Above ground biomass estimation in Mediterranean multiple use systems with high spatial resolution satellite images

Forest biomass has been having an increasing importance in the world economy and in the evaluation of the forests development and monitoring. It was identified as a global strategic reserve, due to its applications in bioenergy, bioproduct development and issues related to reducing greenhouse gas emissions. The estimation of above ground biomass is frequently done with allometric functions per species with plot inventory data. An adequate sampling design and intensity for an error threshold is required. The estimation per unit area is done using an extrapolation method. This procedure is labour demanding and costly. The mail goal of this study is the development of allometric functions for the estimation of above ground biomass with ground cover as independent variable, for forest areas of holm aok (Quercus rotundifolia), cork oak (Quercus suber) and umbrella pine (Pinus pinea) in multiple use systems. Ground cover per species was derived from crown horizontal projection obtained by processing high resolution satellite images, orthorectified, geometrically and atmospheric corrected, with multi-resolution segmentation method and object oriented classification. Forest inventory data were used to estimate plot above ground biomass with published allometric functions at tree level. The developed functions were fitted for monospecies stands and for multispecies stands of Quercus rotundifolia and Quercus suber, and Quercus suber and Pinus pinea. The stand composition was considered adding dummy variables to distinguish monospecies from multispecies stands. The models showed a good performance. Noteworthy is that the dummy variables, reflecting the differences between species, originated improvements in the models. Significant differences were found for above ground biomass estimation with the functions with and without the dummy variables. An error threshold of 10% corresponds to stand areas of about 40 ha. This method enables the overall area evaluation, not requiring extrapolation procedures, for the three species, which occur frequently in multispecies stands.

Above ground biomass functions with vegetation indices for multiple use systems of two evergreen oaks

Remote sensing is a promising approach for above ground biomass estimation, as forest parameters can be obtained indirectly. The analysis in space and time is quite straight forward due to the flexibility of the method to determine forest crown parameters with remote sensing. It can be used to evaluate and monitoring for example the development of a forest area in time and the impact of disturbances, such as silvicultural practices or deforestation. The vegetation indices, which condense data in a quantitative numeric manner, have been used to estimate several forest parameters, such as the volume, basal area and above ground biomass. The objective of this study was the development of allometric functions to estimate above ground biomass using vegetation indices as independent variables. The vegetation indices used were the Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI), Simple Ratio (SR) and Soil-Adjusted Vegetation Index (SAVI). QuickBird satellite data, with 0.70 m of spatial resolution, was orthorectified, geometrically and atmospheric corrected, and the digital number were converted to top of atmosphere reflectance (ToA). Forest inventory data and published allometric functions at tree level were used to estimate above ground biomass per plot. Linear functions were fitted for the monospecies and multispecies stands of two evergreen oaks (Quercus suber and Quercus rotundifolia) in multiple use systems, montados. The allometric above ground biomass functions were fitted considering the mean and the median of each vegetation index per grid as independent variable. Species composition as a dummy variable was also considered as an independent variable. The linear functions with better performance are those with mean NDVI or mean SR as independent variable. Noteworthy is that the two better functions for monospecies cork oak stands have median NDVI or median SR as independent variable. When species composition dummy variables are included in the function (with stepwise regression) the best model has median NDVI as independent variable. The vegetation indices with the worse model performance were EVI and SAVI.

Can birds play a role as High Nature Value indicators of montado system?

Montados form a heterogeneous landscape of wooded matrix dominated by cork and/or holm oak with open areas characterized by fuzzy boundaries. Montado supports a high biological diversity associated to low intensity management and a landscape diversity provided by a continuous gradient of land cover. Among other features this permits the classification of montados as a High Nature Value (HNV) system. We assessed the role of birds as HNV indicators for montado, and tested several bird groups—farmland, edge, forest generalists and forest specialists species; and some universal indicators such as species conservation status, Shannon’s diversity index and species richness. Our study areas covered the North–South distribution of cork oak in Portugal, and we surveyed the breeding bird communities across 117 sampling sites. In addition to variables related to management and sanitary status, we considered variables that characterize the landscape heterogeneity inside the montado—trees and shrub density and richness of woody vegetation. Our results suggest that specific bird guilds can be used as HNV indicators of particular typologies of montado, and highlight the need to develop an indicator that could be transversally applied to all types of montado.

Creative Practices Around the Production of Cork

Cork, as a natural product provided by the bark of the cork oak tree, is an important staple of the Portuguese economy and important to Portuguese culture. It is a sustainable product with a positive ecological footprint, from harvesting to industrial production, with the advantage of creating a local economic model through regional labour activity and distribution. Within the balance between nature-human-economy to create a sustainable system, cork production in Portugal represents a human and social dimension. By focusing on that dimension and by creating an awareness of the cultural and social impact of the activity and by re-appraising the meaning of the material within the culture, the study reframes a consideration of the actual place of labour and production. The human, geophysical, historical, social, economic, ecological and cultural aspects of the place are observed as regards their relation to work or labour in that physical space. A pilot study is being developed in the village of Azaruja in the district of Évora, Portugal. In this small locality, cork is very important in terms of the relationships between the physical subsistence of their residents and the local natural resources, because it structures the place in its cultural, social and economical dimensions. This paper outlines the theoretical foundations, the process and the outcomes of the participatory ecodesign project titled Creative Practices Around the Production of Cork which was initiated by a Portuguese artist/design researcher and developed further through the collaboration with the other two authors, one a Portuguese visual artist/researcher and the other a Turkish fashion designer/theorist. The investigation focuses on questions that expand the notion of place for artists and designers, filtered through the lenses of manual labourers in order to understand their physical, social, cultural and economic relationship with the environment. To create the process of interaction with the place and the people, a creative collaborative dynamic is developed between the authors with their range of artistic sensibilities and the local population. To adopt a holistic notion of sustainability and cultural identity a process of investigation is designated to: (1) analyse, test and interpret - through the dissemination of life stories, visual representation of the place and the creation of cork objects - the importance of culture related to the labour activity of a local natural resource that determines and structures the region; (2) to give public recognition to those involved, taking into account their sense of belonging to the place and in order to show the value of their sustainable labour activities related to local natural resources; (3) to contribute to the knowledge of the place and to its dynamism through an aesthetic approach to labour activities. With reference to fields of knowledge such as anthropology, the social arts and sustainable design, a practice-based research is conducted with collaborative and participatory design methods to create an open model of interaction which involves local people in the realization of the project. Outcomes of this research will be presented in the paper as a survey analysis with theoretical conclusions.

Water requirements as a bottleneck in the reintroduction of European roe deer to the southern edge of its range

Success rates of reintroduction programs are low, often owing to a lack of knowledge of site-specific ecological requirements. A reintroduction program of European roe deer (Capreolus capreolus (L., 1758)) in a dry Mediterranean region in Israel provides an opportunity to study the bottleneck effect of water requirements on a mesic-adapted species. Four does were hand-reared and released in a 10 ha site consisting of an early succession scrubland and a mature oak forest. We measured daily energy expenditure (DEE) and water turnover (WTO) using the doubly labeled water technique during summer and winter. DEE was similar in the summer and winter, but there was a significant difference in WTO and in the source of gained water. In winter, WTO was 3.3 L/day, of which 67% was obtained from vegetation. In summer, WTO dropped to 2.1 L/day, of which only 20% was obtained from the diet and 76% was gained from drinking. When the water source was moved to a nonpreferred habitat, drinking frequency dropped significantly, but water consumption remained constant. In a dry Mediterranean environment, availability of free water is both a physiological contraint and a behavioral constraint for roe deer. This study demonstrates the importance of physiological and behavioral feasibility studies for reintroduction programs.

Incised palaeo-channels of the Late Middle Pleistocene Thames: age, origins and implications for fluvial palaeogeography and sea-level reconstruction in the southern North Sea Basin.

Multidisciplinary investigations of the infills of steeply-incised buried channels on the coast of Essex, England, provide important insights into late Middle Pleistocene climate and sea-level change and have a direct bearing on the differentiation of MIS 11 and MIS 9 in terrestrial records. New data are presented from Rochford and Burnham-on-Crouch where remnants of two substantial palaeo-channels filled with interglacial sediment can be directly related to the terrace stratigraphy of the Thames. The sediments in both channels accumulated in an estuarine environment early in an interglacial when mixed oak forest was becoming established. Lithological evidence suggests that the interglacial beds post-date the brackish-water infill of an older palaeo-channel ascribed to the Hoxnian and correlated with part of MIS 11, and pre-date terrace gravels (Barling Gravel) ascribed to MIS 8. An MIS 9 attribution is supported by molluscan biostratigraphy, palaeo-salinity and amino-acid racemization data. The relative sea-level record in this area thus includes evidence for two major marine transgressions during MIS 11 and MIS 9, with local maxima of >10 m O.D. Both are associated with sediments that show ‘Hoxnian’ palynological affinities. The wider significance of these findings, and of an intermediate phase of pronounced fluvial incision during MIS 10, is discussed.

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.

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

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

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.

Estudi d'una metal·lotioneïna d'alzina surera (QsMT)

En aquest treball es caracteriza per primera vegada la capacitat de coordinació metàl·lica d'una metal·lotineïna (MT) de planta i es proposa un model de plegament per a les MTs de planta en general. Els resultat mostren que aquestes proteïnes poden tenir un paper molt important en la regulació de l'estat redox de les cèl·lules, probablement a través de la coordinació a Cu. Les MTs de planta són proteïnes molt desconegudes. Es postula que participen en l'homeòstasi del Cu i en la protecció contra l'estrès oxidatiu, però es desconeix la capacitat de coordinació metàl·lica i el plegament. En aquest treball s'han estudiat una metal·lotioneïna d'alzina surera, QsMT, aïllada d'una llibreria de cDNA de fel·lema. Els objectius concrets han estat: (1) estudiar l'expressió de QsMT i la resposta a l'estrès oxidatiu; (2) determinar la capacitat de coordinació metàl·lica i la funcionalitat in vivo; (3) fer una aproximació al plegament de les MTs de planta. L'expressió del gen s'ha estudiat mitjançant hibridació in situ en plàntules i en embrions d'alzina surera. QsMT s'expressa majoritàriament en cèl·lules amb fort estrès oxidatiu, associat a la síntesi de polifenols (suberització i lignificació) i a la senescència. També s'expressa en cèl·lules meristemàtiques, cèl·lules en divisió molt activa on la funció de les MTs podria estar relacionada amb el manteniment de l'estat redox. L'aplicació d'estrès oxidatiu exogen (H2O2 i paraquat) incrementa fortament l'expressió de QsMT en teixits amb expressió constitutiva, confirmant la regulació de l'expressió del gen per estrès oxidatiu. Per l'estudi de les propietats de coordinació metàl·lica es va expressar QsMT en cèl·lules d'E. coli en medi de cultiu suplementat amb Cu, Zn o Cd. Es van aïllar els agregats metàl·lics corresponents i es van analitzar mitjançant tècniques espectroscòpiques i espectromètriques (ICP-OES, ESI-MS i CD). Els resultats mostren que QsMT coordina de forma estable Cu (8 ions metàl·lics/molècula), Zn (4 ions de Zn/molècula) i Cd (6 ions de Cd/molècula), i adopta una estructura especialment quiral en coordinació a Cu. L'elevada capacitat quelant de la proteïna i la quiralitat de l'estructura indiquen que QsMT possiblement té preferència metàl·lica pel Cu i per tant una funció relacionada amb aquest metall in vivo. Estudis de complementació en llevat demostren que QsMT coordina Cu de forma funcional in vivo. En coordinació a Cd QsMT presenta una peculiaritat no observada fins ara en altres MTs: la participació d'ions sulfur en la formació de l'agregat metàl·lic incrementant la capacitat de coordinació metàl·lica (6 ions metàl·lics divalents de Cd enlloc de 4 ions de Zn). A més QsMT coordina Cd de forma funcional en llevat, i per tant la seva funció també podria estar relacionada amb la destoxicació de Cd en la planta. QsMT s'ha utilitzat com a model per fer una aproximació al plegament de les MTs de planta. Amb aquest objectiu vam dissenyar tres pèptids mutants derivats de QsMT: N25 corresponent a la zona rica en cisteïna en posició amino-terminal, C18 corresponent a la zona rica en cisteïna en posició carboxil-terminal, i N25-C18 corresponent a les dues zones riques en cisteïna enllaçades per 4 glicines substituint la zona central de 39 aminoàcids. Es van expressar i estudiar aquests pèptids per les mateixes tècniques utilitzades en l'estudi de QsMT. Els resultats indiquen que QsMT es plega formant un sol agregat metàl·lic per la interacció de les dues zones riques en cisteïna. En aquest model la zona central d'enllaç, típica de les MTs de planta, no participa en la coordinació metàl·lica però és imprescindible per a la funció de la proteïna. El paper de la zona central podria variar en funció del metall que coordina, participant en el plegament i estructura de la proteïna quan coordina Zn i Cd i en la seva regulació i estabilització quan coordina Cu.

Les sHsps en surera: capacitat protectora enfront l'estrés i variabilitat genètica

Els organismes responen a la temperatura i a molts altres estressos sintetitzant un grup de proteïnes anomenat proteïnes de xoc de calor (HSPs). En plantes les sHsps, d'entre 15 i 30 kDa formen el grup més abundant i divers, classificat en funció de la seva localització subcel.lular i homologia en: mitocondrials, cloroplàstiques, de reticle endoplasmàtic i citoplàsmiques de classe I i II. Les sHsps-CI s'ha descrit que s'indueixen per estrès tèrmic, hídric i oxidatiu (peròxid d'hidrògen, llum UV, ozó) i en resposta a algunes hormones. També s'expressen durant el desenvolupament, per exemple durant l'embriogènesi, on es creu que podrien tenir un paper protector de l'embrió enfront la dessecació. Tot i que hi ha abundants treballs que correlacionen la resistència a l'estrès i l'acumulació de sHsps-CI, els mecanismes moleculars d'aquesta activitat són poc conguts. Tot i això, per diverses sHsps-CI ha estat descrita una activitat xaperona in vitro i, més recentment, que la seva sobreexpressió augmenta la viabilitat de cèl.lules d'E.coli en condicions d'estrès tèrmic. L'estudi de l'acumulació de sHsps-CI en surera (Quercus suber) mitjançant immunodetecció en electroforesi bidimensional mostra uns patrons d'acumulació complexos i formats per dos grups d'espècies proteiques principals, a l'entorn dels 10 i 17 kDa respectivament, que mostren una inducció diferencial en funció del teixit i l'estrès. Mentre que les espècies proteiques de 17 kDa s'indueixen per temperatura però no per estrès oxidatiu, les de ca. 10 kDa ho fan per estrès oxidatiu i no per temperatura. Ambdós grups d'espècies proteiques s'acumulen conjuntament en fel.lema. Assajos de PCR i RT-PCR han permès clonar parcialment tres noves sHsps-CI en surera: Qshsp10-CI, QshspC-CI i QshspD-CI. Aquest fet confirma la multigeneïcitat de les sHsps-CI en surera que apuntava el patró bidimensional. Dels nous clons obtinguts destaca especialment Qshsp10-CI, un gen que presenta un codó stop enmig del domini -cristal.lí que fa que a la proteïna que se'n dedueix li manqui un 55% del domini -cristal.lí i tota l'extensió C-terminal. Es tractaria de la sHsp més petita i més truncada descrita fins al moment. L'anàlisi de l'expressió de Qshsp10-CI mitjançant RT-PCR mostra expressió en plantes tractades amb H2O2 però no en les que han estat sotmeses a un xoc de calor. Aprofitant l'oportunitat que oferia aquesta sHsp-CI de ser utilitzada com a model per l'estudi de la importància del domini -cristal.lí i l'extensió C-terminal en l'activitat protectora enfront l'estrès, es va voler determinar la capacitat que tenia d'augmentar la viabilitat de cèl.lules d'E. coli en condicions d'estrès tèrmic i oxidatiu. Els resultats mostren que la proteïna recombinant QsHsp10-CI, tot i la important truncació que té, és capaç de protegir cèl.lules d'E. coli en condicions d'estrès tèrmic i, remarcablement, en condicions d'estrès oxidatiu. Tots aquests resultats indiquen que les espècies proteiques de ca. 10 kDa podrien correspondre a Qshsp10-CI i tenir un paper en les cèl.lules del fel.lema en la protecció enfront l'estrès oxidatiu. L'estrès oxidatiu provoca lesions al DNA que poden produir errors en la replicació, transcripció o traducció i generar proteïnes aberrants. Donades les condicions d'estrès oxidatiu a les quals es troben sotmeses les cèl.lules del fel.lema, s'ha volgut estudiar la variabilitat dels seus àcids nucleics. La determinació de la taxa de mutació de la regió codificant del gen Qshsp17.4-CI en mRNA i DNA de fel.lema i àpex radicular, un teixit jove i en creixement actiu va mostrar unes taxes sorprenentment elevades en l'mRNA (1/1784 pb) i el DNA genòmic (1/1520 pb) del fel.lema. Aquestes taxes són les més altes descrites en un genoma nuclear eucariota i són similars a les dels virus d'RNA d'evolució ràpida com el virus de l'Hepatitis C. Amb aquestes taxes de mutació, un terç dels mRNAs del fel.lema de la surera contindrien missatges aberrants i la supervivència de les cel.lules es veuria compromesa. Això implica que el fel.lema hauria de ser considerat com un mosaic de cèl.lules genèticament heterogènies i, per tant, una sola seqüència no defineix en tota la seva amplitud un gen en aquest teixit. No es va detectar cap mutació en àpex de rel. Amb l'objectiu d'aprofundir en el coneixement de les mutacions que es donen en aquests dos teixits i per tal de poder fer una anàlisi qualitativa més completa que permetés especular sobre el seu origen, es va aplicar un mètode de selecció de seqüències mutants en base a la utilització d'enzims de restricció. Les mutacions detectades en fel.lema es corresponen amb les relacionades, en altres sistemes no nuclears (plasmidis, fags i DNA bacterià), amb l'estrès oxidatiu. En conseqüència, l'estrès oxidatiu al qual estan sotmeses les cèl.lules del fel.lema podria ser el causant de l'elevada taxa de mutació detectada. D'acord amb això, el tipus majoritari de productes d'oxidació de les bases del DNA que s'acumulen en brots de plàntules de surera en resposta al peròxid d'hidrògen produeixen el mateix tipus de mutacions detectades en l'mRNA del fel.lema de la surera. La major sensibilitat d'aquest nou mètode ha permès, a més, detectar mutacions en molècules d'mRNA de rel, un teixit en el qual no s'havia trobat cap mutació utilitzant el mètode de clonatge i seqüenciació directa. Tot i això, el tipus de mutacions predominants no estan relacionades amb l'estrès oxidatiu sinó amb erros en la reparació dels àcids nucleics.

Landscape typology in the Mediterranean context: a tool for habitat restoration

Despite the wide use of Landscape Character Assessment (LCA) as a tool for landscape planning in NW Europe, there are few examples of its application in the Mediterranean. This paper reports on the results from the development of a typology for LCA in a study area of northern Sardinia, Italy to provide a spatial framework for the analysis of current patterns of cork oak distribution and future restoration of this habitat. Landscape units were derived from a visual interpretation of map data stored within a GIS describing the physical and cultural characteristics of the study area. The units were subsequently grouped into Landscape Types according to the similarity of shared attributes using Two Way Indicator Species Analysis (TWINSPAN). The preliminary results showed that the methodology classified distinct Landscape Types but, based on field observations, there is a need for further refinement of the classification. The distribution and properties of two main cork oak habitats types was examined within the identified Landscape Types namely woodlands and wood pastures using Patch Analyst. The results show very clearly a correspondence between the distribution of cork oak pastures and cork oak woodland and landscape types. This forms the basis of the development of strategies for the maintenance, restoration and recreation of these habitat types within the study area, ultimately for the whole island of Sardinia. Future work is required to improve the landscape characterisation , particularly with respect to cultural factors, and to determine the validity of the landscape spatial framework for the analysis of cork oak distribution as part of a programme of habitat restoration and re-creation.

Laboratory and field measurements of enantiomeric and non-enantiomeric biogenic VOCs and anthropogenic BTEX compounds

This doctoral thesis was focused on the investigation of enantiomeric and non-enantiomeric biogenic organic compound (BVOC) emissions from both leaf and canopy scales in different environments. In addition, the anthropogenic compounds benzene, toluene, ethylbenzene, and xylenes (BTEX) were studied. BVOCs are emitted into the lower troposphere in large quantities (ca. 1150 Tg C ·yr-1), approximately an order of magnitude greater than the anthropogenic VOCs. BVOCs are particularly important in tropospheric chemistry because of their impact on ozone production and secondary organic aerosol formation or growth. The BVOCs examined in this study were: isoprene, (-)/ (+)-α-pinene, (-)/ (+)-ß-pinene, Δ-3-carene, (-)/ (+)-limonene, myrcene, eucalyptol and camphor, as these were the most abundant BVOCs observed both in the leaf cuvette study and the ambient measurements. In the laboratory cuvette studies, the sensitivity of enantiomeric enrichment change from the leaf emission has been examined as a function of light (0-1600 PAR) and temperature (20-45°C). Three typical Mediterranean plant species (Quercus ilex L., Rosmarinus officinalis L., Pinus halepensis Mill.) with more than three individuals of each have been investigated using a dynamic enclosure cuvette. The terpenoid compound emission rates were found to be directly linked to either light and temperature (e.g. Quercus ilex L.) or mainly to temperature (e.g. Rosmarinus officinalis L., Pinus halepensis Mill.). However, the enantiomeric signature showed no clear trend in response to either the light or temperature; moreover a large variation of enantiomeric enrichment was found during the experiment. This enantiomeric signature was also used to distinguish chemotypes beyond the normal achiral chemical composition method. The results of nineteen Quercus ilex L. individuals, screened under standard conditions (30°C and 1000 PAR) showed four different chemotypes, whereas the traditional classification showed only two. An enclosure branch cuvette set-up was applied in the natural boreal forest environment from four chemotypes of Scots pine (Pinus sylvestris) and one chemotype of Norway spruce (Picea abies) and the direct emissions compared with ambient air measurements above the canopy during the HUMPPA-COPEC 2010 summer campaign. The chirality of a-pinene was dominated by (+)-enantiomers from Scots pine while for Norway spruce the chirality was found to be opposite (i.e. Abstract II (-)-enantiomer enriched) becoming increasingly enriched in the (-)-enantiomer with light. Field measurements over a Spanish stone pine forest were performed to examine the extent of seasonal changes in enantiomeric enrichment (DOMINO 2008). These showed clear differences in chirality of monoterpene emissions. In wintertime the monoterpene (-)-a-pinene was found to be in slight enantiomeric excess over (+)-a-pinene at night but by day the measured ratio was closer to one i.e. racemic. Samples taken the following summer in the same location showed much higher monoterpene mixing ratios and revealed a strong enantiomeric excess of (-)-a-pinene. This indicated a strong seasonal variance in the enantiomeric emission ratio which was not manifested in the day/night temperature cycles in wintertime. A clear diurnal cycle of enantiomeric enrichment in a-pinene was also found over a French oak forest and the boreal forest. However, while in the boreal forest (-)-a-pinene enrichment increased around the time of maximum light and temperature, the French forest showed the opposite tendency with (+)-a-pinene being favored. For the two field campaigns (DOMINO 2008 and HUMPPA-COPEC 2010), the BTEX were also investigated. For the DOMINO campaign, mixing ratios of the xylene isomers (meta- and para-) and ethylbenzene, which are all well resolved on the ß-cyclodextrin column, were exploited to estimate average OH radical exposures to VOCs from the Huelva industrial area. These were compared to empirical estimates of OH based on JNO2 measured at the site. The deficiencies of each estimation method are discussed. For HUMPPA-COPEC campaign, benzene and toluene mixing ratios can clearly define the air mass influenced by the biomass burning pollution plume from Russia.

Habitat Associations of the Golden-Winged Warbler in Honduras

The global population of the Neotropical migrant Golden-winged Warbler (Vermivora chrysoptera) has declined steadily over the past fifty years. While factors influencing this decline have been well researched on the breeding grounds, little is known about the distribution and habitat requirements of this warbler on its stationary non-breeding range. Recent efforts to quantify the non-breeding habitat requirements of this warbler have focused on Colombia and Costa Rica, though the species ranges as far north as the Yucatan Peninsula, Mexico. To address the gap in knowledge from the northern portion of the non-breeding range, I conducted 80 serial point-count surveys targeting Goldenwinged Warblers at eight field sites in Honduras, Central America. I found that Goldenwinged Warblers occupy a greater variety of habitats than previously recognized, including pine-oak forest and semi-deciduous broadleaf forest. I also documented habitat associations that have not been observed in other parts of the non-breeding range with respect to elevation, rainfall, and spatial segregation by sex. These results demonstrate the need to consider the entire non-breeding range in conservation planning, as Goldenwinged Warbler habitat associations appear to vary regionally.

Pollen records and lithology of profiles from Lobsigensee, Switzerland

Lobsigensee is a small kettle hole lake 15 km north-west of Bern on the Swiss Plateau, at an altitude of 514 m asl. Its surface is 2ha today, its maximum depth 2.7 m; it has no inlet and the overflow functions mainly during snow melting. The area was covered by Rhone ice during the Last Glaciation (map in Fig.2). Local geology, climate and vegetation are summarized in Figure 3A-C, the history of settlement in Figures 5-7. In order to reconstruct the vegetational and environmental history of the lake and its surroundings pollen analysis and other bio- and isotope stratigraphies were applied to twelve profiles cored across the basin with modified Livingstone corers (Fig.3 D). (1) The standard diagram: The central core LQ-90 is described as the standard pollen diagram (Chapter 3) with 10 local pollen assemblage zones of the Late-Glacial (local PAZ Ll to Ll0, from about 16'000(7) to 10'000 years BP) and 20 PAZ of the Holocene (local PAZ L11 to L30), see Figs. 8-10 and 20-24. Local PAZ L 1 to L3 are in the Late-Glacial clay and record the vegetational development after the ice retreat: L1 shows very low pollen concentration and high Pinus percentages due to long-distance transport and reworking; the latter mechanism is corroborated by the findings of thermophilous and pre-Quaternary taxa. Local PAZ L2 has a high di versi ty of non-arboreal pollen (NAP) and reflects the Late-Glacial steppe rich in heliophilous species. Local PAZ L3 is similar but additionally rich in Betula nana and Sal1x, thus reflecting a "shrub tundra". The PAZ L1 to L3 belong to the Oldest Dryas biozone. Local PAZ L4 to L 10 are found in the gyttja of the profundal or in the lake marl of the littoral and record the Late-Glacial forests. L4 is the shrub phase of reforestation with very high Junlperus and rapidly increasing Betula percentages. L5 is the PAZ with a first, L7 with a second dominance of tree-birches, separated by L6 showing a depression in the Betula curve. L4 to L7 can be assigned to the Balling biozone. Possible correlation of the Betula depression to the Older Dryas biozone is discussed. In local PAZ L8 Plnus immigrates and expands. L9 shows a facies difference in that Plnus dominates over Betula in littoral but not in profundal spectra. L8 and L9 belong to the Allerod biozone. In its youngest part the volcanic ash from Laach/Eifel is regularly found (11,000 BP). The local PAZ Ll0 corresponds to the Younger Dryas blozone. The merely slight increase of the NAP indicates that the pine forests of the lowland were not strongly affected by a cooler climate. In order to evaluate the significance of the littoral accumulation of coniferous pollen the littoral profile LQ-150 is compared to the profundal. Radiocarbon stratigraphies derived from different materials are presented in Figures 13 and 14 and in Tables 2 and 3. The hard-water errors in the gyttja samples and the carbonate samples are similar. The samples of terrestrial plant macrofossils are not affected by hard-water errors. Two plateaux of constant age appear in the age-depth relationship; their consequence for biostratigraphy as well as pollen concentration and influx diagrams are discussed. Radiocarbon ages of the Late-Glacial pollen zones are shown in Table 10. The Holocene vegetational history is recorded in the local PAZ L 11 to L30. After a Preboreal (PAZ L11) dominated by pine and birch the expansions of Corylus, Ulmus and Quercus are very rapid. Among these taxa Corylus dominates dur ing the Boreal (PAZ L 12 and L 1 3), whereas the components of the mixed oak forest dominate in the Older Atlantic (PAZ L14 to L16). In the Younger Atlantic (PAZ L 17 to L 19) Fagus and Alnus play an increasing, the mixed oak forest a decreasing role. During the period of local PAZ L19 Neolithic settlers lived on the shore of Lobsigensee. During the Subboreal (PAZ L20 and L21) and the Older Subatlantic (L22 to L25) strong fluctuations of Fagus and often antagonistic peaks of NAP, Alnus, Betula and Corylus can be interpreted as signs of human impact on vegetation. L23 is characterized not only by high values of NAP (especially apophytes and anthropochorous species) but also by the appearance of Juglans, Castanea and Secale which point to the Roman colonization of the area. For a certain period during the Younger Subatlantic (PAZ L26 to L30) the lake was used for retting hemp (Cannabis). Later the dominance of Quercus pollen indicates the importance of wood pastures. The youngest sediments reflect the wide-spread agricultural grass lands and the plantation of Pinus and Picea. Radiocarbon dates for the Holocene are given in Figure 23 and Table 4, the extrapolated ages of the Holocene pollen zones in Table 15. (2) The cross sections: Figures 25 and 26 give a summary of the litho- and palynostratigraphy of the two cross sections. Based on 11 Late-Glacial and 9 Holocene pollen diagrams (in addition to the standard ones), the consistency of the criteria for the definition of the pollen zones is examined in Tables 7 and 8 for the Late-Glacial and in Tables 11 to 14 for the Holocene. Sediment thicknesses across the basin for each pollen zone are presented in these tables as well as in Figures 43 to 45 for the Late-Glacial and in Figures 59 to 65 for the Holocene. Sediment focusing can explain differences between the gyttja cores of the profundal. Focusing is more than compensated for through "stretching" by carbonate precipitation on the littoral terrace. Pollen influx to the cross section are discussed (Chapters 4.1.5. and 4.2.3.). (3) The regional pollen zones: Based on some selected sites between Lake Geneva and Lake Constance regional pollen zones are proposed (Table 16, 17 and 19). (4) Paleoecology: Climatic change in the Late-Glacial can be inferred from Coleoptera, Trichoptera, Chironomidae and d18O of carbonates: a distinct warming is recorded around 12' 600 BP and around 10' 000 BP. The Younger Dryas biozone (10'700-10'000 BP) was the only cooling found in the Late-Glacial. The Betula depression often correlated wi th the Older Dryas biozone was possibl not colder but dryer than the previous period. During the Holocene the lowland site is not very sensitive to the minor climatic changes. Table 22 summarizes climatic and trophic changes before 8'000 BP as deduced from various biostratigraphies studied by a number of authors. Ostracods, Chironomids and fossil pigments indicate that anoxic conditions prevailed during the BoIling (possibly meromixis). Changes in the lake level are illustrated in Figure 74. A first lake-level lowering occurred in the early Holocene (10'000 to 9'000 BP), a second during the Atlantic (about 6'800 to 5'200 BP). The first "shrinking" of the lake volume resulted in a eutrophication recorded by laminations in the profundal and by pigments of Cyanophyceae. The second fall in water level corresponds to an increase of Nymphaeaceae. Human impact can be inferred in three ways: eutrophication of the lake (since the Neolithic), changes of terrestrial vegetation by deforestations (cyclicity of Fagus, see Figures 78 to 80), and enhanced erosion (increasing sedimentation rates by inwashed clay, particularly since the Roman Colonization, see Figures 49 and 81). Summary: This paper was planned as the final report on Lobsigensee. However, a number of issues are not answered but can only be asked more precisely, for example: (1) For the two periods with the highest rates of change, Le. the Bolling and the Preboreal biozones, pollen influx may reflect vegetation dynamics. Detailed investigations of these periods in annually laminated sediments are planned. (2) Biostratigraphies other than palynostratigraphy are needed to estimate the degree of linkage or independence in the development of terrestrial and lacustrine ecosystems. Often our sampling intervals were not identical, thus influencing our temporal resolution. (3) 6180- and 14C-stratigraPhies with high resolution will elucidate the leads and lags of these dynamic periods. Plateaux of constant age in the age-depth relationship have a strong bearing on both biological and geophysical understanding of Late-Glacial and early Holocene developments. (4) Numerical methods applied to the pollen diagrams of the cross section will help to quantify the significance of similari ties and dissimilarities across a single basin (with Prof. Birks). (5) Numerical methods applied to different sites on the Swiss Plateau and on the transect across the Alps will be helpful in evaluating the influence of different environmental factors (with Prof. Birks). (6) A new map 1: 1000 with 50cm-contour lines prov ided by Prof. Zurbuchen will be combined with a grid of cores sampling the transition from lake marl to peat enabling us to calculate paleo-volumes of the lake. This is interesting for the two "shrinking periods" (in Fig. 74A numbers 2-6 and 7-10), both accompanied by eutrophication. The pal eo-volume during the Neoli thic set tlement of the Cortaillod culture linked wi th an est l.mate of trophic change derived from diatoms (Prof. Smol in prep.) could possibly give an indication of the size of the human population of this period. (7) For the period with the antagonism between Fagus peaks and ABC-peaks close collaboration between palynologists, geochemists and archeologists should enable us to determine the influence of prehistoric and historic people on vegetation (collaboration with Prof. Stockli and Prof. Herzig). (8) The core LL-75 taken with a "cold letter box" will be analysed for major and trace elements by Dr. Sturm for 210pb and 137Cs by Prof.von Gunten and for pollen. We will see if our local PAZ L30 really corresponds to the surface sediment and if the small seepage lake reflects modern pollution.