Phage-displayed peptides as capture antigens in an innovative assay for Taenia saginata-infected cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Host-specificity and morphometrics of female Haemonchus contortus, H. placei and H. similis (Nematoda: Trichostrongylidae) in cattle and sheep from shared pastures in Sao Paulo State, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Shared Escovopsis parasites between leaf-cutting and non-leaf-cutting ants in the higher attine fungus-growing ant symbiosis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Shared Feed as a Means of Deer-to-Deer Transmission of Mycobacterium bovis

To determine the ability of experimentally inoculated white-tailed deer (Odocoileus virginianus) to transmit Mycobacterium bovis to naive deer through the sharing of feed, four deer were intratonsillarly inoculated with 4x105 colony-forming units of M. bovis. On a daily basis, feed not consumed by inoculated deer after approximately 8 hr was offered to four naıve deer maintained in a separate pen, where direct contact, aerosol transmission, or transmission through personnel were prevented. After 150 days, naıve deer were euthanized and examined. All naıve deer had lesions consistent with tuberculosis and M. bovis was isolated from various tissues. The most commonly affected tissues were lung, tracheobronchial lymph nodes, and mediastinal lymph nodes. This study demonstrates the potential for indirect transmission of M. bovis through the sharing of feed. Intentional or unintentional feeding of deer by wildlife or agricultural interests in regions where M. bovis infection is endemic should be avoided because both direct and indirect transmission through sharing of feed are enhanced.

Survivable Lightpath Provisioning in WDM Mesh Networks Under Shared Path Protection and Signal Quality Constraints

This paper addresses the problem of survivable lightpath provisioning in wavelength-division-multiplexing (WDM) mesh networks, taking into consideration optical-layer protection and some realistic optical signal quality constraints. The investigated networks use sparsely placed optical–electrical–optical (O/E/O) modules for regeneration and wavelength conversion. Given a fixed network topology with a number of sparsely placed O/E/O modules and a set of connection requests, a pair of link-disjoint lightpaths is established for each connection. Due to physical impairments and wavelength continuity, both the working and protection lightpaths need to be regenerated at some intermediate nodes to overcome signal quality degradation and wavelength contention. In the present paper, resource-efficient provisioning solutions are achieved with the objective of maximizing resource sharing. The authors propose a resource-sharing scheme that supports three kinds of resource-sharing scenarios, including a conventional wavelength-link sharing scenario, which shares wavelength links between protection lightpaths, and two new scenarios, which share O/E/O modules between protection lightpaths and between working and protection lightpaths. An integer linear programming (ILP)-based solution approach is used to find optimal solutions. The authors also propose a local optimization heuristic approach and a tabu search heuristic approach to solve this problem for real-world, large mesh networks. Numerical results show that our solution approaches work well under a variety of network settings and achieves a high level of resource-sharing rates (over 60% for O/E/O modules and over 30% for wavelength links), which translate into great savings in network costs.

A Load-Balancing Shared-Protection-Path Reconfiguration Approach in WDM Wavelength-Routed Networks

Wavelength-routed networks (WRN) are very promising candidates for next-generation Internet and telecommunication backbones. In such a network, optical-layer protection is of paramount importance due to the risk of losing large amounts of data under a failure. To protect the network against this risk, service providers usually provide a pair of risk-independent working and protection paths for each optical connection. However, the investment made for the optical-layer protection increases network cost. To reduce the capital expenditure, service providers need to efficiently utilize their network resources. Among all the existing approaches, shared-path protection has proven to be practical and cost-efficient [1]. In shared-path protection, several protection paths can share a wavelength on a fiber link if their working paths are risk-independent. In real-world networks, provisioning is usually implemented without the knowledge of future network resource utilization status. As the network changes with the addition and deletion of connections, the network utilization will become sub-optimal. Reconfiguration, which is referred to as the method of re-provisioning the existing connections, is an attractive solution to fill in the gap between the current network utilization and its optimal value [2]. In this paper, we propose a new shared-protection-path reconfiguration approach. Unlike some of previous reconfiguration approaches that alter the working paths, our approach only changes protection paths, and hence does not interfere with the ongoing services on the working paths, and is therefore risk-free. Previous studies have verified the benefits arising from the reconfiguration of existing connections [2] [3] [4]. Most of them are aimed at minimizing the total used wavelength-links or ports. However, this objective does not directly relate to cost saving because minimizing the total network resource consumption does not necessarily maximize the capability of accommodating future connections. As a result, service providers may still need to pay for early network upgrades. Alternatively, our proposed shared-protection-path reconfiguration approach is based on a load-balancing objective, which minimizes the network load distribution vector (LDV, see Section 2). This new objective is designed to postpone network upgrades, thus bringing extra cost savings to service providers. In other words, by using the new objective, service providers can establish as many connections as possible before network upgrades, resulting in increased revenue. We develop a heuristic load-balancing (LB) reconfiguration approach based on this new objective and compare its performance with an approach previously introduced in [2] and [4], whose objective is minimizing the total network resource consumption.

A Heuristic with Bounded Guarantee to Compute Diverse Paths under Shared Protection in WDM Mesh Networks

Establishing a fault-tolerant connection in a network involves computation of diverse working and protection paths. The Shared Risk Link Group (SRLG) [1] concept is used to model several types of failure conditions such as link, node, fiber conduit, etc. In this work we focus on the problem of computing optimal SRLG/link diverse paths under shared protection. Shared protection technique improves network resource utilization by allowing protection paths of multiple connections to share resources. In this work we propose an iterative heuristic for computing SRLG/link diverse paths. We present a method to calculate a quantitative measure that provides a bounded guarantee on the optimality of the diverse paths computed by the heuristic. The experimental results on computing link diverse paths show that our proposed heuristic is efficient in terms of number of iterations required (time taken) to compute diverse paths when compared to other previously proposed heuristics.

Survivable Virtual Topology Routing under Shared Risk Link Groups in WDM Networks

Network survivability is one of the most important issues in the design of optical WDM networks. In this work we study the problem of survivable routing of a virtual topology on a physical topology with Shared Risk Link Groups (SRLG). The survivable virtual topology routing problem against single-link failures in the physical topology is proved to be NP-complete in [1]. We prove that survivable virtual topology routing problem against SRLG/node failures is also NP-complete. We present an improved integer linear programming (ILP) formulation (in comparison to [1]) for computing the survivable routing under SRLG/node failures. Using an ILP solver, we computed the survivable virtual topology routing against link and SRLG failures for small and medium sized networks efficiently. As even our improved ILP formulation becomes intractable for large networks, we present a congestion-based heuristic and a tabu search heuristic (which uses the congestion-based heuristic solution as the initial solution) for computing survivable routing of a virtual topology. Our experimental results show that tabu search heuristic coupled with the congestion based heuristic (used as initial solution) provides fast and near-optimal solutions.

Evidence that a single bioluminescent system is shared by all known bioluminescent fungal lineages

Since the early 20th century, many researchers have attempted to determine how fungi are able to emit light. The first successful experiment was obtained using the classical luciferin-luciferase test that consists of mixing under controlled conditions hot (substrate/luciferin) and cold (enzyme/luciferase) water extracts prepared from bioluminescent fungi. Failures by other researchers to reproduce those experiments using different species of fungi lead to the hypothesis of a non-enzymatic luminescent pathway. Only recently, the involvement of a luciferase in this system was proven, thus confirming its enzymatic nature. Of the 100 000 described species in Kingdom Fungi, only 71 species are known to be luminescent and they are distributed unevenly amongst four distantly related lineages. The question we address is whether the mechanism of bioluminescence is the same in all four evolutionary lineages suggesting a single origin of luminescence in the Fungi, or whether each lineage has a unique mechanism for light emission implying independent origins. We prepared hot and cold extracts of numerous species representing the four bioluminescent fungal lineages and performed cross-reactions (luciferin x luciferase) in all possible combinations using closely related non-luminescent species as controls. All cross-reactions with extracts from luminescent species yielded positive results, independent of lineage, whereas no light was emitted in cross-reactions with extracts from non-luminescent species. These results support the hypothesis that all four lineages of luminescent fungi share the same type of luciferin and luciferase, that there is a single luminescent mechanism in the Fungi, and that fungal luciferin is not a ubiquitous molecule in fungal metabolism.

Modelling shared attention through relational reinforcement learning

Shared attention is a type of communication very important among human beings. It is sometimes reserved for the more complex form of communication being constituted by a sequence of four steps: mutual gaze, gaze following, imperative pointing and declarative pointing. Some approaches have been proposed in Human-Robot Interaction area to solve part of shared attention process, that is, the most of works proposed try to solve the first two steps. Models based on temporal difference, neural networks, probabilistic and reinforcement learning are methods used in several works. In this article, we are presenting a robotic architecture that provides a robot or agent, the capacity of learning mutual gaze, gaze following and declarative pointing using a robotic head interacting with a caregiver. Three learning methods have been incorporated to this architecture and a comparison of their performance has been done to find the most adequate to be used in real experiment. The learning capabilities of this architecture have been analyzed by observing the robot interacting with the human in a controlled environment. The experimental results show that the robotic head is able to produce appropriate behavior and to learn from sociable interaction.

Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions

Abstract Background: Schistosoma mansoni is a blood helminth parasite that causes schistosomiasis, a disease that affects 200 million people in the world. Many orthologs of known mammalian genes have been discovered in this parasite and evidence is accumulating that some of these genes encode proteins linked to signaling pathways in the parasite that appear to be involved with growth or development, suggesting a complex co-evolutionary process. Results: In this work we found 427 genes conserved in the Deuterostomia group that have orthologs in S. mansoni and no members in any nematodes and insects so far sequenced. Among these genes we have identified Insulin Induced Gene (INSIG), Interferon Regulatory Factor (IRF) and vasohibin orthologs, known to be involved in mammals in mevalonate metabolism, immune response and angiogenesis control, respectively. We have chosen these three genes for a more detailed characterization, which included extension of their cloned messages to obtain full-length sequences. Interestingly, SmINSIG showed a 10-fold higher expression in adult females as opposed to males, in accordance with its possible role in regulating egg production. SmIRF has a DNA binding domain, a tryptophan-rich N-terminal region and several predicted phosphorylation sites, usually important for IRF activity. Fourteen different alternatively spliced forms of the S. mansoni vasohibin (SmVASL) gene were detected that encode seven different protein isoforms including one with a complete C-terminal end, and other isoforms with shorter C-terminal portions. Using S. mansoni homologs, we have employed a parsimonious rationale to compute the total gene losses/gains in nematodes, arthropods and deuterostomes under either the Coelomata or the Ecdysozoa evolutionary hypotheses; our results show a lower losses/gains number under the latter hypothesis. Conclusion: The genes discussed which are conserved between S. mansoni and deuterostomes, probably have an ancient origin and were lost in Ecdysozoa, being still present in Lophotrochozoa. Given their known functions in Deuterostomia, it is possible that some of them have been co-opted to perform functions related (directly or indirectly) to host adaptation or interaction with host signaling processes.

Analysis of the influence of epitope flanking regions on MHC class I restricted antigen presentation

Peptides presented by MHC class I molecules for CTL recognition are derived mainly from cytosolic proteins. For antigen presentation on the cell surface, epitopes require correct processing by cytosolic and ER proteases, efficient TAP transport and MHC class I binding affinity. The efficiency of epitope generation depends not only on the epitope itself, but also on its flanking regions. In this project, the influence of the C-terminal region of the model epitope SIINFEKL (S8L) from chicken ovalbumin (aa 257-264) on antigen processing has been investigated. S8L is a well characterized epitope presented on the murine MHC class I molecule, H-2Kb. The Flp-In 293Kb cell line was transfected with different constructs each enabling the expression of the S8L sequence with different defined C-terminal flanking regions. The constructs differed at the two first C-terminal positions after the S8L epitope, so called P1’ and P2’. At these sites, all 20 amino acids were exchanged consecutively and tested for their influence on H-2Kb/S8L presentation on the cell surface of the Flp-In 293Kb cells. The detection of this complex was performed by immunostaining and flow cytometry. The prevailing assumption is that proteasomal cleavages are exclusively responsible for the generation of the final C-termini of CTL epitopes. Nevertheless, recent publications showed that TPPII (tripeptidyl peptidase II) is required for the generation of the correct C-terminus of the HLA-A3-restricted HIV epitope Nef(73-82). With this background, the dependence of the S8L generation on proteasomal cleavage of the designed constructs was characterized using proteasomal inhibitors. The results obtained indicate that it is crucial for proteasomal cleavage, which amino acid is flanking the C-terminus of an epitope. Furthermore, partially proteasome independent S8L generation from specific S8L-precursor peptides was observed. Hence, the possibility of other existing endo- or carboxy-peptidases in the cytosol that could be involved in the correct trimming of the C-terminus of antigenic peptides for MHC class I presentation was investigated, performing specific knockdowns and using inhibitors against the target peptidases. In parallel, a purification strategy to identify the novel peptidase was established. The purified peaks showing an endopeptidase activity were further analyzed by mass spectrometry and some potential peptidases (like e.g. Lon) were identified, which have to be further characterized.

Identification of preferentially targeted tumor-associated antigens in melanoma patients via mRNA stimulation of CD8+ blood lymphocytes

Until now, therapeutic vaccination of cancer patients has mainly relied on rather few T cell epitopes processed from structurally normal shared tumor antigens and presented by frequent HLA alleles. So far the design of these studies has not addressed the individuality of tumor-host interactions, which are not only determined by the antigenic tumor phenotype or the natural HLA polymorphism, but also by the individual T cell repertoire. The procedure described herein was developed to identify the preferential targets of the individual repertoire from a panel of known shared tumor-associated antigens. Lymphocytes were isolated from the peripheral blood of cancer patients or healthy donors and stimulated twice with autologous mRNA-transfected FastDC (Dauer et al., J Immunol. 170:4069, 2003). FastDC were generated from blood monocytes and separately transfected via lipofection with in vitro transcribed mRNAs encoding the panel antigens. Responder lymphocytes were tested on day 12 in a 20-hour IFN-g ELISPOT assay for recognition of 293T cells co-transfected pairwise with plasmids encoding the stimulation antigens and the respective individual’s HLA class I alleles. In a first step, stimulation parameters were optimized for the detection of anti-HCMV pp65 responses. A maximum amplification of pp65-specific CD8+ T cell responses was obtained at a rather low IL-2 concentration (25 IU/ml) and at a minimum APC-to-effector ratio of 1:10. Addition of IL-4, IL-7 or IL-15 did not substantially improve the stimulatory potential. The test was applied to the human melanoma models D05 and MZ2, in both of which multiple T cell-defined antigens had previously been identified by expression screening. Blood lymphocytes were stimulated in parallel with autologous tumor cells and with mRNA-transfected FastDC. In D05, T cell reactivities against three out of eleven epitopes induced by stimulation with tumor cells were also found after stimulation with mRNA-transfected FastDC. Two further T cell target epitopes were identified with mRNA but not with tumor cell stimulation. In MZ2, T cell responses against five distinct epitopes were detected on day 12 after stimulation with mRNA transfectants. The same responses were detectable after stimulation with tumor cells only on day 32. mRNA stimulations against 21 tumor-associated antigens in addition to HCMV pp65 were performed in four healthy individuals. In all cases, CD8+ T cells against HCMV pp65 could be expanded. Among tumor-associated antigens, only reactivity against Melan-A/MART-1 in association with HLA-A*0201 was detectable in one of the donors. The vaccination of patients with targets a priori known to be recognized by their T cell repertoire may help to improve the outcome of therapeutic vaccination.