ICONA: Inter Cluster ONOS Network Application

Several Network Operating Systems (NOS) have been proposed in the last few years for Software Defined Networks; however, a few of them are currently offering the resiliency, scalability and high availability required for production environments. Open Networking Operating System (ONOS) is an open source NOS, designed to be reliable and to scale up to thousands of managed devices. It supports multiple concurrent instances (a cluster of controllers) with distributed data stores. A tight requirement of ONOS is that all instances must be close enough to have negligible communication delays, which means they are typically installed within a single datacenter or a LAN network. However in certain wide area network scenarios, this constraint may limit the speed of responsiveness of the controller toward network events like failures or congested links, an important requirement from the point of view of a Service Provider. This paper presents ICONA, a tool developed on top of ONOS and designed in order to extend ONOS capability in network scenarios where there are stringent requirements in term of control plane responsiveness. In particular the paper describes the architecture behind ICONA and provides some initial evaluation obtained on a preliminary version of the tool.Comment: Paper submitted to a conferenc

Tandem quadruplication of HMA4 in the zinc (Zn) and cadmium (Cd) hyperaccumulator noccaea caerulescens

Zinc (Zn) and cadmium (Cd) hyperaccumulation may have evolved twice in the Brassicaceae, in Arabidopsis halleri and in the Noccaea genus. Tandem gene duplication and deregulated expression of the Zn transporter, HMA4, has previously been linked to Zn/Cd hyperaccumulation in A. halleri. Here, we tested the hypothesis that tandem duplication and deregulation of HMA4 expression also occurs in Noccaea. A Noccaea caerulescens genomic library was generated, containing 36,864 fosmid pCC1FOSTM clones with insert sizes ~20–40 kbp, and screened with a PCR-generated HMA4 genomic probe. Gene copy number within the genome was estimated through DNA fingerprinting and pooled fosmid pyrosequencing. Gene copy numbers within individual clones was determined by PCR analyses with novel locus specific primers. Entire fosmids were then sequenced individually and reads equivalent to 20-fold coverage were assembled to generate complete whole contigs. Four tandem HMA4 repeats were identified in a contiguous sequence of 101,480 bp based on sequence overlap identities. These were flanked by regions syntenous with up and downstream regions of AtHMA4 in Arabidopsis thaliana. Promoter-reporter b-glucuronidase (GUS) fusion analysis of a NcHMA4 in A. thaliana revealed deregulated expression in roots and shoots, analogous to AhHMA4 promoters, but distinct from AtHMA4 expression which localised to the root vascular tissue. This remarkable consistency in tandem duplication and deregulated expression of metal transport genes between N. caerulescens and A. halleri, which last shared a common ancestor >40 mya, provides intriguing evidence that parallel evolutionary pathways may underlie Zn/Cd hyperaccumulation in Brassicaceae

Context-Dependent Dual Role of SKI8 Homologs in mRNA Synthesis and Turnover

Eukaryotic mRNA transcription and turnover is controlled by an enzymatic machinery that includes RNA polymerase II and the 3′ to 5′ exosome. The activity of these protein complexes is modulated by additional factors, such as the nuclear RNA polymerase II-associated factor 1 (Paf1c) and the cytoplasmic Superkiller (SKI) complex, respectively. Their components are conserved across uni- as well as multi-cellular organisms, including yeast, Arabidopsis, and humans. Among them, SKI8 displays multiple facets on top of its cytoplasmic role in the SKI complex. For instance, nuclear yeast ScSKI8 has an additional function in meiotic recombination, whereas nuclear human hSKI8 (unlike ScSKI8) associates with Paf1c. The Arabidopsis SKI8 homolog VERNALIZATION INDEPENDENT 3 (VIP3) has been found in Paf1c as well; however, whether it also has a role in the SKI complex remains obscure so far. We found that transgenic VIP3-GFP, which complements a novel vip3 mutant allele, localizes to both nucleus and cytoplasm. Consistently, biochemical analyses suggest that VIP3–GFP associates with the SKI complex. A role of VIP3 in the turnover of nuclear encoded mRNAs is supported by random-primed RNA sequencing of wild-type and vip3 seedlings, which indicates mRNA stabilization in vip3. Another SKI subunit homolog mutant, ski2, displays a dwarf phenotype similar to vip3. However, unlike vip3, it displays neither early flowering nor flower development phenotypes, suggesting that the latter reflect VIP3's role in Paf1c. Surprisingly then, transgenic ScSKI8 rescued all aspects of the vip3 phenotype, suggesting that the dual role of SKI8 depends on species-specific cellular context

Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana.

Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality–drafted genomes assembled based on reference genomes that can have highly divergent or haplotypic regions. The self-fertilizing nature of Arabidopsis thaliana poses an advantage to sequencing projects because its genome is mostly homozygous. To determine the accuracy of an Arabidopsis drafted genome in less conserved regions, we performed a resequencing experiment on a 3 ~71-kb genomic interval in the Landsberg erecta (Ler-0) accession. We identified novel structural variations (SVs) between Ler-0 and the reference accession Col-0 using a long-range polymerase chain reaction approach to generate an Illumina data set that has positional information, that is, a data set with reads that map to a known location. Positional information is important for accurate genome assembly and the resolution of SVs particularly in highly duplicated or repetitive regions. Sixty-one regions with misassembly signatures were identified from the Ler-0 draft, suggesting the presence of novel SVs that are not represented in the draft sequence. Sixty of those were resolved by iterative mapping using our data set. Fifteen large indels (>100 bp) identified from this study were found to be located either within protein-coding regions or upstream regulatory regions, suggesting the formation of novel alleles or altered regulation of existing genes in Ler-0. We propose future genome-sequencing experiments to follow a clone-based approach that incorporates positional information to ultimately reveal haplotype-specific differences between accessions

Paradigms of Healthcare Systems, Law, and Regulation: A Transatlantic Conversation

This chapter assesses how the law creates and sustains healthcare systems. It considers six paradigm concepts which are important in the structures of healthcare systems and how the law seeks to support and encourage the effective provision of healthcare to relevant populations. These concepts are quality/accessibility; health citizenship and a “right to health”; individual liberty; market competition; economic productivity; and “health justice” and integrated social services. The chapter then discusses five structures for health system regulation, starting with the simplest: public provision of health services, publicly funded but privately supplied health services, self-regulating health professions, public–private partnerships, and nonprofit and charitable organizations. Finally, it compares European and American approaches to the geographical dimensions of health system law and regulation, discussing paradigms of federalism and localism

Analysis of Communication Models in Web Service Compositions

In this paper we describe an approach for the verification of Web service compositions dened by sets of BPEL processes. The key aspect of such a verification is the model adopted for representing the communications among the services participating in the composition. Indeed, these communications are asynchronous and buffered in the existing execution frameworks, while most verication approaches assume a synchronous communication model for efficiency reasons. In our approach, we develop a parametric model for describing Web service compositions, which allows us to capture a hierarchy of communication models, ranging from synchronous communications to asynchronous communications with complex buffer structures. Moreover, we develop a technique to associate with a Web service composition the most adequate communication model, i.e., the simplest model that is sufficient to capture all the behaviors of the composition. This way, we can provide an accurate model of a wider class of service composition scenarios, while preserving as much as possible an efficient performance in verification

Hybrid IP/SDN Networking: Open Implementation and Experiment Management Tools

The introduction of SDN in large-scale IP provider networks is still an open issue and different solutions have been suggested so far. In this paper, we propose a hybrid approach that allows the coexistence of traditional IP routing with SDN based forwarding within the same provider domain. The solution is called OSHI-Open Source Hybrid IP/SDN networking, as we have fully implemented it combining and extending open source software. We discuss the OSHI system architecture and the design and implementation of advanced services like pseudo wires and virtual switches. In addition, we describe a set of open source management tools for the emulation of the proposed solution using either the Mininet emulator or distributed physical testbeds. We refer to this suite of tools as Mantoo (management tools). Mantoo includes an extensible Web-based graphical topology designer, which provides different layered network "views" (e.g., from physical links to service relationships among nodes). The suite can validate an input topology, automatically deploy it over a Mininet emulator or a distributed SDN testbed and allows access to emulated nodes by opening consoles in the web GUI. Mantoo provides also tools to evaluate the performance of the deployed nodes