On the molecular biology and evolution of plant parasitism by nematodes

Plant-parasitic nematodes (PPN) are among the most devastating plant pathogens. However, our understanding of how nematodes adapted to plant parasitism, and the molecular mechanisms that PPN use during infection is limited. Among the most important genomic changes that occurred in the free-living nematode ancestors of PPN were multiple horizontal gene transfer (HGT) events from bacteria. Though it is clear that HGT helped shape the genomes of many PPN, how this process occurred is unknown. Also, it is evident that successful parasitism occurs from the delivery of proteinaceous effectors into plant roots to hijack and modify host cellular processes. The research included in this dissertation aims at addressing several important questions regarding HGT in PPN, and investigates important molecular, cellular and developmental processes that are determined critical for successful parasitism. Of particular emphasis throughout this dissertation is the soybean cyst nematode, Heterodera glycines, due to a highly specialized and agronomically important interaction with its soybean host. Major findings for HGT in PPN include the identification of eighteen new H. glycines effectors, three of which are determined to have been part of more ancient HGT events from rhizosphere bacteria. Additionally, homologs of two of the three HGT genes are shown to have been transferred numerous different times from bacteria to diverse eukaryotes and archaea. The latter findings indicate the likely evolutionary advantages that these genes provided not just to PPN, but many different taxa. Intriguingly, we reveal that a group of retroviruses specific to distal nematode clades is genomically associated with HGT genes in PPN genomes. These retroviruses potentially have all of the elements that would be necessary for HGT to occur in PPN. Thus, we propose the tempting hypothesis that this specific group of retroviruses might have contributed to HGT in these nematodes. We also reveal several novelties for plant-nematode interactions. Major findings include the discovery of a strongly expressed H. glycines effector that is essential for virulence and efficiently targets plant cell nucleoli for suppression of innate immune responses. Also, this H. glycines effector contains marginal, but significant sequence similarity with an immunosuppressive effector found only in Plasmodium spp., the malaria parasites. Extensive database searches, phylogenetic analyses, and functional complementation experiments conclude that the similarities are best explained by sequence convergence due to similar immunosuppressive functions. Furthermore, we determine that a specific microRNA network in soybean that is essential for plant development delineates the formation of the H. glycines feeding site, and interfering with this network renders soybean roots much less susceptible to infection. In conclusion, the major findings included in this dissertation reveal novel insights into how nematodes adapted to plant parasitism, and for how PPN manipulate their host plants during infection to establish compatible interactions. Moreover, these findings will undoubtedly provide foundations for developing novel control measures against these important plant pathogens

The CARE 3 Phase 3 Report: Test and Evaluation

CARE 3 (Computer-Aided Reliability Estimation, version three) is a computer program designed to help estimate the reliability of complex, redundant systems; although the program can model a wide variety of redundant structures, it was developed specifically for fault-tolerant avionics systems, systems distinguished by the need for extremely reliable performance since a system failure could well result in the loss of human life. CARE 3 further generalizes the class of system structures that can be modeled and greatly expands the coverage model to take into account such effects as intermittent and transient faults, latent faults, error propagation, etc. The initial test and evaluation of CARE 3 are reported

A Semantic Framework for Proof Evidence

International audienceTheorem provers produce evidence of proof in many different formats, such as proof scripts, natural deductions, resolution refutations, Herbrand expansions, and equational rewritings. In implemented provers, numerous variants of such formats are actually used: consider, for example, such variants of or restrictions to resolution refu-tations as binary resolution, hyper-resolution, ordered-resolution, paramodulation, etc. We propose the foundational proof certificates (FPC) framework for defining the semantics of a broad range of proof evidence. This framework allows both producers of proof certificates and the checkers of those certificates to have a clear formal definition of the semantics of a wide variety of proof evidence. Employing the FPC framework will allow one to separate a proof from its provenance and to allow anyone to construct their own proof checker for a given style of proof evidence. The foundation on which FPC relies is that of proof theory, particularly recent work into focused proof systems: such proof systems provide protocols by which a checker extracts information from the certificate (mediated by the so called clerks and experts) as well as performs various deterministic and non-deterministic computations. While we shall limit ourselves to first-order logic in this paper, we shall not limit ourselves in many other ways. The FPC framework is described for both classical and intuitionistic logics and for proof structures as diverse as resolution refutations, natural deduction, Frege proofs, and equality proofs

Quantum fields and machine learning

In this thesis, we use detector models to study various properties of quantum fields. One such property is the correlations present in fields. It is known that two uncorrelated detectors, upon coupling to a quantum field, can become correlated, i.e. they harvest correlations from the field. In this work, we study the effect of the presence of extra detectors in correlation harvesting protocols. Our first main result is that a single interloper detector can sabotage the harvesting of classical and quantum correlations. The second main result in this thesis is that machines can learn to extract different features of a quantum field by processing the outcomes of local probes. As proof-of-principle, we show how a neural network can distinguish a field's boundary conditions, predict the temperature of a field and of how it can distinguish between a Fock state and a phase-averaged coherent state

Coronectomy of deeply impacted lower third molar : incidence of outcomes and complications after one year follow-up

Objectives: The purpose of present study was to assess the surgical management of impacted third molar with proximity to the inferior alveolar nerve and complications associated with coronectomy in a series of patients undergoing third molar surgery. Material and Methods: The position of the mandibular canal in relation to the mandibular third molar region and mandibular foramen in the front part of the mandible (i.e., third molar in close proximity to the inferior alveolar nerve [IAN] or not) was identified on panoramic radiographs of patients scheduled for third molar extraction. Results: Close proximity to the IAN was observed in 64 patients (35 females, 29 males) with an impacted mandibular third molar. Coronectomy was performed in these patients. The most common complication was tooth migration away from the mandibular canal (n = 14), followed by root exposure (n = 5). Re-operation to remove the root was performed in cases with periapical infection and root exposure. Conclusions: The results indicate that coronectomy can be considered a reasonable and safe treatment alternative for patients who demonstrate elevated risk for injury to the inferior alveolar nerve with removal of the third molars. Coronectomy did not increase the incidence of damage to the inferior alveolar nerve and would be safer than complete extraction in situations in which the root of the mandibular third molar overlaps or is in close proximity to the mandibular canal

Genetic diversity of structural species, and stability of populations and ecosystems

Anthropogenic actions are responsible for changes in the environment with irreversible consequences on ecosystems worldwide. The positive effect of greater biodiversity in the stability of communities, stability or productivity of ecosystems and resistance to disturbances such as disease and invasion is often debated, but usually accepted. However, the influence of the genetic component of biodiversity on higher levels of biological organization remains poorly examined. Some empirical data have shown that the genetic composition of key plant populations can have a strong effect at the level of the community and ecosystem. In ecosystems dominated by one or a few species, such as seagrass meadows or algae stands, the loss of genetic diversity resulting from habitat loss and population fragmentation of that structural species may have consequences on the overall biodiversity and function of the community . In this study we used a key-species of the intertidal system of the Ria Formosa to combine field studies and manipulative experiments in order to assess the relationship between genetic diversity and the stability (resilience or resistance) of populations. We have determined the sub-lethal temperature of Z. noltei in the Ria Formosa to be approx.. 38ºC, and assessed the physiological response of Z. noltei shoots from two distinct populations under high temperature stress conditions, as well as the gene expression variations at distinct steps of the stress treatment. We also showed that survival of Z noltei shoots can be favoured by higher levels of genotypic and allelic richness, after suffering a diatom bloom.Universidade do Algarve, Faculdade de Ciências e Tecnologi