Oleoresin glands in copaiba (Copaifera trapezifolia Hayne: Leguminosae), a Brazilian rainforest tree

Although studies have addressed the chemical analysis and the biological activity of oleoresin in species of Copaifera, the cellular mechanisms of oleoresin production, storage, and release have rarely been investigated. This study detailed the distribution, ontogeny, and ultrastructure of secretory cavities and canals distributed in leaf and stem, respectively, of Copaifera trapezifolia, a Brazilian species included in a plant group of great economic interest. Axillary vegetative buds, leaflets, and portions of stem in primary and secondary growth were collected and processed in order to study the anatomy, histolocalization of substances, and ultrastructure. Secretory cavities are observed in the foliar blade and secretory canals in the petiolule and stem. They are made up of a uniseriate epithelium delimiting an isodiametric or elongated lumen. Biseriate epithelium is rarely observed and is a novelty for Leguminosae. Cavities and canals originate from ground meristem cells and the lumen is formed by schizogenesis. The content of the cavities and canals of both stem and leaf is oily and resinous, which suggests that the oleoresin could be extracted from the leaf instead of the stem. Phenolic compounds are also detected in the epithelial cell cytoplasm. Cavities and canals in the beginning of developmental stages have polarized epithelial cells. The cytoplasm is rich in smooth and rough endoplasmic reticula connected to vesicles or plastids. Smooth and rough endoplasmic reticulum and plastids were found to be predominant in the epithelial cells of the secretory cavities and canals of C. trapezifolia. Such features testify the quantities of oleoresin found in the lumen and phenolic compounds in the epithelial cell cytoplasm of these glands. Other studies employing techniques such as correlative light electron microscopy could show the vesicle traffic and the compartmentalization of the produced substances in such glands.

Solar-Terrestrial Signal Record in Tree Ring Width Time Series from Brazil

This work investigates the behavior of the sunspot number and Southern Oscillation Index (SOI) signal recorded in the tree ring time series for three different locations in Brazil: Humaita in Amaznia State, Porto Ferreira in So Paulo State, and Passo Fundo in Rio Grande do Sul State, using wavelet and cross-wavelet analysis techniques. The wavelet spectra of tree ring time series showed signs of 11 and 22 years, possibly related to the solar activity, and periods of 2-8 years, possibly related to El Nio events. The cross-wavelet spectra for all tree ring time series from Brazil present a significant response to the 11-year solar cycle in the time interval between 1921 to after 1981. These tree ring time series still have a response to the second harmonic of the solar cycle (5.5 years), but in different time intervals. The cross-wavelet maps also showed that the relationship between the SOI x tree ring time series is more intense, for oscillation in the range of 4-8 years.

Substrate specificity of the Chamaerops excelsa palm tree peroxidase. A steady-state kinetic study

The steady state kinetic mechanism of the H(2)O(2)-supported oxidation of different organic substrates by peroxidase from leaves of Chamaerops excelsa palm trees (CEP) has been investigated. An analysis of the initial rates vs. H(2)O(2) and reducing substrate concentrations is consistent with a substrate-inhibited Ping-Pong Bi Bi reaction mechanism. The phenomenological approach expresses the peroxidase Ping-Pong mechanism in the form of the Michaelis-Menten equation and leads to an interpretation of the effects in terms of the kinetic parameters K(m)(H2O2)center dot K(m)(AH2)center dot k(cat)center dot K(SI)(AH2) and of the microscopic rate constants k(1) and k(3) of the shared three-step catalytic cycle of peroxidases. (C) 2011 Elsevier B.V. All rights reserved.

A new eriophyoid mite genus and species, Gymnaceria cupuassu (Acari: Eriophyidae), described from the cupuacu tree in Brazil

A new eriophyoid mite genus and species, Gymnaceria cupuassu n. sp. et n. gen. (Acari: Eriophyidae: Eriophyinae: Aceriini), is described from young fruits and other plant parts of the cupuacu tree, Theobroma grandiflorum (Willd. Ex Spreng.) K. Schum. (Sterculiaceae), from the State of Bahia, northeastern Brazil. No visible damage symptoms were observed.

Tree species richness, does it play a key role on a forest restoration plantation?

The Brazilian Atlantic forest is considered one of the world's biodiversity conservation hotspot. Today there is less than ten percent remaining. Therefore it is necessary to restore these ecosystems. There are many ways of achieving restoration's main goals, but there is a lack of ecological studies that analyzes tree species richness as a variable. Thus, this study's goal is to investigate if there is a difference between a forest restoration in a gradient of tree species richness that varies from 20, 60 to 120 species, by using the litterfall as an indicator. Every month, for one year the forest litter was collected from litter traps that were previously installed. Results revealed that stands produced litterfall by the increasing gradient of species was of 5,370, 5,909 and 6,432 kg ha(-1) yr(-1). The statistical analyses revealed no significant difference among them. Therefore this six-year-old forest restoration plantation shows no difference on the litter production by the tree species richness.

Yield mapping, soil fertility and tree gaps in an orange orchard

The current high competition on Citrus industry demands from growers new management technologies for superior efficiency and sustainability. In this context, precision agriculture (PA) has developed techniques based on yield mapping and management systems that recognize field spatial variability, which contribute to increase profitability of commercial crops. Because spatial variability is often not perceived the orange orchards are still managed as uniform and adoption of PA technology on citrus farms is low. Thus, the objective of the present study was to characterize the spatial variability of three factors: fruit yield, soil fertility and occurrence of plant gaps caused by either citrus blight or huanglongbing (HLB) in a commercial Valencia orchard in Brotas, São Paulo State, Brazil. Data from volume, geographic coordinates and representative area of the bags used on harvest were recorded to generate yield points that were then interpolated to produce the yield map. Soil chemical characteristics were studied by analyzing samples collected along planting rows and inter-rows in 24 points distributed in the field. A map of density of tree gaps was produced by georeferencing individual gaps and later by counting the number of gaps within 500 m² cells. Data were submitted to statistical and geostatistical analyses. A t test was used to compare means of soil chemical characteristics between sampling regions. High variation on yield and density of tree gaps was observed from the maps. It was also demonstrated overlapping regions of high density of plant absence and low fruit yield. Soil fertility varied depending on the sampling region in the orchard. The spatial variability found on yield, soil fertility and on disease occurrence demonstrated the importance to adopt site specific nutrient management and disease control as tools to guarantee efficiency of fruit production.

Vegetation mapping in an area of Ombrophilous Dense Forest at Parque Estadual da Serra do Mar, São Paulo State, Brazil, and floristic composition of the tree component of some physiognomies*

This study aimed to map phytophysiognomies of an area of Ombrophilous Dense Forest at Parque Estadual da Serra do Mar and characterize their floristic composition. Photointerpretation of aerial photographs in scale of 1:35,000 was realized in association with field work. Thirteen physiognomies were mapped and they were classified as Montane Ombrophilous Dense Forest, Alluvial Ombrophilous Dense Forest or Secondary System. Three physiognomies identified at Casa de Pedra streamlet's basin were studied with more details. Riparian forest (RF), valley forest (VF), and hill forest (HF) presented some floristic distinction, as confirmed by Detrended Correspondence Analysis (DCA) and Indicator Species Analysis (ISA) conducted here. Anthropic or natural disturbances and heterogeneity of environmental conditions may be the causes of physiognomic variation in the vegetation of the region. The results presented here may be useful to decisions related to management and conservation of Núcleo Santa Virgínia forests, in general.

3D reconstruction from a vascular tree model

[EN] In this paper, we present a vascular tree model made with synthetic materials and which allows us to obtain images to make a 3D reconstruction.We have used PVC tubes of several diameters and lengths that will let us evaluate the accuracy of our 3D reconstruction. In order to calibrate the camera we have used a corner detector. Also we have used Optical Flow techniques to follow the points through the images going and going back. We describe two general techniques to extract a sequence of corresponding points from multiple views of an object. The resulting sequence of points will be used later to reconstruct a set of 3D points representing the object surfaces on the scene. We have made the 3D reconstruction choosing by chance a couple of images and we have calculated the projection error. After several repetitions, we have found the best 3D location for the point.

Kernel Methods for Tree Structured Data

Machine learning comprises a series of techniques for automatic extraction of meaningful information from large collections of noisy data. In many real world applications, data is naturally represented in structured form. Since traditional methods in machine learning deal with vectorial information, they require an a priori form of preprocessing. Among all the learning techniques for dealing with structured data, kernel methods are recognized to have a strong theoretical background and to be effective approaches. They do not require an explicit vectorial representation of the data in terms of features, but rely on a measure of similarity between any pair of objects of a domain, the kernel function. Designing fast and good kernel functions is a challenging problem. In the case of tree structured data two issues become relevant: kernel for trees should not be sparse and should be fast to compute. The sparsity problem arises when, given a dataset and a kernel function, most structures of the dataset are completely dissimilar to one another. In those cases the classifier has too few information for making correct predictions on unseen data. In fact, it tends to produce a discriminating function behaving as the nearest neighbour rule. Sparsity is likely to arise for some standard tree kernel functions, such as the subtree and subset tree kernel, when they are applied to datasets with node labels belonging to a large domain. A second drawback of using tree kernels is the time complexity required both in learning and classification phases. Such a complexity can sometimes prevents the kernel application in scenarios involving large amount of data. This thesis proposes three contributions for resolving the above issues of kernel for trees. A first contribution aims at creating kernel functions which adapt to the statistical properties of the dataset, thus reducing its sparsity with respect to traditional tree kernel functions. Specifically, we propose to encode the input trees by an algorithm able to project the data onto a lower dimensional space with the property that similar structures are mapped similarly. By building kernel functions on the lower dimensional representation, we are able to perform inexact matchings between different inputs in the original space. A second contribution is the proposal of a novel kernel function based on the convolution kernel framework. Convolution kernel measures the similarity of two objects in terms of the similarities of their subparts. Most convolution kernels are based on counting the number of shared substructures, partially discarding information about their position in the original structure. The kernel function we propose is, instead, especially focused on this aspect. A third contribution is devoted at reducing the computational burden related to the calculation of a kernel function between a tree and a forest of trees, which is a typical operation in the classification phase and, for some algorithms, also in the learning phase. We propose a general methodology applicable to convolution kernels. Moreover, we show an instantiation of our technique when kernels such as the subtree and subset tree kernels are employed. In those cases, Direct Acyclic Graphs can be used to compactly represent shared substructures in different trees, thus reducing the computational burden and storage requirements.

Impact of forest fragmentation and disturbance on the endangered tropical tree Prunus africana (Rosaceae)

Anthropogene Fragmentierung und Störung von Wäldern beeinflussen ökologische Prozesse. Darüber hinaus werden genetische Drift und Inzucht verstärkt und die Fitness von Populationen beeinträchtigt. Um die Einflüsse von Fragmentierung und Störung auf die Biodiversität und Prozesse in tropischen Wäldern zu ermitteln, habe ich im „Kakamega Forest“, West-Kenia, die Baumart Prunus africana genauer untersucht. Dabei lag der Fokus auf (i) der Frugivorengemeinschaft und Samenausbreitung, (ii) der Kleinsäugergemeinschaft im Kontext der Samenprädation und (iii) der genetische Populationsstruktur von Keimlingen und adulten Bäumen. Der Vergleich von Keimlingen mit adulten Bäumen ermöglicht es, Veränderungen im Genfluss zwischen Generationen festzustellen. Die Ergebnisse zeigten, dass im untersuchten Waldgebiet insgesamt 49 frugivore Arten (Affen und Vögel) vorkommen. Dabei lag die Gesamtartenzahl im zusammenhängenden Wald höher als in den isoliert liegenden Fragmenten. An den Früchten von P. africana konnten insgesamt 36 Arten fressend beobachtet werden. Hier jedoch wurden in Fragmenten eine leicht erhöhte Frugivorenzahl sowie marginal signifikant erhöhte Samenausbreitungsraten nachgewiesen. Der Vergleich von stark gestörten mit weniger gestörten Flächen zeigte eine höhere Gesamtartenzahl sowie eine signifikant höhere Frugivorenzahl in P. africana in stark gestörten Flächen. Entsprechend war die Samenausbreitungsrate in stark gestörten Flächen marginal signifikant erhöht. Diese Ergebnisse deuten darauf hin, dass die quantitative Samenausbreitung in fragmentierten und gestörten Flächen etwas erhöht ist und somit eine gewisse Artenredundanz besteht, die den Verlust einzelner Arten ausgleichen könnte. Prunus africana Samen, die auf dem Boden lagen, wurden hauptsächlich von einer Nagerart (Praomys cf. jacksonii) erbeutet. Dabei war in gestörten Waldbereichen eine tendenziell höhere Prädatoraktivität zu beobachten als in weniger gestörten. Zudem waren einzelne Samen im Gegensatz zu Samengruppen in gestörten Flächen signifikant höherem Prädationsdruck ausgesetzt. Diese Ergebnisse zeigen, dass Fragmentierung sowie anthropogene Störungen auf unterschiedliche Prozesse im Lebenszyklus eines tropischen Baumes gegensätzliche Effekte haben können. Eine Extrapolation von einem auf einen anderen Prozess kann somit nicht erfolgen. Die genetische Differenzierung der adulten Baumpopulationen war gering (FST = 0.026). Der Großteil ihrer Variation (~ 97 %) lag innerhalb der Populationen, was intensiven Genfluss in der Vergangenheit widerspiegelt. Die genetische Differenzierung der Keimlinge war etwas erhöht (FST = 0.086) und ~ 91 % ihrer Variation lag innerhalb der Populationen. Im Gegensatz zu den adulten Bäumen konnte ich für Keimlinge ein „Isolation-by-distance“-Muster feststellen. Somit sind erste Hinweise auf begrenzten Genfluss im Keimlingsstadium infolge von Fragmentierung gegeben. Obwohl die Momentaufnahmen im Freiland keine Abnahme in der Frugivorenzahl und Samenausbreitung von P. africana als Folge von Fragmentierung beobachten ließen, weisen die Ergebnisse der genetischen Studie auf einen bereits reduzierten Genaustausch zwischen den Populationen hin. Somit lässt sich feststellen, dass die Faktoren Fragmentierung und Störung genetische Diversität, ökologische Prozesse und Artendiversität in Wäldern jeweils auf unterschiedliche Weise beeinflussen. Um Konsequenzen derartiger Einflüsse folgerichtig abschätzen zu können, sind Studien auf unterschiedlichen Diversitätsebenen unabdingbar.

Study of Italian isolates of Alternaria spp.: molecular and morphological characterization and pathogenesis on apple tree

It was decided to carry out a morphological and molecular characterization of the Italian Alternaria isolatescollected from apple , and evaluate their pathogenicity and subsequently combining the data collected. The strain collection (174 isolates) was constructed by collecting material (received from extension service personnel) between June and August of 2007, 2008, and 2009. A Preliminary bioassays were performed on detached plant materials (fruit and leaf wounded and unwounded), belonging to the Golden cultivar, with two different kind of inoculation (conidial suspension and conidial filtrate). Symptoms were monitored daily and a value of pathogenicity score (P.S.) was assigned on the basis of the diameter of the necrotic area that developed. On the basis of the bioassays, the number of isolates to undergo further molecular analysis was restricted to a representative set of single spore strains (44 strains). Morphological characteristics of the colony and sporulation pattern were determined according to previous systematic work on small-spored Alternaria spp. (Pryor and Michaelides, 2002 and Hong et al., 2006). Reference strains (Alternaria alternata, Alternaria tenuissima, Alternaria arborescens and four Japanese strains of Alternaria alternata mali pathotype), used in the study were kindly provided by Prof. Barry Pryor, who allows a open access to his own fungal collection. Molecular characterization was performed combining and comparing different data sets obtained from distinct molecular approach: 1) investigation of specific loci and 2) fingerprinting based on diverse randomly selected polymorphic sites of the genome. As concern the single locus analysis, it was chosen to sequence the EndoPG partial gene and three anonymous region (OPA1-3, OPA2- and OPa10-2). These markers has revealed a powerful tool in the latter systematic works on small-spored Alternaria spp. In fact, as reported in literature small-spored Alternaria taxonomy is complicated due to the inability to resolve evolutionary relationships among the taxa because of the lack of variability in the markers commonly used in fungi systematic. The three data set together provided the necessary variation to establish the phylogenetic relationships among the Italian isolates of Alternaria spp. On Italian strains these markers showed a variable number of informative sites (ranging from 7 for EndoPg to 85 for OPA1-3) and the parsimony analysis produced different tree topologies all concordant to define A. arborescens as a mophyletic clade. Fingerprinting analysis (nine ISSR primers and eight AFLP primers combination) led to the same result: a monophyleic A. arborescens clade and one clade containing both A. tenuissima and the A. alternata strains. This first attempt to characterize Italian Alternaria species recovered from apple produced concordant results with what was already described in a similar phylogenetic study on pistachio (Pryor and Michaelides, 2002), on walnut and hazelnut (Hong et al., 2006), apple (Kang et al., 2002) and citurus (Peever et al., 2004). Together with these studies, this research demonstrates that the three morphological groups are widely distributed and occupy similar ecological niches. Furthermore, this research suggest that these Alternaria species exhibit a similar infection pattern despite the taxonomic and pathogenic differences. The molecular characterization of the pathogens is a fundamental step to understanding the disease that is spreading in the apple orchards of the north Italy. At the beginning the causal agent was considered as Alteraria alternata (Marshall and Bertagnoll, 2006). Their preliminary studies purposed a pathogenic system related to the synthesis of toxins. Experimental data of our bioassays suggest an analogous hypothesis, considering that symptoms could be induced after inoculating plant material with solely the filtrate from pathogenic strains. Moreover, positive PCR reactions using AM-toxin gene specific primers, designed for identification of apple infecting Alternaria pathovar, led to a hypothesis that a host specific toxin (toxins) were involved. It remains an intriguing challenge to discover or not if the agent of the “Italian disease” is the same of the one previously typified as Alternaria mali, casual agent of the apple blotch disease.

Frugivores, seed dispersal and tree regeneration along a human disturbance gradient in East African tropical rainforests

Samenausbreitung und Regeneration von Bäumen sind wichtig für den langfristigen Bestand von Baum- und Frugivorengemeinschaften in tropischen Regenwäldern. Zunehmende Rohdung und Degradation gefährden den Ablauf dieser mutualistischen Prozesse in diesem Ökosystem. Um den Einfluss von kleinräumiger menschlicher Störung auf die Frugivorengemeinschaft und die zentralen Ökosystemprozesse Samenausbreitung und Regeneration zu erforschen, habe ich 1) die Frugivorengemeinschaft und die Samenausbreitungsrate von Celtis durandii (Ulmaceae) und 2) den Zusammenhang zwischen Baumarten mit fleischigen Früchten, Frugivoren und der Etablierung von Keimlingen dieser Baumarten in unterschiedlich stark gestörten Flächen dreier ostafrikanischer tropischer Regenwälder untersucht. Insgesamt konnte ich 40 frugivore Vogel- und Primatenarten in den drei untersuchten Waldgebieten nachweisen. Auf gering gestörten Flächen wurden mehr Frugivore als auf stark gestörten Flächen aufgenommen. Auch die Beobachtungen an C. durandii ergaben mehr frugivore Besucher in Bäumen auf gering gestörten als auf stark gestörten Flächen. Dies führte zu einer marginal signifikant höheren Samenausbreitungsrate auf den gering gestörten Flächen. Diese Ergebnisse waren auf regionaler Ebene in allen drei untersuchten Wäldern konsistent. Dies zeigt, dass kleinräumige Störung einen umfassenderen negativen Einfluss auf Frugivore und ihre Funktion als Samenausbreiter hat als zuvor angenommen. Bei der Vegetationserfassung nahm ich 131 verschiedene Baumarten mit fleischigen Früchten in den drei Regenwäldern auf. Kleinräumige menschliche Störung erhöhte den Artenreichtum dieser Baumarten marginal signifikant, hatte jedoch keinen direkten Einfluss auf die Frugivorendichte und den Artenreichtum von Keimlingen dieser Baumarten. Der Artenreichtum von Baumarten mit fleischigen Früchten zeigte einen marginal signifikant positiven Einfluss auf die Frugivorendichte, allerdings nicht auf die Keimlinge. Allerdings führte die Dichte der Frugivoren zu signifikant erhöhtem Artenreichtum der Keimlinge. Folglich scheint kleinräumige Störung die Keimlingsetablierung indirekt durch erhöhten Baumartenreichtum und erhöhte Frugivorendichte zu beeinflussen. Die Frugivorendichte hatte einen größeren Einfluss auf die Waldregeneration als kleinräumige Störung und Baumartenreichtum. Demnach scheint kleinräumige menschliche Störung sowohl positive als auch negative Effekte auf Samenausbreitung und Regeneration zu haben. Somit sind weitere Studien notwendig, die den Einfluss von kleinräumiger menschlicher Störung auf Mutualismen tropischer Regenwälder aufklären.

Genetic dynamics across early life stages in the tropical tree Prunus africana (Rosaceae)

In many plant species, the genetic template of early life-stages is formed by animal-mediated pollination and seed dispersal and has profound impact on further recruitment and population dynamics. Understanding the impact of pollination and seed dispersal on genetic patterns is a central issue in plant population biology. In my thesis, I investigated (i) contemporary dispersal and gene flow distances as well as (ii) genetic diversity and spatial genetic structure (SGS) across subsequent recruitment stages in a population of the animal-pollinated and dispersed tree Prunus africana in Kakamega Forest, West Kenya. Using microsatellite markers and parentage analyses, I inferred distances of pollen dispersal (father-to-mother), seed dispersal/maternal gene flow (mother-to-offspring) as well as paternal gene flow (father-to-offspring) for four early life stages of the species (seeds and fruits, current year seedlings, seedlings ≤ 3yr, seedlings > 3yr). Distances of pollen and seed dispersal as well as paternal gene flow were significantly shorter than expected from the spatial arrangement of trees and sampling plots. They were not affected by the density of conspecific trees in the surrounding. At the propagule stage, mean pollen dispersal distances were considerably (23-fold) longer than seed dispersal distances, and paternal gene flow distances exceeded maternal gene flow by a factor of 25. Seed dispersal distances were remarkably restricted, potentially leading to a strong initial SGS. The initial genetic template created by pollination and seed dispersal was extensively altered during later recruitment stages. Potential Janzen-Connell effects led to markedly increasing distances between offspring and both parental trees in older life stages. This showed that distance and density-dependent mortality factors are not exclusively related to the mother tree, but also to the father. Across subsequent recruitment stages, the pollen to seed dispersal ratio and the paternal to maternal gene flow ratio dropped to 2.1 and 3.4, respectively, in seedlings > 3yr. The relative changes in effective pollen dispersal, seed dispersal, and paternal gene flow distances across recruitment stages elucidate the mechanisms affecting the contribution of the two processes pollen and seed dispersal to overall gene flow. Using the same six microsatellite loci, I analyzed genetic diversity and SGS across five life stages, from seed rain to adults. Levels of genetic diversity within the studied P. africana population were comparable to other Prunus species and did not vary across life stages. In congruence with the short seed dispersal distances, I found significant SGS in all life stages. SGS decreased from seed and early seedling stages to older juvenile stages, and it was higher in adults than in late juveniles of the next generation. A comparison of the data with direct assessments of contemporary gene flow patterns indicate that distance- or density-dependent mortality, potentially due to Janzen-Connell effects, led to the initial decrease in SGS. Intergeneration variation in SGS could have been driven by variation in demographic processes, the effect of overlapping generations, and local selection processes. Overall, my study showed that complex sequential processes during recruitment contribute to the spatial genetic structure of tree populations. It highlights the importance of a multistage perspective for a comprehensive understanding of the impact of animal-mediated pollen and seed dispersal on spatial population dynamics and genetic patterns of trees.