of subtelomeric heterochromatin remain unknown. Here, we describe the purification and characterization of PfSIP2, a member of the ApiAP2 family of putative transcription factors, as the unknown nuclear factor interacting specifically with cis-acting SPE2 motif arrays in subtelomeric domains. Interestingly, SPE2 is not bound by the full-length protein but rather by a 60kDa N-terminal domain, PfSIP2-N, which is released during schizogony. Our experimental re-definition of the SPE2/PfSIP2-N interaction highlights the strict requirement of both adjacent AP2 domains and a conserved bipartite SPE2 consensus motif for high-affinity binding. Genome-wide in silico mapping identified 777 putative binding sites, 94% of which cluster in heterochromatic domains upstream of subtelomeric var genes and in telomere-associated repeat elements. Immunofluorescence and chromatin immunoprecipitation (ChIP) assays revealed co-localization of PfSIP2-N with PfHP1 at chromosome ends. Genome-wide ChIP demonstrated the exclusive binding of PfSIP2-N to subtelomeric SPE2 landmarks in vivo but not to single chromosome-internal sites. Consistent with this specialized distribution pattern, PfSIP2-N over-expression has no effect on global gene transcription. Hence, contrary to the previously proposed role for this factor in gene activation, our results provide strong evidence for the first time for the involvement of an ApiAP2 factor in heterochromatin formation and genome integrity. These findings are highly relevant for our understanding of chromosome end biology and variegated expression in P. falciparum and other eukaryotes, and for the future analysis of the role of ApiAP2-DNA interactions in parasite biology

Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite

The molecular mechanisms underlying transcriptional regulation in apicomplexan parasites remain poorly understood. Recently, the Apicomplexan AP2 (ApiAP2) family of DNA binding proteins was identified as a major class of transcriptional regulators that are found across all Apicomplexa. To gain insight into the regulatory role of these proteins in the malaria parasite, we have comprehensively surveyed the DNA-binding specificities of all 27 members of the ApiAP2 protein family from Plasmodium falciparum revealing unique binding preferences for the majority of these DNA binding proteins. In addition to high affinity primary motif interactions, we also observe interactions with secondary motifs. The ability of a number of ApiAP2 proteins to bind multiple, distinct motifs significantly increases the potential complexity of the transcriptional regulatory networks governed by the ApiAP2 family. Using these newly identified sequence motifs, we infer the trans-factors associated with previously reported plasmodial cis-elements and provide evidence that ApiAP2 proteins modulate key regulatory decisions at all stages of parasite development. Our results offer a detailed view of ApiAP2 DNA binding specificity and take the first step toward inferring comprehensive gene regulatory networks for P. falciparum

The photodissociation dynamics of ozone at 226 and 248 nm: O(3PJ) atomic angular momentum polarization.

Speed distributions, and spatial anisotropy and atomic angular momentum polarization parameters have been determined for the O((3)P(J)) products following the photodissociation of ozone at 248 and 226 nm using velocity map ion imaging. The data have been interpreted in terms of two dissociation mechanisms that give rise to fast and slow products. In both cases, excitation is believed to occur to the B state. Consistent with previous interpretations, the speed distributions, translational anisotropy parameters, and angular momentum polarization moments support the assignment of the major pathway to curve crossing from the B to the repulsive R surface, generating fast fragments in a wide range of vibrational states. For the slow fragments, it is proposed that following excitation to the B state, the system crosses onto the A state. The crossing seam is only accessible to molecules that are highly vibrationally excited and therefore possess modest recoil speeds. Once on the A state, the wavepacket is thought to funnel through a conical intersection to the ground state. The velocity distributions, spatial anisotropy parameters, spin-orbit populations and polarization data each lend support to this mechanism

Detecting RNA base methylations in single cells by in situ hybridization

Methylated bases in tRNA, rRNA and mRNA control a variety of cellular processes, including protein synthesis, antimicrobial resistance and gene expression. Currently, bulk methods that report the average methylation state of ~104–107 cells are used to detect these modifications, obscuring potentially important biological information. Here, we use in situ hybridization of Molecular Beacons for single-cell detection of three methylations (m62A, m1G and m3U) that destabilize Watson–Crick base pairs. Our method—methylation-sensitive RNA fluorescence in situ hybridization—detects single methylations of rRNA, quantifies antibiotic-resistant bacteria in mixtures of cells and simultaneously detects multiple methylations using multicolor fluorescence imaging

The POLIPO Security Framework

Systems of systems are dynamic coalitions of distributed, autonomous and heterogeneous systems that collaborate to achieve a common goal. While offering several advantages in terms of scalability and flexibility, the systems of systems paradigm has a significant impact on systems interoperability and on the security requirements of the collaborating systems. In this chapter we introduce POLIPO, a security framework that protects the information exchanged among the systems in a system of systems, while preserving systems’ autonomy and interoperability. Information is protected from unauthorized access and improper modification by combining context-aware access control with trust management. Autonomy and interoperability are enabled by the use of ontology-based services. More precisely, each authority may refer to different ontologies to define the semantics of the terms used in the security policy of the system it governs and to describe domain knowledge and context information. A semantic alignment technique is then employed to map concepts from different ontologies and align the systems’ vocabularies. We demonstrate the applicability of our solution with a prototype implementation of the framework for a scenario in the maritime safety and security domain