Stand density management in rainforest plantations

Trees in plantations established for timber production are usually grown at a sufficiently high density that canopy closure occurs within a relatively short time after planting. The trees then shade and outcompete most herbs, shrubs or grasses growing at the site. The closer the spacing (i.e. the greater the density) the faster this will occur. Subsequently, as the trees grow larger, this between-species competition is replaced by within-species competition. If unmanaged, this competition can reduce the commercial productivity of the plantation. Thus, there are two management dilemmas. One is knowing the best initial planting density. The second is knowing how to management the subsequent between-tree competition in order to optimize overall plantation timber productivity. In this chapter we consider initial spacing and thinning for high value timber trees grown in single and mixed species plantations. From growth studies in stands of different ages recommendations are proposed for managing both types of plantations where the primary objective is timber production. It seems that many rainforest species will require more space to achieve optimal growth than most eucalypts and conifers. On the other hand many rainforest species do not have strong apical dominance. Care will be needed to balance these two attributes.

RNA Virus Evolution: a Cross-scale, Disease Dynamic Perspective

RNA viruses are an important cause of global morbidity and mortality. The rapid evolutionary rates of RNA virus pathogens, caused by high replication rates and error-prone polymerases, can make the pathogens difficult to control. RNA viruses can undergo immune escape within their hosts and develop resistance to the treatment and vaccines we design to fight them. Understanding the spread and evolution of RNA pathogens is essential for reducing human suffering. In this dissertation, I make use of the rapid evolutionary rate of viral pathogens to answer several questions about how RNA viruses spread and evolve. To address each of the questions, I link mathematical techniques for modeling viral population dynamics with phylogenetic and coalescent techniques for analyzing and modeling viral genetic sequences and evolution. The first project uses multi-scale mechanistic modeling to show that decreases in viral substitution rates over the course of an acute infection, combined with the timing of infectious hosts transmitting new infections to susceptible individuals, can account for discrepancies in viral substitution rates in different host populations. The second project combines coalescent models with within-host mathematical models to identify driving evolutionary forces in chronic hepatitis C virus infection. The third project compares the effects of intrinsic and extrinsic viral transmission rate variation on viral phylogenies.

Scaling limits of a model for selection at two scales

The dynamics of a population undergoing selection is a central topic in evolutionary biology. This question is particularly intriguing in the case where selective forces act in opposing directions at two population scales. For example, a fast-replicating virus strain outcompetes slower-replicating strains at the within-host scale. However, if the fast-replicating strain causes host morbidity and is less frequently transmitted, it can be outcompeted by slower-replicating strains at the between-host scale. Here we consider a stochastic ball-and-urn process which models this type of phenomenon. We prove the weak convergence of this process under two natural scalings. The first scaling leads to a deterministic nonlinear integro-partial differential equation on the interval $[0,1]$ with dependence on a single parameter, $\lambda$. We show that the fixed points of this differential equation are Beta distributions and that their stability depends on $\lambda$ and the behavior of the initial data around $1$. The second scaling leads to a measure-valued Fleming-Viot process, an infinite dimensional stochastic process that is frequently associated with a population genetics.

Temperature and the synchrony of plant-insect interactions

Increasing temperatures resulting from climate change have within recent years been shown to advance phenological events in a large number of species worldwide. Species can differ in their response to increasing temperatures, and understanding the mechanisms that determine the response is therefore of great importance in order to understand and predict how a warming climate can influence both individual species, but also their interactions with each other and the environment. Understanding the mechanisms behind responses to increasing temperatures are however largely unexplored. The selected study system consisting of host plant species of the Brassicaceae family and their herbivore Anthocharis cardamines, is assumed to be especially vulnerable to climatic variations. Through the use of this study system, the aim of this thesis is to study differences in the effect of temperature on development to start of flowering within host plant species from different latitudinal regions (study I), and among host plant species (study II). We also investigate whether different developmental phases leading up to flowering differ in sensitivity to temperature (study II), and if small-scale climatic variation in spring temperature influence flowering phenology and interactions with A. cardamines (study III). Finally, we investigate if differences in the timing of A. cardamines relative to its host plants influence host species use and the selection of host individuals differing in phenology within populations (study IV). Our results showed that thermal reaction norms differ among regions along a latitudinal gradient, with the host plant species showing a mixture of co-, counter- and mixed gradient patterns (study I). We also showed that observed differences in the host plant species order of flowering among regions and years might be caused by both differences in the distribution of warm days during development and differences in the sensitivity to temperature in different phases of development (study II). In addition, we showed that small-scale variations in temperature led to variation in flowering phenology among and within populations of C. pratensis, impacting the interactions with the butterfly herbivore A. cardamines. Another result was that the less the mean plant development stage of a given plant species in the field deviated from the stage preferred by the butterfly for oviposition, the more used was the species as a host by the butterfly (study IV). Finally, we showed that the later seasonal appearance of the butterflies relative to their host plants, the higher butterfly preference for host plant individuals with a later phenology, corresponding to a preference for host plants in earlier development stages (study IV). For our study system, this thesis suggest that climate change will lead to changes in the interactions between host plants and herbivore, but that differences in phenology among host plants combined with changes in host species use of the herbivore might buffer the herbivore against negative effects of climate change. Our work highlights the need to understand the mechanisms behind differences in the responses of developmental rates to temperature between interacting species, as well as the need to account for differences in temperature response for interacting organisms from different latitudinal origins and during different developmental phases in order to understand and predict the consequences of climate change. 

Colonization of Onions by Endophytic Fungi and Their Impacts on the Biology of Thrips tabaci

Endophytic fungi, which live within host plant tissues without causing any visible symptom of infection, are important mutualists that mediate plant-herbivore interactions. Thrips tabaci (Lindeman) is one of the key pests of onion, Allium cepa L., an economically important agricultural crop cultivated worldwide. However, information on endophyte colonization of onions, and their impacts on the biology of thrips feeding on them, is lacking. We tested the colonization of onion plants by selected fungal endophyte isolates using two inoculation methods. The effects of inoculated endophytes on T. tabaci infesting onion were also examined. Seven fungal endophytes used in our study were able to colonize onion plants either by the seed or seedling inoculation methods. Seed inoculation resulted in 1.47 times higher mean percentage post-inoculation recovery of all the endophytes tested as compared to seedling inoculation. Fewer thrips were observed on plants inoculated with Clonostachys rosea ICIPE 707, Trichoderma asperellum M2RT4, Trichoderma atroviride ICIPE 710, Trichoderma harzianum 709, Hypocrea lixii F3ST1 and Fusarium sp. ICIPE 712 isolates as compared to those inoculated with Fusarium sp. ICIPE 717 and the control treatments. Onion plants colonized by C. rosea ICIPE 707, T. asperellum M2RT4, T. atroviride ICIPE 710 and H. lixii F3ST1 had significantly lower feeding punctures as compared to the other treatments. Among the isolates tested, the lowest numbers of eggs were laid by T. tabaci on H. lixii F3ST1 and C. rosea ICIPE 707 inoculated plants. These results extend the knowledge on colonization of onions by fungal endophytes and their effects on Thrips tabaci.

Dynamic set pieces for CAMBADA team

Robotics is an emergent branch of engineering that involves the conception, manufacture, and control of robots. It is a multidisciplinary field that combines electronics, design, computer science, artificial intelligence, mechanics and nanotechnology. Its evolution results in machines that are able to perform tasks with some level of complexity. Multi-agent systems is a researching topic within robotics, thus they allow the solving of higher complexity problems, through the execution of simple routines. Robotic soccer allows the study and development of robotics and multiagent systems, as the agents have to work together as a team, having in consideration most problems found in our quotidian, as for example adaptation to a highly dynamic environment as it is the one of a soccer game. CAMBADA is the robotic soccer team belonging to the group of research IRIS from IEETA, composed by teachers, researchers and students of the University of Aveiro, which annually has as main objective the participation in the RoboCup, in the Middle Size League. The purpose of this work is to improve the coordination in set pieces situations. This thesis introduces a new behavior and the adaptation of the already existing ones in the offensive situation, as well as the proposal of a new positioning method in defensive situations. The developed work was incorporated within the competition software of the robots. Which allows the presentation, in this dissertation, of the experimental results obtained, through simulation software as well as through the physical robots on the laboratory.

Goal detection using laser range finder for goalkeeper and striker from CAMBADA team

For a robot be autonomous and mobile, it requires being attached with a set of sensors that helps it to have a better perception of the surrounding world, to manage to localize itself and the surrounding objects. CAMBADA is the robotic soccer team of the IRIS research group, from IEETA, University of Aveiro, that competes in the Middle-Size League of RoboCup. In competition, in order to win, the main objective of the game it's to score more goals than the conceded, so not conceding goals, and score as much as possible it's desirable, thus, this thesis focus on adapt an agent with a better localization capacity in defensive and offensive moments. It was introduced a laser range finder to the CAMBADA robots, making them capable of detecting their own and the opponent goal, and to detect the opponents in specific game situations. With the new information and adapting the Goalie and Penalty behaviors, the CAMBADA goalkeeper is now able to detect and track its own goal and the CAMBADA striker has a better performance in a penalty situation. The developed work was incorporated within the competition software of the robots, which allows the presentation, in this thesis, of the experimental results obtained with physical robots on the laboratory field.

Advances in gastropod immunity from the study of the interaction between the snail Biomphalaria glabrata and its parasites: A review of research progress over the last decade

This review summarizes the research progress made over the past decade in the field of gastropod immunity resulting from investigations of the interaction between the snail Biomphalaria glabrata and its trematode parasites. A combination of integrated approaches, including cellular, genetic and comparative molecular and proteomic approaches have revealed novel molecular components involved in mediating Biomphalaria immune responses that provide insights into the nature of host-parasite compatibility and the mechanisms involved in parasite recognition and killing. The current overview emphasizes that the interaction between B. glabrata and its trematode parasites involves a complex molecular crosstalk between numerous antigens, immune receptors, effectors and anti-effector systems that are highly diverse structurally and extremely variable in expression between and within host and parasite populations. Ultimately, integration of these molecular signals will determine the outcome of a specific interaction between a B. glabrata individual and its interacting trematodes. Understanding these complex molecular interactions and identifying key factors that may be targeted to impairment of schistosome development in the snail host is crucial to generating new alternative schistosomiasis control strategies.

Grazers and diggers: Exploitation competition and coexistence among foragers with different feeding strategies on a single resource

A mathematical model is presented that describes a system where two consumer species compete exploitatively for a single renewable resource. The resource is distributed in a patchy but homogeneous environment; that is, all patches are intrinsically identical. The two consumer species are referred to as diggers and grazers, where diggers deplete the resource within a patch to lower densities than grazers. We show that the two distinct feeding strategies can produce a heterogeneous resource distribution that enables their coexistence. Coexistence requires that grazers must either move faster than diggers between patches or convert the resources to population growth much more efficiently than diggers. The model shows that the functional form of resource renewal within a patch is also important for coexistence. These results contrast with theory that considers exploitation competition for a single resource when the resource is assumed to be well mixed throughout the system.

Modeling the Competition Between Viruses in a Complex Plant-Pathogen System

In this article, we propose a mathematical model that describes the competition between two plant virus strains (MAV and PAV) for both the host plant (oat) and their aphid vectors. We found that although PAV is transmitted by two aphids and MAV by only one, this fact, by itself, does not explain the complete replacement of MAV by PAV in New York State during the period from 1961 through 1976; an interpretation that is in agreement with the theories of A. G. Power. Also, although MAV wins the competition within aphids, we assumed that, in 1961, PAV mutated into a new variant such that this new variant was able to overcome MAV within the plants during a latent period. As shown below, this is sufficient to explain the swap of strains; that is, the dominant MAV was replaced by PAV, also in agreement with Power`s expectations.

Early expression of the type III secretion system of Parachlamydia acanthamoebae during a replicative cycle within its natural host cell Acanthamoeba castellanii.

The type three secretion system (T3SS) operons of Chlamydiales bacteria are distributed in different clusters along their chromosomes and are conserved at both the level of sequence and genetic organization. A complete characterization of the temporal expression of multiple T3SS components at the transcriptional and protein levels has been performed in Parachlamydia acanthamoebae, replicating in its natural host cell Acanthamoeba castellanii. The T3SS components were classified in four different temporal clusters depending on their pattern of expression during the early, mid- and late phases of the infectious cycle. The putative T3SS transcription units predicted in Parachlamydia are similar to those described in Chlamydia trachomatis, suggesting that T3SS units of transcriptional expression are highly conserved among Chlamydiales bacteria. The maximal expression and activation of the T3SS of Parachlamydia occurred during the early to mid-phase of the infectious cycle corresponding to a critical phase during which the intracellular bacterium has (1) to evade and/or block the lytic pathway of the amoeba, (2) to differentiate from elementary bodies (EBs) to reticulate bodies (RBs), and (3) to modulate the maturation of its vacuole to create a replicative niche able to sustain efficient bacterial growth.

Capacity and transformational development within the 2005 Canada Summer Games host society

Although capacity has been used in recent federal government accords and policies related to the voluntary and amateur sport sectors, there is little consensus over the meaning of the term. Consequently, the purpose of this qualitative case study was to explore the concept of organizational capacity within a temporary voluntary sport organization. Specifically, the nature of organizational capacity was examined within the case of the Volunteers Division of the 2005 Canada Summer Games (CSG) Host Society. Data were collected from executive planning and middle management CSG volunteers through the use of a variety of methods: verbal journals, interviews, observations, documents and a focus group. Findings indicated several challenges associated with the volunteer management model utilized by the host society, varying levels of importance among six elements of capacity, and key aspects of the relationship between organizational capacity and transformational development. Implications focused upon the importance of highlighting individuals rather than the organizational as a whole in order to build capacity, and utilizing a brain or hybrid brain-machine organizational form to enhance capacity. Recommendations are provided for both the Canada Games Council and Canada Games host societies.

Growth and flowering of petunia and impatiens: effects of competition and reduced water content within a container

The primary objective of this research was to determine how the presence of more than one plant and more than one species in a container influence plant quality, particularly when the volume of water given to the container is reduced. Petunia xhybrida 'Hurrah White' and Impatiens 'Cajun Violet' were chosen as typical bedding plant species. Plants were grown in 2 1 containers either under "100% ETp" (i.e., replacing all the water lost by evapotranspiration in the previous 24 h) or under a moisture-restrictive regime of "25% ETp," in which plants received 25% of the "100% ETp" value. An ancillary experiment investigated whether low watering resulted in floral buds being aborted. Results demonstrated that watering requirements of Petunia under "100% ETp" (i.e., replacing all the water lost by evapotranspiration in the previous 24 h) were on average 30% greater than those of Impatiens. However, when two Petunia plants were growing in the same container, the volume of water required to maintain soil moisture content at container capacity was on average only 10% greater than for a single plant. Under a "25% ETp" regime in which plants received 25% of the "100% ETp" value, flower number, plant height, and flower size were reduced by 50%,33%, and 13%,respectively,in Petunia compared with "100% ETp." For example, flower numbers decreased from an average of 71 to 33 flowers per plant in "100% ETp" and "25% ETp," respectively. Petunia plants in the "25% ETp" regime, however, were more efficient at producing both biomass and flowers in relation to the volume of water applied. Petunia plants that experienced both competition from other plants in the container and lower irrigation rates had enhanced efficiency of flower production (i.e., more flowers per unit biomass). For Impatiens, however, the growing of single plants at "25% ETp" was plausible, but the addition of a Petunia plant at "25% ETp" was detrimental to plant quality (Impatiens flower numbers reduced by 75%).

An evaluation of the costs of making specific secondary metabolites: does the yield penalty incurred by host plant resistance to insects due to competition for resources?

The presumption that the synthesis of 'defence' compounds in plants must incur some 'trade-off' or penalty in terms of annual crop yields has been used to explain observed inverse correlations between resistance to herbivores and rates of growth or photosynthesis. An analysis of the cost of making secondary compounds suggests that this accounts for only a small part of the overall carbon budget of annual crop plants. Even the highest reported amounts of secondary metabolites found in different crop species (flavonoids, allylisothiocyanates, hydroxamic acids, 2-tridecanone) represent a carbon demand that can be satisfied by less than an hour's photosynthesis. Similar considerations apply to secondary compounds containing nitrogen or sulphur, which are unlikely to represent a major investment compared to the cost of making proteins, the major demand for these elements. Decreases in growth and photosynthesis in response to stress are more likely the result of programmed down-regulation. Observed correlations between yield and low contents of unpalatable or toxic compounds may be the result of parallel selection during the refinement of crop species by humans.