Electron-impact excitation of beryllium and its ions

Inelastic electron scattering from light atomic species is of fundamental importance and has significant applications in fusion-plasma modeling. Therefore, it is of interest to apply advanced nonperturbative, close-coupling methods to the determination of electron-impact excitation for these atoms. Here we present the results of R matrix with pseudostate (RMPS) calculations of electron-impact excitation cross sections through the n=4 terms in Be, Be+, Be2+, and Be3+. In order to determine the effects of coupling of the bound states to the target continuum in these species, we compare the RMPS results with those from standard R-matrix calculations. In addition, we have performed time-dependent close-coupling calculations for excitation from the ground and the metastable terms of Be+ and the metastable term of Be3+. In general, these results are found to agree with those from our RMPS calculations. The full set of data resulting from this work is now available on the Oak Ridge National Laboratory Controlled Fusion Atomic Data Center web site, and will be employed for collisional-radiative modeling of Be in magnetically confined plasmas.

Bursaphelenchus xylophilus : opportunities in comparative genomics and molecular host–parasite interactions

Most Bursaphelenchus species are fungal feeding nematodes that colonize dead or dying trees. However, Bursaphelenchus xylophilus , the pine wood nematode, is also a pathogen of trees and is the causal agent of pine wilt disease. B. xylophilus is native to North America and here it causes little damage to trees. Where it is introduced to new regions it causes huge damage. The most severely affected areas are found in the Far East but more recently B. xylophilus has been introduced into Portugal and the potential for damage here is also high. As incidence and severity of pine wilt disease are linked to temperature we suggest that climate change is likely to exacerbate the problems caused by B. xylophilus and, in addition, will extend (northwards in Europe) the range in which pine wilt disease can occur. Here we review what is currently known about the interactions of B. xylophilus with its hosts, including recent developments in our understanding of the molecular biology of pathogenicity in the nematode. We also examine the potential developments that could be made by more widespread use of genomics tools to understand interactions between B. xylophilus , bacterial pathogens that have been implicated in disease and host trees.

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.

Developmental biology and cytogenetics of B. xylophilus

The pine wood nematode Bursaphelenchus xylophilus reproduces bisexually: a haploid sperm fertilizes a haploid oocyte, and the two pronuclei rearrange, move together, fuse, and begin diploid development. Early embryonic events taking place in the B. xylophilus embryo are similar to those of Caenorhabditis elegans, although the anterior-posterior axis appeares to be determined oppositely to that observed for C. elegans. Thai is, in the B. xylophilus embryo, the male pronucleus emerges at the future anterior end, whereas the female pronucleus appeares laterally. To understand the evolution of nematode developmental systems, we cloned the full length of Bx-tbb-1 (beta tubulin) from B. xylophilus cDNA and attempted to apply reverse genetics analysis to B. xylophilus. Several lengths of double stranded RNA (dsRNA) for the Bx-tbb-1 gene were synthesized by in vitro transcription, and both B. xylophilus and C. elegans were soaked in dsRNA for RNAi. Both nematodes could suck up the dsRNA, and we could detect the abnormal phenotypes caused by Bx-tbb-1 dsRNA in C. elegans, but not in B. xylophilus. We suspect that systemic RNAi might be suppressed in B. xylophilus and are attempting to establish other methods for functionally analyzing B. xylophilus genes.

Taxonomic databases for Bursaphelenchus and other aphelenchoid nematodes

Nematodes are the most abundant metazoans, comprising more than 80% of all animals alive today. Since 1743, when Needham (Needham, 1743) described the first nematode, approximately 20,000 - 30,000 species have been named, with estimates of species remaining to be described ranging from 100,000 to 1 million (Blaxter, 2004; De Ley, 2000). Unfortunately, the taxonomic community is woefully inadequate for this task. The number of taxonomists currently describing new species of nematodes around the world is less than 100, and significant increases are not expected. If each of these taxonomists were able to describe 10 new species every year, it would take between 100 to 1,000 years to name these yet to be described species.

Isolation of Aeromonas hydrophila in piglets

The production of Alentejano breed pig started a recovery two decades ago due to increasing demand for gourmet products. These pigs are raised in rotational semi-extensive or extensive outdoor production systems in the “Montado” (green and cork oak forest), grazing and feeding acorns and other associated food resources. Bacteria of the genus Aeromonas are considered as emerging pathogens of importance for man and animals, but its involvement in swine is not well documented. In the context of a study made at the University of Évora to assess the specific diseases of Alentejano swine, diseased piglets from two farms were submitted for pathological and bacteriological examinations. Pathological examinations revealed changes characteristic of septicemia, and Aeromonas hydrophila was isolated in pure culture from multiple organs of piglets from both farms. Antibiotic sensitivity tests showed that the isolates from one of the farms were susceptible to gentamicin, oxitetracycline, neomycin, enrofloxacin, colistin sulfate, trimethoprim, ceftiofur, and amoxicillin plus clavulanic acid. In contrast, the A. hydrophila isolated in the other farm was resistant to all drugs tested but enrofloxacin. This is the first report in the world showing the relationship between septicemia and A. hydrophila infection in piglets. The importance of this finding is further reinforced by the fact that these bacteria can be highly resistant to antimicrobial agents.

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.

Assessment of the genetic diversity of the pinewood nematode, Bursaphelenchus xylophilus, in Portugal

O nemátode da madeira do pinheiro (NMP), Bursaphelenchus xylophiius, tem uma extensa distribuição na América do Norte, e encontra-se atualmente distribuído ao longo da maioria dos territórios de Canadá e dos Estados Unidos. Durante o último século, esta espécie foi transportada pelo Homem para outras regiões do mundo (não-nativas), associadas com o comércio e o fluxo global de produtos de origem florestal. Atualmente, esta espécie invasiva está reportada para algumas regiões do SE asiático (China, Japão, Coreia e Taiwan) e mais recentemente para a Europa (Portugal). Devido ao impacto que este organismo agente da doença da murchidão dos pinheiros causa nas florestas nativas destas regiões esta espécie assume uma elevada importância económica a nível mundial Em Portugal, a distribuição do NMP encontra-se confinada a uma área restrita e limitada (500 000 ha), a sul de Lisboa (península de Setúbal); contudo, constitui uma das maiores ameaças às florestas de pinheiro do país e da UE. Ate recentemente, nenhum consenso existia quanto à origem do NMP em Portugal. Diversas hipóteses têm sido colocadas para explicar esta introdução, nomeadamente a partir de zonas onde o nematode ocorre naturalmente (América do Norte), ou de outras áreas (não-nativas) onde o nematode se comporta como uma espécie invasiva (Leste da Ásia). A fim de avaliar a variabilidade genética do NMP proveniente da área afetada em Portugal, foram utilizadas várias técnicas moleculares, designadamente o random amplified polymorphic DNA (RAPD-PCR) e o satellite DNA (satDNA). No caso do RAPD-PCR, foram utilizados 24 isolados do NMP provenientes de Portugal, 1 proveniente da América do Norte e 1 da Ásia, tendo sido utilizado como out-group um isolado de B. mucronatus. A partir dos 28 RAPD primers utilizados obtiveram-se 640 fragmentos. No caso do satDNA, foram utilizados 21 isolados do NMP provenientes de Portugal, obtendo-se no total 206 sequências da família MspI. Ambos os métodos revelaram uma elevada similaridade genética entre os vários isolados do NMP da área afetada em Portugal O nível reduzido de diversidade genética obtido entre os isolados portugueses do NMP, permite concluir que se trata de uma única introdução deste organismo em Portugal, e proveniente de uma região asiática. A inexistência de uma de correlação entre a variabilidade genética e a distribuição geográfica do NMP dentro da área afetada em Portugal, indica que o NMP se encontra distribuído de forma uniforme ao longo de toda a área afetada, provavelmente relacionado com a distribuição e a expansão natural do inseto vector. The pinewood nematode (PWN), Bursaphelenchus xylophilus, has a wide distribution in North America, and is present throughout most of the territories of Canada and the United Stata. During the last century, this species has been transported by man to several non-native regions of the world, associated with trade and the global flow of forest products. Up to date, this invasive species has been reported from Asia (PR China, Japan, Korea and Taiwan) and more recently in Europe (Portugal). Due to the impact on native pine forests of these regions, this nematode species, the causal agent of pine wilt disease, is of great economic importance worldwide. In Portugal, the distribution of the PWN has been constrained to a relatively small area (500 000 ha) in the south of Lisbon (Setúbal Peninsula); however, it has become the most serious threat to pine forests in the country. Until recently, no consensus had emerged on the possible pathway of the PWN introduction in Portugal. Several hypotheses have been put forward to explain this introduction, such as an origin from endemic areas where the nematode naturally occurs (North America), or non-endemic areas where the nematode behaves as an exotic pest (East Asia). Random amplified polymorphic DNA (RAPD-PCR) and satellite DNA (satDNA) techniques were used in order to assess the level of genetic variability and genetic relationships, among several isolates of the PWN, representative of the entire affected area in Portugal. In the case of RAPD-PCR, 24 Portuguese isolates, plus two additional isolates of B. xylophilus, representing North America and East Asia were included. B. mucronatus was used as an out-group. Twenty-eight random primers generated a total of 640 DNA fragments. With satDNA, 206 Mspl sequence repeats were obtained from 21 Portuguese isolates of B. xylophilus. Both molecular methods revealed a high genetic similarity among the Portuguese isolates, and the low level of genetic diversity strongly suggests that they were dispersed recently from a single introduction, and from East Asia. The lack of apparent relationship between the genetic variability and the geographic distribution of the PWN within the affected area, suggests that the recent introduction of this pest (and pathogen) in Portugal has been uniformly distributed since its establishment, probably following the natural distribution and expansion of the insect vector.

A influência dos factores humanos, ambientais e do pastoreio na ocorrência de geneta (Genetta genetta) no Sítio Monfurado

O presente estudo determina e analisa a importância relativa de diversos descritores ambientais, de pastoreio e de influência humana directa na distribuição da geneta (Genetta genetta L., 1758). O estudo decorreu em Monfurado, Sítio de Importância Comunitária, no Sul de Portugal. A área de estudo é predominantemente agrícola, maioritariamente ocupada por montado. A análise do padrão de distribuição deste carnívoro através de partição da variância e de ITMC (lnformation Theoretic Model Comparison) teve como objectivo orientar as prioridades na gestão das actividades humanas, compatíveis com a presença da espécie. Os resultados mostram que a distribuição da geneta é maioritariamente influenciada pelos descritores ambientais, apresentando uma relação positiva com densidade de montado com matos, conteúdo de matéria orgânica do solo e índice de Shannon de diversidade vertical da vegetação. A sua presença parece também ser promovida por níveis intermédios de pastoreio e fora das zonas de caça do regime cinegético especial. ABSTRACT; This study determines and analyses the relative importance of several environmental, livestock and human descriptors in the distribution of the common genet (Genetta genetta L., 1758). The study was conducted in Monfurado, a Site of Communitary lmportance, in South Portugal. The study area is Mediterranean farmland and is dominated by evergreen oak tree stands, named "montado". Modeling the distribution of this carnivore species was evaluated on the basis of ITMC (lnformation Theoretic Model Comparison) and variation partitioning techniques aiming to define human management activities compatible with the species conservation. The results show that the species distribution is mainly influenced by the environmental descriptors, and is positively related with montado and shrubs density, soil organic matter and Shannon's index of vertical vegetation diversity. Genet presence is favoured by intermediate levels of grazing and outside of game estates areas.

Molecular regulation of cork development: the QsMYB1 gene

Cork is a natural and renewable material obtained as a sustainable product from cork oak (Quercus suber L.) during the tree’s life. Cork formation is a secondary growth derived process resulting from the activity of cork cambium. However, despite its economic importance, only very limited knowledge is available about the molecular mechanisms underlying the regulation of cork biosynthesis and differentiation. The work of this PhD thesis was focused on the characterization of an R2R3-MYB transcription factor, the QsMYB1, previously identified as being putatively involved in the regulatory network of cork development. The first chapter introduces cork oak and secondary growth, with special emphasis on cork biosynthesis. Some findings concerning transcriptional regulation of secondary growth are also described. The MYB superfamily and the R2R3-MYB family (in particular) of transcription factors are introduced. Chapter II presents the complete QsMYB1 gene structure with the identification of two alternative splicing variants. Moreover, the results of QsMYB1 expression analysis, done by real-time PCR, in several organs and tissues of cork oak are also reported. Chapter III is dedicate to study the influence of abiotic stresses (drought and high temperature) and recovery on QsMYB1 expression levels. The effects of exogenous application of phytohormones on the expression profile of QsMYB1 gene are evaluated on Chapter IV. Chapter V describes the reverse genetic approach to obtain transgenic lines of Populus tremula L. x tremulóides Michx. overexpressing the QsMYB1 gene. Finally, in Chapter VI the final conclusions of this PhD thesis are presented and some future research directions are pointed based on the obtained results.

Infection mechanism of Diplodia corticola

Diplodia corticola is regarded as the most virulent fungus involved in cork oak decline, being able to infect not only Quercus species (mainly Q. suber and Q. ilex), but also grapevines (Vitis vinifera) and eucalypts (Eucalyptus sp.). This endophytic fungus is also a pathogen whose virulence usually manifests with the onset of plant stress. Considering that the infection normally culminates in host death, there is a growing ecologic and socio-economic concern about D. corticola propagation. The molecular mechanisms of infection are hitherto largely unknown. Accordingly, the aim of this study was to unveil potential virulence effectors implicated in D. corticola infection. This knowledge is fundamental to outline the molecular framework that permits the fungal invasion and proliferation in plant hosts, causing disease. Since the effectors deployed are mostly proteins, we adopted a proteomic approach. We performed in planta pathogenicity tests to select two D. corticola strains with distinct virulence degrees for our studies. Like other filamentous fungi D. corticola secretes protein at low concentrations in vitro in the presence of high levels of polysaccharides, two characteristics that hamper the fungal secretome analysis. Therefore, we first compared several methods of extracellular protein extraction to assess their performance and compatibility with 1D and 2D electrophoretic separation. TCA-Acetone and TCA-phenol protein precipitation were the most efficient methods and the former was adopted for further studies. The proteins were extracted and separated by 2D-PAGE, proteins were digested with trypsin and the resulting peptides were further analysed by MS/MS. Their identification was performed by de novo sequencing and/or MASCOT search. We were able to identify 80 extracellular and 162 intracellular proteins, a milestone for the Botryosphaeriaceae family that contains only one member with the proteome characterized. We also performed an extensive comparative 2D gel analysis to highlight the differentially expressed proteins during the host mimicry. Moreover, we compared the protein profiles of the two strains with different degrees of virulence. In short, we characterized for the first time the secretome and proteome of D. corticola. The obtained results contribute to the elucidation of some aspects of the biology of the fungus. The avirulent strain contains an assortment of proteins that facilitate the adaptation to diverse substrates and the identified proteins suggest that the fungus degrades the host tissues through Fenton reactions. On the other hand, the virulent strain seems to have adapted its secretome to the host characteristics. Furthermore, the results indicate that this strain metabolizes aminobutyric acid, a molecule that might be the triggering factor of the transition from a latent to a pathogenic state. Lastly, the secretome includes potential pathogenicity effectors, such as deuterolysin (peptidase M35) and cerato-platanin, proteins that might play an active role in the phytopathogenic lifestyle of the fungus. Overall, our results suggest that D. corticola has a hemibiotrophic lifestyle, switching from a biotrophic to a necrotrophic interaction after plant physiologic disturbances.This understanding is essential for further development of effective plant protection measures.

Traditional algarvian distillats and liqueurs historic scientific aspects

All the evidence indicates that distillation and liqueurs preparation began in Monchique mountain because this place was pointed as a possible capital of the oldest population of Algarve and an important Arabic village (Barreto, 1972: 19). It was possible to find lots of vestiges like the alembic produced by Arabic population near the X century (Telo, 1988: 77). Traditionally the Algarvian people produce the Arbutus unedo L., fig, carob, grape distillates. At the same time they produce liqueur-using maceration of parts of plants or fruits in some kinds of distillates. Most of the work about Algarvian distillates started by studying the basic compounds of Arbutus unedo spirits by gas chromatography (GC) and mass spectrometry (MS) as well as other physical-chemical properties. In a second phase aged distillates were studied by their phenolic compounds evolution using high resolution liquid chromatography (HPLC). Volatile compounds of traditional liqueurs were identified by head space micro extraction solid phase (HE-SPME) and also analysed by gas chromatography mass spectrometry (GC-MS) and when possible confirmed with standards. Total phenols were determined by Folin-Ciocalteur method. Flavenoids were studied by high performance liquid chromatography (HPLC). Sensorial analysis was also done in every drink studies. The results showed that the arbutus distillate doesn’t present a high level of methanol according to the current legislation. The excesses of acidity or ethyl acetate present normal values when the fermentation is well done (Galego, et al. 1995: 341; Galego, et al. 1995: 685). During the aging process, the colour of spirits tend to become darker, the colour changes occurred more rapidly in the arbutus spirits located in cellars with higher temperatures (Galego, et al. 2001: 432). In the sensory evaluation of samples aged during 12 months into 50 L medium toasting level oak wood barrels, panellists considered that samples of arbutus spirit had too much wood flavour and they were not able to detect the characteristic aroma of arbutus fruit (Galego, et al., 2001: 183). Differences in liqueurs were observed using HS-SPME-GC, HS-SPME-GC-MS or HPLC analysis and this observation was confirmed by a sensorial panel (Galego, et al. 2003: 60).

Evaluation of the in vitro biological activities of extracts from carob tree and mediterranean oaks

Dissertação mest., Engenharia Biológica, Universidade do Algarve, 2009

A tomada de decisão e o envolvimento no jogo em doentes com Parkinson

Os processos de tomada de decisão na doença de Parkinson (DP) têm sido cada vez mais investigados nos últimos anos e têm estado associados à presença de perturbações de controlo de impulsos, nomeadamente o jogo patológico. De acordo com a literatura estas alterações comportamentais têm estado relacionadas a uma desregulação dopaminérgica nos circuitos ventromediais do córtex pré-frontal. O objetivo deste trabalho consistiu em compreender se os DP têm défices na tomada de decisão comparativamente ao grupo de controlo, estando associado a um risco acrescido destes doentes poderem tornar-se jogadores patológicos. Foram comparados 20 sujeitos com DP e sem demência e 20 indivíduos saudáveis sem doença neurológica, em tarefas de tomada de decisão (Iowa Gambling Task), risco de jogo patológico (South Oak Gambling Screen) e níveis de impulsividade (Barratt Impulsiveness Scale-11). Os resultados revelaram uma diminuição do desempenho na prova de tomada de decisão por parte dos DP e níveis de impulsividade ligeiramente superiores ao do grupo de controlo, particularmente da impulsividade não-planeada. Contudo não foram encontradas diferenças significativas entre grupos quanto ao risco de jogo patológico. De um modo geral, os DP têm dificuldade na tomada de decisão que poderá ser causada por uma disfunção no processamento do feedback emocional da recompensa e/ou punição. No entanto, não demonstraram um risco adicional em adotar condutas aditivas pelo jogo.

Study of transcripts and reactive oxygen species involved in the defence responses of Quercus suber against Phytophthora cinnamomi

The present work has the merit of exploring an insight into the activation of defence genes of Quercus suber during response to infection by Phytophthora cinnamomi. Thus, cDNA-AFLP methodology was used to identify gene fragments differentially present in the mRNA profiles of host cells of micropropagated Q. suber plantlets roots infected with zoospores of P. cinnamomi at different post challenge time points. Six candidate genes were selected based on their interesting cDNA-AFLP expression patterns and homology to genes known to play a role in defence. These six genes encode a cinnamyl alcohol dehydrogenase 2 (QsCAD2), a protein disulphide isomerase (QsPDI), a CC-NBS-LRR resistance protein (QsRPc), thaumatin-like protein (QsTLP), chitinase (QsCHI) and a 1,3-beta glucanase (QsGLU). The current work has been successful in evaluation of the expression of these genes by qRT-PCR. Data analysis revealed that transcript levels of QsRPc, QsCHI, QsCAD2 and QsPDI increased during the early hours of inoculation, while transcript profiles of thaumatin-like protein showed decreasing. No expression was detected for 1,3-beta-glucanase (QsGLU). Furthermore, the choice of suitable reference genes in any new experimental system is absolutely crucial in qRT-PCR; for this reason in this study and for the first time a set of potential reference genes were analyzed and validated for qRT-PCR normalization in the patho-system Phytophthora-Q. suber. Four candidate reference genes polimerase II (QsRPII), eukaryotic translation initiation factor 5A(QsEIF-5A), b-tubulin (QsTUB) and a medium subunit family protein of Clathrin adaptor complexes (QsCACs) were evaluated to determine the most stable internal references in Q. suber. Analysis of stability of genes was carried out using Genex software. Results indicated all these four potential reference genes assumed stable expression. Data analysis revealed that QsRPII and QsCACs were the two most stable genes, while genes QsTUB and QsEIF-5A were the third and the fourth most stable gene, respectively. In this study, a plasmid-based quantitative PCR method was developed to measure P. cinnamomi colonization during infection process of Q. suber. Plasmid-based detection of P. cinnamomi showed a gradual accumulation of the pathogen DNA in cork oak root tips up to 24 h post infection. The higher increase in P. cinnamomi/plasmid DNA ratio occurred between 18 and 24 h. One of the primary objectives of this research was to study the effect of cinnamomins (elicitins secreted by P. cinnamomin) on inducing defence mechanism against the pathogen, as recent histological and ultra-structural studies showed that P. cinnamomi was restricted to the outer cortex root fragments pre-treated with capsicien and cryptogein, suggesting that elicitins can stimulate plant defence reactions against P. cinnamomi. To complement these studies and to have a clear view of the nature of the interaction, the role of cinnamomins in the production of the oxidative burst [ROS and ROS scavenging enzymes such as superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD)] and in the defence responses was evaluated. Cork oak seedlings were pretreated with alpha-cinnamomin and then inoculated with P. cinnamomi mycelia. Results showed a significant higher production of reactive oxygen species (ROS) (H2O2 and O2•-) in elicitin and non-elicitin treated roots in interaction with P. cinnamomi in comparison to the corresponding control. The plant group inoculated with the pathogen after cinnamomin treatment showed an earlier increase in H2O2 production but this was lower as compared with that group inoculated with P. cinnamomi alone. Also, in elicitin pre-treated group generally, a lower level of O2•− production during infection was observed as compared with inoculated roots with P. cinnamomi alone without elicitin treatment. Furthermore, in this study, we evaluated activities of antioxidant enzymes upon challenge with P. cinnamomi, with and without pretreatment with alpha cinnamomin. Results indicated that the activities of defense enzymes POD, SOD and CAT increased after P. cinnamomi inoculation when compared with those in the control group. Also, in the group treated with alpha-cinnamomin followed by P. cinnamomi inoculation, a higher level of enzymatic activities was detected as compared with elicitin non-treated group, which suggest the protective effect of alpha-cinnamomin against the pathogen due to higher elevated levels of defense enzymes POD, SOD and CAT during the infection period. Furthermore, a sensitive qPCR method was applied to measure the pathogen biomass in elicited and non-elicited Q. suber roots challenged with P. cinnamomi to elucidate the effect of cinnamomins on the colonization of P. cinnamomi. Plasmid-based quantification of P. cinnamomi showed a significant decrease in accumulation of the pathogen DNA in cork oak roots after treatment with alpha and beta-cinnamomins which attest the role of cinnamomins in promoting defense responses in cork oak against P. cinnamomi invasion.