Multifunctional Delivery Systems for Cancer Gene Therapy

This chapter examines key concepts with respect to cancer gene therapy and the current issues with respect to non-viral delivery. The biological and molecular barriers that need to be overcome before effective non-viral delivery systems can be appropriately designed for oncology applications are highlighted and ways to overcome these are discussed. Strategies developed to evade the immune response are also described and targeted gene delivery is examined with the most effective strategies highlighted. Finally, this chapter proposes a new way forward based on a growing body of evidence that supports a multifunctional delivery approach involving the creation of vectors, with a unique molecular architecture designed using a bottom-up approach.

A Compositional and Interpretable Semantic Space

Vector Space Models (VSMs) of Semantics are useful tools for exploring the semantics of single words, and the composition of words to make phrasal meaning. While many methods can estimate the meaning (i.e. vector) of a phrase, few do so in an interpretable way. We introduce a new method (CNNSE) that allows word and phrase vectors to adapt to the notion of composition. Our method learns a VSM that is both tailored to support a chosen semantic composition operation, and whose resulting features have an intuitive interpretation. Interpretability allows for the exploration of phrasal semantics, which we leverage to analyze performance on a behavioral task.

Geostatistical Fisher discriminant analysis

A geostatistical version of the classical Fisher rule (linear discriminant analysis) is presented.This method is applicable when a large dataset of multivariate observations is available within a domain split in several known subdomains, and it assumes that the variograms (or covariance functions) are comparable between subdomains, which only differ in the mean values of the available variables. The method consists on finding the eigen-decomposition of the matrix W-1B, where W is the matrix of sills of all direct- and cross-variograms, and B is the covariance matrix of the vectors of weighted means within each subdomain, obtained by generalized least squares. The method is used to map peat blanket occurrence in Northern Ireland, with data from the Tellus
survey, which requires a minimal change to the general recipe: to use compositionally-compliant variogram tools and models, and work with log-ratio transformed data.

POU2F1 activity regulates HOXD10 and HOXD11 promoting a proliferative and invasive phenotype in head and neck cancer

HOX genes are master regulators of organ morphogenesis and cell differentiation during embryonic development, and continue to be expressed throughout post-natal life. To test the hypothesis that HOX genes are dysregulated in head and neck squamous cell carcinoma (HNSCC) we defined their expression profile, and investigated the function, transcriptional regulation and clinical relevance of a subset of highly expressed HOXD genes. Two HOXD genes, D10 and D11, showed strikingly high levels in HNSCC cell lines, patient tumor samples and publicly available datasets. Knockdown of HOXD10 in HNSCC cells caused decreased proliferation and invasion, whereas knockdown of HOXD11 reduced only invasion. POU2F1 consensus sequences were identified in the 5' DNA of HOXD10 and D11. Knockdown of POU2F1 significantly reduced expression of HOXD10 and D11 and inhibited HNSCC proliferation. Luciferase reporter constructs of the HOXD10 and D11 promoters confirmed that POU2F1 consensus binding sites are required for optimal promoter activity. Utilizing patient tumor samples a significant association was found between immunohistochemical staining of HOXD10 and both the overall and the disease-specific survival, adding further support that HOXD10 is dysregulated in head and neck cancer. Additional studies are now warranted to fully evaluate HOXD10 as a prognostic tool in head and neck cancers.

Calmodulin disruption impacts growth and motility in juvenile liver fluke

Background: Deficiencies in effective flukicide options and growing issues with drug resistance make current strategies for liver fluke control unsustainable, thereby promoting the need to identify and validate new control targets in Fasciola spp. parasites. Calmodulins (CaMs) are small calcium-sensing proteins with ubiquitous expression in all eukaryotic organisms and generally use fluctuations in intracellular calcium levels to modulate cell signalling events. CaMs are essential for fundamental processes including the phosphorylation of protein kinases, gene transcription, calcium transport and smooth muscle contraction. In the blood fluke Schistosoma mansoni, calmodulins have been implicated in egg hatching, miracidial transformation and larval development. Previously, CaMs have been identified amongst liver fluke excretory-secretory products and three CaM-like proteins have been characterised biochemically from adult Fasciola hepatica, although their functions remain unknown.

Methods: In this study, we set out to investigate the biological function and control target potential of F. hepatica CaMs (FhCaMs) using RNAi methodology alongside novel in vitro bioassays.

Results: Our results reveal that: (i) FhCaMs are widely expressed in parenchymal cells throughout the forebody region of juvenile fluke; (ii) significant transcriptional knockdown of FhCaM1-3 was inducible by exposure to either long (~200 nt) double stranded (ds) RNAs or 27 nt short interfering (si) RNAs, although siRNAs were less effective than long dsRNAs; (iii) transient long dsRNA exposure-induced RNA interference (RNAi) of FhCaMs triggered transcript knockdown that persisted for ≥ 21 days, and led to detectable suppression of FhCaM proteins; (iv) FhCaM RNAi significantly reduced the growth of juvenile flukes maintained in vitro; (v) FhCaM RNAi juveniles also displayed hyperactivity encompassing significantly increased migration; (vi) both the reduced growth and increased motility phenotypes were recapitulated in juvenile fluke using the CaM inhibitor trifluoperazine hydrochloride, supporting phenotype specificity.

Conclusions: These data indicate that the Ca(2+)-modulating functions of FhCaMs are important for juvenile fluke growth and movement and provide the first functional genomics-based example of a growth-defect resulting from gene silencing in liver fluke. Whilst the phenotypic impacts of FhCaM silencing on fluke behaviour do not strongly support their candidature as new flukicide targets, the growth impacts encourage further consideration, especially in light of the speed of juvenile fluke growth in vivo.

Ferroelectric Vortices and Related Configurations

This chapter discusses that the theoretical studies, using both atomistic and phenomenological approaches, have made clear predictions about the existence and behaviour of ferroelectric (FE) vortices. Effective Hamiltonians can be implemented within both Monte Carlo (MC) and molecular dynamics (MD) simulations. In contrast to the effective Hamiltonian method, which is atomistic in nature, the phase field method employs a continuum approach, in which the polarization field is the order parameter. Properties of FE nanostructures are largely governed by the existence of a depolarization field, which is much stronger than the demagnetization field in magnetic nanosystems. The topological patterns seen in rare earth manganites are often referred to as vortices and yet this claim never seems to be explicitly justified. By inspection, the form of a vortex structure is such that there is a continuous rotation in the orientation of dipole vectors around the singularity at the centre of the vortex.

Spatio-temporal Rich Model Based Video Steganalysis on Cross Sections of Motion Vector Planes

A rich model based motion vector steganalysis benefiting from both temporal and spatial correlations of motion vectors is proposed in this work. The proposed steganalysis method has a substantially superior detection accuracy than the previous methods, even the targeted ones. The improvement in detection accuracy lies in several novel approaches introduced in this work. Firstly, it is shown that there is a strong correlation, not only spatially but also temporally, among neighbouring motion vectors for longer distances. Therefore, temporal motion vector dependency along side the spatial dependency is utilized for rigorous motion vector steganalysis. Secondly, unlike the filters previously used, which were heuristically designed against a specific motion vector steganography, a diverse set of many filters which can capture aberrations introduced by various motion vector steganography methods is used. The variety and also the number of the filter kernels are substantially more than that of used in previous ones. Besides that, filters up to fifth order are employed whereas the previous methods use at most second order filters. As a result of these, the proposed system captures various decorrelations in a wide spatio-temporal range and provides a better cover model. The proposed method is tested against the most prominent motion vector steganalysis and steganography methods. To the best knowledge of the authors, the experiments section has the most comprehensive tests in motion vector steganalysis field including five stego and seven steganalysis methods. Test results show that the proposed method yields around 20% detection accuracy increase in low payloads and 5% in higher payloads.

A synopsis of the genus Bursaphelenchus Fuchs, 1937 (Aphelenchida: Parasitaphelenchidae) with keys to species

The 75 valid species of the genus Bursaphelenchus are listed together with their synonyms. Diagnostic characters and their states are discussed and illustrated. Tabular and traditional text keys are provided for the genus. Two new subspecies are proposed to distinguish populations of B. piniperdae and B. poligraphi, as described by Rühm (1956), from the original descriptions of these species published by Fuchs (1937). Known records of Bursaphelenchus species with their associated natural vectors, plants and plant families are given. Dendrograms of species relationships (UPGMA, standard distance: mean character difference) based on combined taxonomic characters and also on spicule characters only, are provided. Discussion as to whether the species groups are natural or artificial (and therefore purely diagnostic) is based on their relationships in the dendrogram and the vector and associated plant ranges of the species. Of the six species groups distinguished, two appear to represent natural assemblages, these being the xylophilus-group (with ten species) and the hunti-group (seven species), of which two, B. cocophilus and B. dongguanensis, form the cocophilus-cluster which is separated on the dendrogram from the main clusters. The remaining four species groups appear to be artificial and purely diagnostic in function, namely the aberrans-group (four species); the eidmanni-group (six species); the borealis-group (five species), and the piniperdae-group (43 species). Two new subspecies, both in the piniperdae-group, viz. B. piniperdae ruehmpiniperdae n. subsp. and B. poligraphi ruehmpoligraphi n. subsp., are proposed and diagnosed from B. piniperdae piniperdae and B. poligraphi poligraphi the respective type subspecies. Bursaphelenchus dongguanensis is regarded as being a valid member of the genus and its transfer to Parasitaphelenchus is rejected.

Review of the genus Bursaphelenchus Fuchs, 1937 (Nematoda, Aphelenchida) with some conclusions on the host-parasite and vector-parasite evolution.

INTRODUCTION AND GOALS: Genus Bursaphelenchus includes several pests of the world importance for the rural economy, the most dangerous are the Bursaphelenchus xylophilus (the pinewood nematode caused decline of the pine trees in south Asia and in one spot area in Europe, Portugal, Peninsula de Setubal) and the Bursaphelenchus cocophilus, causing the decline of coco-palm plantations in Carribean and Latin American regions. The peculiarity of the host-parasite association of the genus that the nematode life cycle includes three trophic components: plant (mostly a tree), insect vector and a fungus. Goals of the presentation is to list all species of the world fauna and all efficient diagnostic characters, then create the identification tool and analyze the similarity of species and possible ways and causes of the host-parasite evolution of the group. RESULTS: Complete list of species with synonymy and a catalogue of all efficient diagnostic characters with their states, selected from papers of the most experienced taxonomists of the genus, are given for the genus Bursaphelenchus. List of known records of Bursaphelenchus species with names of natural vectors and plants and their families is given (for world pests the most important groups of trees and insects are listed). The tabular, traditional and computer-aided keys are presented. Dendrograms of species relationships (UPGMA, standard distance: mean character difference) based on all efficient taxonomic characters and separately on the spicule characters only, are given. Discussion whether the species groups are natural or purely diagnostic ones is based on the relationships dendrograms and the vector and associated plant ranges of Bursaphelenchus species; the xylophilus species group (B. xylophilus, B. abruptus, B. baujardi, B. conicaudatus, B. eroshenkii, B. fraudulentus, B. kolymensis, B. luxuriosae; B. mucronatus), the hunti group (B. hunti, B. seani, B. kevini and B. fungivorus) are probably the natural ones. CONCLUSIONS: The parasitic nematode association includes three trophic components: plant, insect vector and fungus. The initial insect-plant complex Scolytidae-Pinaceae is changeable and only in rare occasions the change of the preferred vector to Cerambycidae (the xylophilus group), Hymenoptera (the hunti group) led to formation of the natural species-groups. From the analysis it is clear that although the vector range is changeable it is comparatively more important for the evolution of the genus Bursaphelenchus than associations with plants at the family level. Data on the fungi species (3rd component in natural Bursaphelenchus associations) are insufficient for the detailed comparative analysis.

The Pine Wood Nematode: a personal view

The first report of the disease (“pine wilt disease”) associated with the pinewood nematode, goes back to 1905, when Yano reported an unusual decline of pines from Nagasaki. For a long time thereafter, the cause of he disease was sought, but without success. Because of the large number of insect species that were usually seen around and on infected trees, it had always been assumed that the causal agent would prove to be one of these. However, in 1971, Kiyohara and Tokushike found a nematode of the genus Bursaphelenchus in infected trees. The nematode found was multiplied on fungal culture, inoculated into healthy trees and then re-isolated from the resulting wilted trees. The subsequent published reports were impressive: this Bursaphelenchus species could kill fully-grown trees within a few months in the warmer areas of Japan, and could destroy complete forests of susceptible pine species within a few years. Pinus densiflora, P. thunbergii und P. luchuensis were particularly affected. In 1972, Mamiya and Kiyohara described the new species of nematode extracted from the wood of diseased pines; it was a named Bursaphelenchus lignicolus. Since 1975, the species has spread to the north of Japan, with the exception of the most northerly prefectures. In 1977, the loss of wood in the west of the country reached 80%. Probably as a result of unusually high summer temperatures and reduced rainfall in the years 1978 and 1979, the losses were more than 2 million m3 per year. From the beginning, B. lignicolus was always considered by Japanese scientists to be an exotic pest. But where did it come from? That this nematode could also cause damage in the USA became clear in 1979 when B. lignicolus was isolated in great numbers from wood of a 39 year-old pine tree (Pinus nigra) in Missouri which had suddenly died after the colour of its needles changed to a reddish-brown colour (Dropkin und Foudin, 2 1979). In 1981, B. lignicolus was synonymised by Nickle et al. with B. xylophilus which had been found for the first time in the USA as far back as 1929, and reported by Steiner and Buhrer in 1934. It had originally been named Aphelenchoides xylophilus, the wood-inhabiting Aphelenchoides but was recognised by Nickle, in 1970,to belong in the genus Bursaphelenchus. Its common name in the USA was the "pine wood nematode" (PWN. After its detection in Missouri, it became known that B. xylophilus was widespread throughout the USA and Canada. It occurred there on native species of conifers where, as a rule, it did not show the symptoms of pine wilt disease unless susceptible species were stressed eg., by high temperature. This fact was an illuminating piece of evidence that North America could be the homeland of PWN. Dwinell (1993) later reported the presence of B. xylophilus in Mexico. The main vector of the PWN in Japan was shown to be the long-horned beetle Monochamus alternatus, belonging to the family Cerambycidae. This beetle lays its eggs in dead or dying trees where the developing larvae then feed in the cambium layer. It was already known in Japan in the 19th century but in the 1930s, it was said to be present in most areas of Japan, but was generally uncommon. However, with the spread of the pine wilt disease, and the resulting increase of weakened trees that could act as breeding sites for beetles, the populations of Monochamus spp. increased significantly In North America, other Monochamus species transmit PWN, and the main vector is M. carolinensis. In Japan, there are also other, less efficient vectors in the genus Monochamus. Possibly, all Monochamus species that breed in conifers can transmit the PWN. The occasional transmission by less efficient species of Monochamus or by some of the many other beetle genera in the bark or wood is of little significance. In Europe, M. galloprovincialis and M. sutor transmits the closely related species B. mucronatus. Some speculate that these two insect species are “standing by” and waiting for the arrival of B. xylophilus. In 1982, the nematode was detected and China. It was first found in dead pines near the Zhongshan Monument of Nanjing (CHENG et. al. 1983); 265 trees were then killed by pine wilt disease. Despite great efforts at eradication in China, the nematode spread further and pine wilt disease has been 3 reported from parts of the provinces of Jiangsu, Anhui, Guangdong, Shandong, Zhejiang and Hubei (YANG, 2003). In 1986, the spread of the PWN to Taiwan was discovered and in 1989, the nematode was reported to be present in the Republic of Korea where it had first been detected in Pinus thunbergii and P. densiflora. It was though to have been introduced with packing material from Japan. PWN was advancing. In 1984, B. xylophilus was found in wood chips imported into Finland from the USA and Canada, and this was the impetus to establish phytosanitary measures to prevent any possible spread into Europe. Finland prohibited the import of coniferous wood chips from these sources, and the other Nordic countries soon followed suit. EPPO (the European and Mediterranean Plant Protection Organization) made a recommendation to its member countries in 1986 to refuse wood imports from infested countries. With its Directive of 1989 (77/93 EEC), the European Community (later called the European Union or EU) recognised the potential danger of B. xylophilus for European forests and imposed restrictions on imports into the Europe. PWN was placed on the quarantine list of the EU and also of other European countries. Later, in 1991, a dispensation was allowed by the Commission of the EU(92/13 EEC) for coniferous wood from North America provided that certain specified requirements were fulfilled that would prevent introduction.

Pine wilt disease: global issues, trade and economic impact

Pine wilt disease (PWD) is perhaps the most serious threat to pine forests worldwide. Since it´s discovery in the early XXth century by Japanese forest researchers, and the relationship with its causative agent, the pinewood nematode (PWN) Bursaphelenchus xylophilus, in the 1970s, PWD has wreaked havoc wherever it appears. Firstly in the Far East (Japan, China and Korea) and now, more recently in 1999, in the EU (Portugal). The forest sector in Portugal plays a major role in the Portuguese economy with a 12% contribution to the industrial gross domestic product, 3.2% of the gross domestic product, 10% of foreign trade and 5% of national employment. Maritime pine (Pinus pinaster) is one of the most important pine productions, and industrial activity, such as the production of wood and resin, as well as coastal protection associated with sand dunes. Also, stone pine (Pinus pinea) plays an important role in the economy with a share derived from the exports of high-quality pineon seed. Thus, the tremendous economical and ecological impact of the introduction of a pest and pathogen such as the PWN, although as far as is known, the only species susceptible to the nematode is maritime pine. Immediately following detection, the research team involved (Univ. Évora, INIAP) informed the national plant quarantine and forest authorities, which relayed the information to Brussels and the appropriate EU authorities. A task force (GANP), followed by a national program (PROLUNP) was established. Since then, national surveys have been taking place, involving MADRP (Ministry of Agriculture), the University of Évora and several private corporations (e.g. UNAC). Forest growers in the area are particularly interested and involved since the area owned by the growers organizations totals 700 000 ha, largely affected by PWD. Detection of the disease has led to serious consequences and restrictions regarding exploration and commercialization of wood. A precautionary phytosanitary strip, 3 km-wide, has been recently (2007) established surrounding the affected area. The Portuguese government, through its national program PROLUNP, has been deeply involved since 1999, and in conjunction with the EU (Permanent Phytosanitary Committee, and FVO) and committed to controlling this nematode and the potential spread to the rest of the country and to the rest of the EU. The global impact of the presence of Bursaphelenchus xylophilus or the threat of its introduction and the resulting pine wilt disease in forested areas in different parts of the world is of increasing concern economically. The concern is exacerbated by the prevailing debate on climate change and the putative impact this could have on the vulnerability of the world’s pine forests to this disease. The scientific and regulatory approach taken in different jurisdictions to the threat of pine wilt disease varies from country to country depending on the perceived vulnerability of their pine forests to the disease and/or to the economic cost due to lost trade in wood products. Much of the research surrounding pine wilt disease has been located in the northern hemisphere, especially in southern Europe and in the warmer, coastal, Asian countries. However, there is an increased focus on this problem also in those countries in the southern hemisphere where plantations of susceptible pine have been established over the years. The forestry sector in Australia and New Zealand are on “high alert” for this disease and are practicing strict quarantine procedures at all ports of entry for wood products. As well, there is heightened awareness, as there is worldwide, for the need to monitor wood packaging materials for all imported goods. In carrying out the necessary monitoring and assessment of products for B. xylophilus and its vectors substantial costs are incurred especially when decisions have to be made rapidly and regardless of whether the outcome is positive or negative. Australia’s response recently to the appearance of some dying pines in a plantation illustrated the high sensitivity of some countries to this disease. Some $200,000 was spent on the assessment in order to save a potential loss of millions of dollars to the disease. This rapid, co-ordinated response to the report was for naught, because once identified it was found not to be B. xylophilus. This illustrates the particular importance of taking the responsibility at all levels of management to secure the site and the need of a rapid, reliable diagnostic method for small nematode samples for use in the field. Australia is particularly concerned about the vulnerability of its 1million hectares of planted forests, 80% of which are Pinus species, to attack from incursions of one or more species of the insect vector. Monochamus alternatus incursions in wood pallets have been reported from Brisbane, Queensland. The climate of this part of Australia is such that the Pinus plantations are particularly vulnerable to the potential outcome of such incursions, and the state of Queensland is developing a risk management strategy and a proactive breeding programme in response to this putative threat. New Zealand has 1.6 million hectares of planted forests and 89% of the commercial forest is Pinus radiata. Although the climate where these forests are located tends to be somewhat cooler than that in Australia the potential for establishment and development of the disease in that country is believed to be high. The passage alone of 200,000 m³/year of wood packaging through New Zealand ports is itself sufficient to require response. The potential incursion of insect vectors of pinewood nematode through the port system is regarded as high and is monitored carefully. The enormous expansion of global trade and the continued use of unprocessed/inadequately-processed wood for packaging purposes is a challenge for all trading nations as such wood packaging material often harbours disease or pest species. The extent of this problem is readily illustrated by the expanding economies and exports of countries in south-east Asia. China. Japan and Korea have significant areas of forestland infested with B. xylophilus. These countries too are among the largest exporting countries of manufactured goods. Despite the attempts of authorities to ensure that only properly treated wood is used in the crating and packaging of goods B. xylophilus and/or its insect vector infested materials is being recorded at ports worldwide. This reminds us, therefore, of the ease with which this nematode pest can gain access to forest lands in new geographic locations through inappropriate use, treatment or monitoring of wood products. It especially highlights the necessity to find an alternative to using low-grade lumber for packaging purposes. Lest we should believe that all wood products are always carriers of B. xylophilus and its vectors, it should be remembered that international trade of all kinds has occurred for thousands of years and that lumber-born pests and diseases do not have worldwide distribution. Other physico-biological factors have a significant role in the occurrence, establishment and sustainability of a disease. The question is often raised as to why the whole of southern Europe doesn’t already have B. xylophilus and pine wilt disease. European countries have traded with countries that are infested with B. xylophilus for hundreds of years. Turkey is an example of a country that appears to be highly vulnerable to pine wilt disease due to its extensive forests in the warm, southern region where the vector, Monochamus galloprovincialis, occurs. However, there is no record of the presence of B. xylophilus occurring there despite the importation of substantial quantities of wood from several countries In many respects, Portugal illustrates both the challenge and the dilemma. In recent times B. xylophilus was discovered there in the warm coastal region. The research, administrative and quarantine authorities responded rapidly and B. xylophilus appears to have been confined to the region in which it was found. The rapid response would seem to have “saved the day” for Portugal. Nevertheless, it raises again the long-standing questions, how long had B. xylophilus been in Portugal before it was found? If Lisbon was the port of entry, which seems very likely, why had B. xylophilus not entered Lisbon many years earlier and established populations and the pine wilt disease? Will the infestation in Portugal be sustainable and will it spread or will it die out within a few years? We still do not have sufficient understanding of the biology of this pest to know the answers to these questions.

Morphobiometric and molecular characterization of Bursaphelenchus Fuchs, 1937 (Nematoda: Aphelenchoididae) species associated with Pinus pinaster Ainton in Portugal

Abstract - The genus Bursaphelenchus comprises almost 100 species mainly from the northern hemisphere, with conifers as the most important hosts. Among the various nematode species, the pine wood nematode (PWN), Bursaphelenchus xylophilus, is the casual agent of pine wilt disease (PWD), and the most important forest pest for pines worldwide, classified as an A1 quarantine organism within the European Union. In 1999 this nematode was detected for the first time in Portugal and Europa associated with maritime pine, Pinus pinaster. Following detection, a national program denominated "Programa Nacional de Luta contra o Nemátodo da Madeira do Pinheiro" (PROLUNP) was created to, among other objectives, determine the distribution of the PWN and its associated vector(s) and host(s), and therefore intensive surveys covering the entire country were conducted with thousands of wood samples and suspected insects being analyzed. This thesis presents the listing, distribution, frequency and the insects associated with Bursaphelenchus species found associated with maritime pine in Portugal, identifying and characterizing the various species by morphological, biometrical and molecular biology (ITS-RFLP and rDNA sequencing analysis) techniques. To achieve the objectives, a total of 4813 maritime pine wood samples and 3294 insects from 22 species and six families were individually analyzed. A total of nine Bursaphelenchus species were found, namely: B. antoniae, B. hellenicus, B. leoni, B. mucronatus, B. pinasteri, B. sexdentati, B. teratospicularis, B. tusciae and B. xylophilus, all of them (with the exception of B. xylophilus) being new records for Portugal. Some of the species appear to have a widespread distribution, such as B. leoni, B. teratospicularis and B. tusciae while others were very rarely found and apparently have a localized distribution range within the country, namely B. antoniae and B. mucronatus. The majority of the species is characteristic of the Mediterranean region and can also be found in countries such as Spain, Italy and Greece, reflecting the affinity of our fauna with those locations. The association of B. hellenicus and B. tusciae with maritime pine is here reported for the first time. Six of the Bursaphelenchus species were also found associated with insects, mainly from the family Scolytidae (Coleoptera). Some of these interactions were described for the first time, namely: B. hellenicus with both Ips sexdentatus and Hylurgus ligniperda, B. sexdentati with both H. ligniperda and Orthotomicus erosus and B. tusciae with H. ligniperda. The exclusive association of B. xylophilus with the cerambycid Monochamus galloprovincialis was also confirmed. The nematode's dauer juveniles were usually found in low numbers in the insect vectors (ca 10-100 per insect), although for B. xylophilus a few thousand specimens per insect were sometimes found. The location of the dauer juveniles differed according to the species, although they were more common under the elytra and wings of the adult insects. A species new to science was detected and formally described as B. antoniae, associated with Hylobius sp. (Coleoptera; Curculionidae) beetles. Morphologically, this new species is very similar to B. hylobianum, although it's distinct ITS-RFLP molecular pattern (with only the enzyme Haelll producing comparable restriction bands) and the failure of hybridization supported the two species as distinct entities. Additional phylogenetic analysis of the 18S rDNA sequence further supported the taxonomical proximity of B. antoniae with B. hylobianum. Concerning the PWN, detailed studies on the development and morphology of B. xylophilus were conducted, and comparative measurements of field-collected and laboratory-maintained populations demonstrated that nematodes from the second group displayed larger size in all morphometric parameters, which could derive from more adequate conditions of nourishment and/or temperature. Taxonomical studies on the development stages of B. xylophilus confirmed the existence of four propagative juvenile stages (J1,J2,J3 and J4), an adult stage with both sexes and two dispersal stages (jIII e jIV), with the measurements of the gonad length allowing the separation of the propagative stages. It is hoped that the acquired knowledge will be useful on future surveys of nematodes of the Bursaphelenchus genus collected from either wood material or insect vectors, and facilitate the correct distinction and identification of the various species which are now known to occur. ### Resumo - 0 género Bursaphelenchus compreende quase 100 espécies, distribuídas sobretudo nos países do hemisfério norte do globo terrestre. Embora algumas espécies já tenham sido detectadas em plantas herbáceas, os hospedeiros vegetais mais comuns deste género são as coníferas, particularmente pinheiros. 0 nemátode da madeira do pinheiro (NMP), Bursaphelenchus xylophilus, é considerado a espécie mais importante deste género uma vez que é o agente causal da doença da murchidão dos pinheiros ("pine wilt disease"). Originário dos Estados Unidos, onde não causa grande impacte, o NMP foi introduzido em alguns países da Ásia (China, Japão, Coreia e Taiwan) e mais recentemente na Europa (Portugal). Nestas regiões é responsável pela destruição de milhares de hectares de coníferas, assumindo uma elevada importância económica. Em Portugal, depois da sua detecção em 1999, associado a Pinus pinaster, foi implementado um programa nacional "Programa Nacional de Luta contra o Nemátodo da Madeira do Pinheiro" (PROLUNP) que permitiu determinar a área afectada pela praga (a sul do rio Tejo, península de Setúbal) bem como definir e implementar estratégias de controlo e prevenção da disseminação do NMP a outras zonas de Portugal. Recentemente, em Junho de 2008, foi confirmada a presença de B. xylophilus em outras regiões de Portugal levando as autoridades oficiais a definir todo o território continental como zona afectada e de restrição. As prospecções intensivas realizadas nos últimos anos incluíram a recolha e análise de milhares de amostras de madeira de pinheiro bem como de insectos associados ao pinheiro bravo conduzindo à identificação de várias espécies de Bursaphelenchus. Assim, os estudos conduzidos neste trabalho tiveram como objectivos efectuar uma caracterização morfológica, biométrica e molecular das espécies associadas a P. pinaster em Portugal bem como a sua distribuição geográfica e abundância. Os estudos biométricos foram realizados com populações extraídas directamente do meio natural. Foi ainda realizada uma pesquisa que permitiu identificar os insectos a que estão associadas essas espécies, os seus possíveis vectores. Foram analisadas no total 4813 amostras de P. pinaster e 3294 insectos (22 espécies pertencentes a seis famílias diferentes). Foram identificadas um total de nove espécies: B. antoniae n. sp., B. hellenicus, B. leoni, B. mucronatus, B. pinasteri, B. sexdentati, B. teratospicularis, B. tusciae e B. xylophilus. Foram realizados estudos morfológicos e biométricos de todas as espécies com excepção de B. mucronatus; o reduzido número de exemplares encontrados em apenas uma amostra foram utilizados para efectuar o diagnóstico molecular desta espécie (ITS-RFLP). Apesar de ter havido, sempre que possível, a confirmação molecular, na maioria dos casos a caracterização morfológica e biométrica permitiu a correcta identificação das espécies. Contudo, foi imprescindível a análise molecular em algumas amostras, nomeadamente para a identificação de B. xylophilus e B. sexdentati; dada a grande semelhança entre B. xylophilus e B. mucronatus e tendo sido encontradas algumas populações de B. xylophilus que possuíam fêmeas com cauda mucronada, foi necessária a realização da confirmação molecular. Com excepção de B. xylophilus, todas as outras espécies foram reportadas pela primeira vez em Portugal. Juntamente com B. xylophilus, B. pinasteri foi a espécie encontrada nas amostras de madeira de pinheiro com maior frequência. Algumas destas espécies como B. leoni, B. teratospicularis e B. tusciae foram reportadas em diferentes localidades do norte, centro e sul de Portugal, apresentando uma vasta distribuição geográfica; este resultado está em consonância com a forte associação destas espécies a climas mediterrânicos tal como acontece em Espanha, França, Itália e Grécia. Em oposição, espécies como B. antoniae e B. mucronatus foram encontradas apenas numa ocasião na região centro (Leiria) e norte (Figueira da Foz) do país, respectivamente. Bursaphelenchus mucronatus é igualmente pouco frequente em Espanha onde ocorre sobretudo na região norte, na Galiza. Esta espécie preferirá climas mais frios, ocorrendo com uma maior frequência nas regiões de latitude norte; esta análise é corroborada pela presença constante em países como Alemanha, Finlândia, França, Noruega, Rússia e Suécia. A nível mundial são descritas neste trabalho pela primeira vez as associações das espécies B. hellenicus e B. tusciae ao hospedeiro vegetal P. pinaster.

The role of environmental stress on protein synthesis fidelity

Estudos recentes estabelecem uma ligação entre erros na tradução do mRNA e cancro, envelhecimento e neurodegeneração. RNAs de transferência mutantes que introduzem aminoácidos em locais errados nas proteínas aumentam a produção de espécies reactivas de oxigénio e a expressão de genes que regulam autofagia, ribofagia, degradação de proteínas não-funcionais e protecção contra o stress oxidativo. Erros na tradução do mRNA estão portanto relacionados com stress proteotóxico. Sabe-se agora que o mecanismo de toxicidade do crómio está associado à diminuição da fidelidade de tradução e à agregação de proteínas com malformações que destabilizam a sua estrutura terciária. Desta forma, é possível que os efeitos do stress ambiental ao nível da degeneração celular possam estar relacionados com a alteração da integridade da maquinaria da tradução. Neste estudo procedeu-se a uma avaliação alargada do impacto do stress ambiental na fidelidade da síntese de proteínas, utilizando S. cerevisiae como um sistema modelo. Para isso recorreu-se a repórteres policistrónicos de luciferase que permitiram quantificar especificamente a supressão de codões de terminação e o erro na leitura do codão AUG em células exposta a concentações não letais de metais pesados, etanol, cafeína e H2O2. Os resultados sugerem que a maquinaria de tradução é na generalidade muito resistente ao stress ambiental, devido a uma conjugação de mecanismos de homeostase que muito eficientemente antagonizam o impacto negativo dos erros de tradução. A nossa abordagem quantitativa permitiu-nos a identificar genes regulados por uma resposta programada ao stress ambiental que são também essenciais para mitigar a ocorrência de erros de tradução, nomeadamente, HSP12, HSP104 e RPN4. A exposição prolongada ao stress ambiental conduz à saturação dos mecanismos de homeostase, contribuindo para a acumulação de proteínas contendo erros de tradução e diminuindo a disponibilidade de proteínas funcionais directamente envolvidas na manutenção da fidelidade de tradução e integridade celular. Ao contrário de outras Hsps, a Hsp12p adopta normalmente uma localização membranar em condições de stress, que pode modular a fluidez e estabilidade membranar, sugerindo que a membrana plasmática é um alvo preferencial da perda de fidelidade da tradução. Para melhor compreender as respostas celulares aos erros de tradução, células contendo deleções em genes codificadores das Hsps foram transformadas com tRNAs mutantes que introduzem alterações no proteoma. Os nossos resultados demonstram que para além da resposta geral ao stress, estes tRNAs induzem alterações a nível do metabolismo celular e um aumento de aminoacilação com Metionina em vários tRNAs, sugerindo um mecanismo de protecção contra espécies reactivas de oxigénio. Em conclusão, este estudo sugere um papel para os erros de tradução na gestão de recursos energéticos e na adaptação das células a ambientes desfavoráveis.

Tributyltin (TBT) resistance in Aeromonas molluscorum Av27

O tributilestanho (TBT) é considerado um dos xenobióticos mais tóxicos, produzidos e deliberadamente introduzidos no meio ambiente pelo Homem. Tem sido usado numa variedade de processos industriais e subsequentemente descarregado no meio ambiente. O tempo de meia-vida do TBT em águas marinhas é de várias semanas, mas em condições de anóxia nos sedimentos, pode ser de vários anos, devido à sua degradação mais lenta. Embora o TBT tenha sido descrito como sendo tóxico para eucariotas e procariotas, muitas bactérias podem ser resistentes a este composto. O presente trabalho teve como objetivo principal elucidar o mecanismo de resistência ao TBT em bactérias. Para além disso, pretendeu-se desenvolver um biorepórter para detectar TBT no ambiente. Para atingir estes objetivos foram delineadas várias tarefas cujos principais resultados obtidos se apresentam a seguir. Várias bactérias resistentes ao TBT foram isoladas de sedimento e água do Porto de Pesca Longínqua (PPL) na Ria de Aveiro, Portugal. Entre estas, Aeromonas molluscorum Av27 foi selecionada devido à sua elevada resistência a este composto (concentrações até 3 mM), à sua capacidade de degradar o TBT em compostos menos tóxicos (dibutilestanho, DBT e monobutilestanho, MBT) e também por usar o TBT como fonte de carbono. A. molluscorum Av27 foi caracterizada genotipica e fenotipicamente. Os fatores de virulência estudados mostraram que esta estirpe i) possui atividade lipolítica; ii) não é citotóxica para células de mamíferos, nomeadamente para células Vero; iii) não possui integrões de classe I e II e iv) possui cinco plasmídeos com aproximadamente 4 kb, 7 kb, 10 kb, 100 kb e mais de 100 kb. Estes resultados mostraram que a estirpe Av27 não é tóxica, aumentando assim o interesse nesta bactéria para futuras aplicações, nomeadamente na bioremediação. Os testes de toxicidade ao TBT mostraram que este composto tem um impacto negativo no crescimento desta estirpe, bem como, na densidade, no tamanho e na atividade metabólica das células e é responsável pela formação de agregados celulares. Assim, o TBT mostrou ser bastante tóxico para as bactérias interferindo com a atividade celular geral. O gene Av27-sugE, que codifica a proteína SugE pertencente à família das “small multidrug resistance proteins” (SMR), foi identificado como estando envolvido na resistência ao TBT nesta estirpe. Este gene mostrou ser sobreexpresso quando as células crescem na presença de TBT. O promotor do gene Av27-sugE foi utilizado para construir um bioreporter para detetar TBT, contendo o gene da luciferase do pirilampo como gene repórter. O biorepórter obtido reúne as características mais importantes de um bom biorepórter: sensibilidade (intervalo de limite de detecção de 1-1000 nM), rapidez (3 h são suficientes para a deteção de sinal) e, possivelmente, não é invasivo (pois foi construído numa bactéria ambiental). Usando sedimento recolhido no Porto de Pesca Longínqua da Ria de Aveiro, foi preparada uma experiência de microcosmos com o intuito de avaliar a capacidade de Av27 para bioremediar o TBT, isoladamente ou em associação com a comunidade bacteriana indígena. A análise das amostras de microcosmos por PCR-DGGE e de bibliotecas de 16S rDNA revelaram que a comunidade bacteriana é relativamente estável ao longo do tempo, mesmo quando Av27 é inoculada no sedimento. Para além disso, o sedimento estuarino demonstrou ser dominado por bactérias pertencentes ao filo Proteobacteria (sendo mais abundante as Delta e Gammaproteobacteria) e Bacteroidetes. Ainda, cerca de 13% dos clones bacterianos não revelaram nenhuma semelhança com qualquer dos filos já definidos e quase 100% afiliou com bactérias não cultiváveis do sedimento. No momento da conclusão desta tese, os resultados da análise química de compostos organoestânicos não estavam disponíveis, e por essa razão não foi possível tirar quaisquer conclusões sobre a capacidade desta bactéria remediar o TBT em sedimentos. Esses resultados irão ajudar a esclarecer o papel de A. molluscorum Av27 na remediação de TBT. Recentemente, a capacidade da estirpe Av27 remediar solo contaminado com TBT foi confirmada em bioensaios realizados com plantas, Brassica rapa e Triticum aestivum (Silva 2011a), e também com invertebrados Porcellionides pruinosus (Silva 2011B). Assim, poder-se-á esperar que a bioremediação do sedimento na experiência de microcosmos também tenha ocorrido. No entanto, só a análise química dos compostos organostânicos deverá ser conclusiva. Devido à dificuldade em realizar a análise analítica de organoestânicos, um método de bioensaio fácil, rápido e barato foi adaptado para avaliar a toxicidade do TBT em laboratório, antes de se proceder à análise química das amostras. O método provou a sua utilidade, embora tenha mostrado pouca sensibilidade quando se usam concentrações de TBT baixas. Em geral, os resultados obtidos contribuíram para um melhor entendimento do mecanismo de resistência ao TBT em bactérias e mostraram o potencial biotecnológico de A. molluscorum Av27, nomeadamente, no que refere à sua possível aplicação na descontaminação de TBT no ambiente e também no desenvolvimento de biorepórteres.