Plant feeding insects comprise about 25% of all animal species on earth and play an important role in all ecosystems. Although we understand that their association with plants is a key-factor driving the diversification in this group, we still have large gaps in our knowledge of the underlying processes of this relationship. Female choice of host plant is an important event in the insect life-cycle, as it is a major determinant of the larval food plant. In this Thesis I studied different aspects of insect host plant choice and used butterflies from the family Nymphalidae as my study system. I found that butterflies have a well developed olfactory system and that they use odors when searching for food or host plants. However, the information obtained from the odor of host plants does not seem to be sufficient for the studied species to make a distinction between plants of different qualities. Interestingly, even when in full contact with the leaf they do not make optimal decisions. I show for example that a sub-optimal female choice may be mitigated by larval ability to cope with unfavorable situations. Moreover, species that utilize a broader set of host plants may not be very well adapted to all the hosts they use, but at the same time they may survive in areas where there is only a subset of the plants available. Lastly, differences in the evolution of life-history traits between species can account for differences in how each species realizes its lifestyle. Thus, by incorporating findings on mechanisms of host plant choice with the ecological and evolutionary context of a species, our ability to explain the dynamics of host plant choice and insect-plant interactions can be improved. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

This research work presents the design and implementation of a host-based Intrusion Detection and Prevention System (IDPS) called HIDROID (Host-based Intrusion Detection and protection system for andROID) for Android smartphones. It runs completely on the mobile device, with a minimal computation burden. It collects data in real-time, periodically sampling features that reflect the overall utilisation of scarce resources of a mobile device (e.g. CPU, memory, battery, bandwidth, etc.). The Detection Engine of HIDROID adopts an anomaly-based approach by exploiting statistical and machine learning algorithms. That is, it builds a data-driven model for benign behaviour and looks for the outliers considered as suspicious activities. Any observation failing to match this model triggers an alert and the preventive agent takes proper countermeasure(s) to minimise the risk. The key novel characteristic of the Detection Engine of HIDROID is the fact that it requires no malicious data for training or tuning. In fact, the Detection Engine implements the following two anomaly detection algorithms: a variation of K-Means algorithm with only one cluster and the univariate Gaussian algorithm. Experimental test results on a real device show that HIDROID is well able to learn and discriminate normal from anomalous behaviour, demonstrating a very promising detection accuracy of up to 0.91, while maintaining false positive rate below 0.03. Finally, it is noteworthy to mention that to the best of our knowledge, publicly available datasets representing benign and abnormal behaviour of Android smartphones do not exist. Thus, in the context of this research work, two new datasets were generated in order to evaluate HIDROID. / Fundação para a Ciência e Tecnologia (FCT-Portugal) with reference SFRH/BD/112755/2015, European Regional Development Fund (FEDER), through the Competitiveness and Internationalization Operational Programme (COMPETE 2020), Regional Operational Program of the Algarve (2020), Fundação para a Ciência e Tecnologia; i-Five .: Extensão do acesso de espectro dinâmico para rádio 5G, POCI-01-0145-FEDER-030500, Instituto de telecomunicações, (IT-Portugal) as the host institution.

Call number: LD2668 .T4 1963 E74 / Master of Science

Call number: LD2668 .T4 1979 S73 / Master of Science

Call number: LD2668 .T4 1986 C374 / Master of Science / Plant Pathology

Bovine viral diarrhea virus (BVDV) is a pestivirus that suppresses the innate and adaptive host immune responses. Each of the two classified genotypes (BVDV1 and BVDV2) has two distinct biotypes – cytopathic (cp) and non-cytopathic (ncp) – and evidence has suggested that cytopathic strains may disrupt host interferon (IFN) synthesis and IFN-mediated responses. However, inconsistent results examining ncpBVDV strains have generated controversy regarding whether they also exhibit this capability. The purpose for this study was to determine the occurrence and functionality of IFN-induced responses within the serum cattle infected with ncpBVDV2-1373. Specifically, this involved analysing the changes in both the serum levels of IFN-α and IFN-γ and the expression of genes that are classically regulated by these cytokines. Serum analysis showed that the infected cattle induced both serum IFN-α and IFN-γ during BVDV infection while PBMC analysis showed increased expression of genes that classically respond to IFN-α – Mx-1, OAS-1, and STAT-1 – and IFN-γ – SOCS-1 and SOCS-3. These findings are supported by temporal kinome analysis, which verified activation of the JAK-STAT signalling network within the PBMCs of the virus-infected animals. In addition to establishing evidence for its synthesis, results from this challenge identified IFN-γ as a possible indicator of animal mortality as analysis of its change within the non-surviving, infected animals was statistically greater than the levels of the surviving, infected animals. Collectively, these results demonstrate 1373-mediated induction of, and host cell response to, both IFN-α and IFN–γ, and the potential for IFN-γ to be a predictive marker for mortality during BVDV infection.

<p>Many human monoclonal antibodies that neutralize multiple clades of HIV-1 are polyreactive and bind avidly to mammalian autoantigens. Indeed, the generation of neutralizing antibodies to the 2F5 and 4E10 epitopes of HIV-1 gp41 in man may be proscribed by immune tolerance since mice expressing the VH and VL of 2F5 have an arrested B-cell development characteristic of central tolerance. This developmental blockade implies the presence of tolerizing autoantigens that mitigate effective humoral responses. I hypothesize that discreet human antigens are mimicked by the membrane-proximal external region (MPER) of HIV-1 gp41, and that such mimicry is a wide-spread strategy for HIV-1 to evade immune attacks to its vulnerable neutralizing epitopes.</p><p>In the first part of the study, I propose to identify autoantigens mimicked by the 2F5 and 4E10 epitopes. I used immunoprecipitation coupled with mass spectrometry as well as protein arrays to identify the self-antigens recognized by 2F5 and 4E10. The binding of antigens was confirmed using serological assays and targeted mutagenesis was used to map the binding epitope. We identified human kynureninase (KYNU) and splicing factor 3b subunit 3 (SF3B3) as the primary conserved, vertebrate self-antigens recognized by the 2F5 and 4E10 antibodies, respectively. 2F5 binds the H4 domain of KYNU which contains the complete 2F5 linear epitope (ELDKWA). 4E10 recognizes a conformational epitope of SF3B3 that is strongly dependent on hydrophobic interactions. Opossums carry a rare KYNU H4 domain that abolishes 2F5 binding, but retain all SF3B3 4E10 epitopes. Immunization of opossums with HIV-1 gp140 induced extraordinary titers of serum antibody to the 2F5 ELDKWA epitope but little or nothing to the 4E10 determinant.</p><p>Our identification of structural motif shared by vertebrates and HIV-1 provides direct evidence that immunological tolerance can impair humoral responses to HIV-1. In the second part of the project, I propose to study the mechanisms of immune tolerance to B cells expressing the 2F5 antibodies. To determine the B cell repertoire before and after tolerance checkpoints, I used the Nojima-Kitamura single B-cell culture that supports differentiation into IgG-secreting plasma cells, even autoreactive cells that are normally subject to tolerization in vivo. I found that the pre-tolerance compartment (small pre-B) from 2F5 KI mice are cells that express the 2F5 V(D)J rearrangements and bind HIV-1 gp41, KYNU, and cardiolipin. Mature, post-tolerance B cells from 2F5 KI mice, however, are purged of gp41- and KYNU-reactivity, but retain cardiolipin-binding, and sequence analysis revealed extensive light-chain editing. The anergic B cells in the post-tolerance compartment are enriched with self-reactivity to KYNU and maintain binding to HIV-1 gp41. Our results demonstrate that tolerance of the 2F5 epitope is driven by specific reactivity to KYNU, but not general cross-reactivity to cardiolipin. In addition, that the peripheral anergic B cells retain self-reactivity and binding to HIV-1 gp41 suggests a potential target for activation by immunizations.</p><p>Lastly, we sought to determine whether the host mimicry by 4E10 and 2F5 epitopes is also present in other HIV-1 epitopes, including additional conserved neutralizing epitopes and more importantly, non-neutralizing epitopes. We used protein microarrays to assess autoreactivity of HIV-1 broadly neutralizing antibodies (bnAbs) and non-neutralizing antibodies (nnAbs) and found that as a class, bnAbs are more polyreactive and autoreactive than nnAbs. The poly- and autoreactive property is therefore not a result of chronic inflammation, but rather uniquely associated with neutralization, consistent with the role of heteroligation for HIV-1 neutralizing activity. In addition, mutation frequencies of bNAbs and nnAbs per se do not correlate with poly- and autoreactivity. Our results demonstrate that HIV-1 bnAbs are significantly more polyreactive and self-reactive than non-neutralizers, which may subject them to immunological tolerance control in vivo. Infrequent poly- or autoreactivity among nnAbs implies that their dominance in humoral responses is due to the absence of negative control by immune tolerance.</p><p>The results of this study indicate that mimicry of host antigens by HIV-1 is an effective mechanism to camouflage vulnerable neutralizing epitopes of HIV-1 and evade host immune responses. As a result, protective HIV-1 bnAbs are rare and often poly- or autoreactive, constituting a major hurdle that must be overcome to effectively elicit protective responses by an HIV-1 vaccine.</p> / Dissertation

BACKGROUND:Numerous studies have investigated cospeciation between parasites and their hosts, but there have been few studies concerning parasitoids and insect hosts. The high diversity and host specialization observed in Anicetus species suggest that speciation and adaptive radiation might take place with species diversification in scale insect hosts. Here we examined the evolutionary history of the association between Anicetus species and their scale insect hosts via distance-based and tree-based methods.RESULTS:A total of 94 Anicetus individuals (nine parasitoid species) and 113 scale insect individuals (seven host species) from 14 provinces in China were collected in the present study. DNA sequence data from a mitochondrial gene (COI) and a nuclear ribosomal gene (28S D2 region) were used to reconstruct the phylogenies of Anicetus species and their hosts. The distance-based analysis showed a significant fit between Anicetus species and their hosts, but tree-based analyses suggested that this significant signal could be observed only when the cost of host-switching was high, indicating the presence of parasite sorting on related host species.CONCLUSIONS:This study, based on extensive rearing of parasitoids and species identification, provides strong evidence for a prevalence of sorting events and high host specificity in the genus Anicetus, offering insights into the diversification process of Anicetus species parasitizing scale insects.

Streptococcus pneumoniae is a commensal inhabitant of the human nasopharynx that can sometimes become pathogenic and cause diseases such as pneumonia, otitis media and meningitis. Carbohydrate metabolism is a critical component of S. pneumoniae virulence. Among the myriad of carbohydrate-specific pathways involved in the host-pneumococcus interaction, the N-glycan foraging pathway stands out because of its direct implication in numerous aspects of virulence such as fitness, adhesion/invasion and impairment of the host immune response. Much of the literature has been focussed on the importance of step-wise depolymerisation of N-glycans by the enzymes NanA, BgaA and StrH. However, the importance of the liberation of N-glycans from host glycoconjuguates and their intake by the bacterium has yet to be examined. We have identified a Carbohydrate Processing Locus (CPL) that is highly conserved throughout a large number of Firmicutes and whose individual components appear widespread in bacteria that we hypothesize is active on host N-glycans. This locus encodes for two putative α-mannosidases GH92 and GH38, a characterised α-mannosidase GH125, a putative β-hexosaminidase GH20C, a putative α-fucosidase GH29 and a ROK (Repressor, Open reading frame, Kinase) protein. The genomic context of CPL orthologues suggests that an endo-β-N-acetylglucosaminidase (EndoD) and an ABC transporter (ABCN-glycan) are functionally associated with this locus. Based on our bioinformatic analyses and known functions of these proteins we hypothesize that the CPL encodes a concerted pathway responsible for the liberation, transport, and processing of N-glycans. The objective of this research is to characterize the putative components of this pathway and assess their implication in virulence. Specific focus on ABCN-glycan demonstrated its specificity for a range of N-glycans liberated by EndoD, shedding light on a novel import system for branched N-glycans. Furthermore, we provided evidence that GH92 is an α-1,2-mannosidase that likely removes the terminal mannose residues found on high-mannose N-glycans. EndoD and GH92 are shown to participate in virulence in mice; however, their role in virulence has yet to be determined. This work will significantly advance the construction and validation of a model of N-glycan processing by S. pneumoniae. As the components of this model pathway are conserved amongst a wide variety of bacteria, this work is of fundamental relevance to understanding how microbes from various environments degrade and metabolize N-glycans. / Graduate

The fascinating field of molecular capsules has recently begun to see the creation of structures that, medicated by the encapsulation of guest molecules within their central cavity, are able to change the properties or reactivity of the substrate. The current capsule designs are however, prone to exchange of either part or whole ligands. This exchange or the capsule's subsequent disassembly can lead to loss of the cavity or modification of their external properties, and is a barrier to their more widespread application, a problem this work seeks to address by creating more a robust capsule structure. This thesis presents the design, synthesis and properties displayed by three novel capsules. All the species presented share a similar supramolecular tetrahedral structure, but their properties deviate significantly, showing either switchable behaviour, spin-crossover or a novel synthetic route to a kinetically inert structure. Improvements in the design have led to a final capsule that is water-soluble, robust, non-toxic and has been shown to encapsulate a range of guests. Chapter 1 includes an overview of the types of capsule constructed in literature and their possible application. The fundamental properties of these capsules are identified, with emphasis given to a discussion of mechanisms underlying their encapsulation phenomena. Chapter 2 describes efforts to construct a tetrahedral capsule based on iron(II) and an oxime ligand. While the use of an oxime motif achieved the aim of preventing exchange of the external groups, the capsule also displayed the surprising property of possessing a solvent responsive assembly-disassembly process. This potentially provides a basis for 'on-demand' encapsulation by being able to choose when to have hydrophobic cavity available for guests. Chapter 3 details the synthesis of a tetrahedral capsule containing iron (II) coordinated by a pyridyl-triazole bonding motif. the spin-crossover properties of the complex were initially demonstrated in the solid state, however, when in solution the capsule displayed the unusual ability of spin-crossover mediated structural rearrangement. Chapter 4 demonstrates the synthesis of a robust capsule. The synthetic route shown alleviates the problems surrounding the construction of inert species in a self-assembly process. Based around a cobalt (III) cation, the stability of the capsule to carious conditions is examined and its host-guest chemistry is explored, revealing some insights into the encapsulation behaviour of this structure.