Not the outside but the inside matters : functional analysis of Capricious and Tartan during Drosophila tracheal morphogenesis

The tubular structures, which transport essential gases, liquids, or cells from one site to another, are shared among various divergent organisms. These highly organized tubular networks include lung, kidney, vasculature and mammary gland in mammals as well as trachea and salivary gland in Drosophila melanogaster. Many questions regarding the tubular morphogenesis cannot be addressed sufficiently by investigating the mammalian organs because their structures are extremely complex and therefore, systematic analyses of genetic and cellular programs guiding the development is not possible. In contrast, the Drosophila tracheal development provides an excellent model system since many molecular markers and powerful tools for genetic manipulations are available. Two mechanisms were shown to be important for the outgrowth of tracheal cells: the FGF signaling pathway and the interaction between the tracheal cells and the surrounding mesodermal cells. The Drosophila FGF ligand encoded by branchless (bnl) is localized in groups of cells near tracheal metameres. The tracheal cells expressing the FGF receptor breathless (btl) respond to these sources of FGF ligand and extend towards them. However, this FGF signaling pathway is not sufficient for the formation of continuous dorsal trunk, the only muticellular tube in tracheal system. Recently, it was found out that single mesodermal cells called bridge-cells are essential for the formation of continuous dorsal trunk as they direct the outgrowth of dorsal trunk cells towards the correct targets. The results in this PhD thesis demonstrate that a cell adhesion molecule Capricious (Caps), which is specifically localized on the surface of bridge-cells, plays an essential role in guiding the outgrowing dorsal trunk cells towards their correct targets. When caps is lacking, some bridge-cells cannot stretch properly towards the adjacent posterior tracheal metameres and thus fail to interconnect the juxtaposing dorsal trunk cells. Consequently, discontinuous dorsal trunks containing interruptions at several positions are formed. On the other hand, when caps is ectopically expressed in the mesodermal cells through a twi-GAL4 driver, these mesodermal cells acquire a guidance function through ectopic caps and misguide the outgrowing dorsal trunk cells in abnormal directions. As a result, disconnected dorsal trunks are formed. These loss- and gain-of-function studies suggest that Caps presumably establishes the cell-to-cell contact between the bridge-cells and the tracheal cells and thereby mediates directly the guidance function of bridge-cells. The most similar protein known to Caps is another cell adhesion molecule called Tartan (Trn). Interestingly, trn is expressed in the mesodermal cells but not in the bridge-cells. When trn is lacking, the outgrowth of not only the dorsal trunks but also the lateral trunks are disrupted. However, in contrast to the ectopic expression of caps, the misexpression of trn does not affect tracheal development. Whereas Trn requires only its extracellular domain to mediate the matrix function, Caps requires both its extracellular and intracellular domains to function as a guidance molecule in the bridge-cells. These observations suggest that Trn functions differently from Caps during tracheal morphogenesis. Presumably, Trn mediates a matrix function of mesodermal cells, which support the tracheal cells to extend efficiently through the surrounding mesodermal tissue. In order to determine which domains dictate the functional specificity of Caps, two hybrid proteins CapsEdTrnId, which contains the Caps extracellular domain and the Trn intracellular domain, and TrnEdCapsId, which consists of the Trn extracellular domain and the Caps intracellular domain, were constructed. Gain of function and rescue experiments with these hybrid proteins suggest on one hand that the extracellular domains of Caps and Trn are functionally redundant and on the other hand that the intracellular domain dictates the functional specificity of Caps. In order to identify putative interactors of Caps, yeast two-hybrid screening was performed. An in vivo interaction assay in yeast suggests that Ras64B interacts specifically with the Caps intracellular domain. In addition, an in vitro binding assay reveals a direct interaction between an inactive form of Ras64B and the Caps intracellular domain. ras64B, which encodes a small GTPase, is expressed in the mesodermal cells concurrently as caps. Finally, a gain-of-function study with the constitutively active Ras64B suggests that Ras64B presumably functions downstream of Caps. All these results suggest consistently that the small GTPase Ras64B binds specifically to the Caps intracellular domain and may thereby mediate the guidance function of Caps.

A Modeling Analysis of Changing Global Land Use as affected by Changing Demands for Wood Products

The 21st century has brought new challenges for forest management at a time when globalization in world trade is increasing and global climate change is becoming increasingly apparent. In addition to various goods and services like food, feed, timber or biofuels being provided to humans, forest ecosystems are a large store of terrestrial carbon and account for a major part of the carbon exchange between the atmosphere and the land surface. Depending on the stage of the ecosystems and/or management regimes, forests can be either sinks, or sources of carbon. At the global scale, rapid economic development and a growing world population have raised much concern over the use of natural resources, especially forest resources. The challenging question is how can the global demands for forest commodities be satisfied in an increasingly globalised economy, and where could they potentially be produced? For this purpose, wood demand estimates need to be integrated in a framework, which is able to adequately handle the competition for land between major land-use options such as residential land or agricultural land. This thesis is organised in accordance with the requirements to integrate the simulation of forest changes based on wood extraction in an existing framework for global land-use modelling called LandSHIFT. Accordingly, the following neuralgic points for research have been identified: (1) a review of existing global-scale economic forest sector models (2) simulation of global wood production under selected scenarios (3) simulation of global vegetation carbon yields and (4) the implementation of a land-use allocation procedure to simulate the impact of wood extraction on forest land-cover. Modelling the spatial dynamics of forests on the global scale requires two important inputs: (1) simulated long-term wood demand data to determine future roundwood harvests in each country and (2) the changes in the spatial distribution of woody biomass stocks to determine how much of the resource is available to satisfy the simulated wood demands. First, three global timber market models are reviewed and compared in order to select a suitable economic model to generate wood demand scenario data for the forest sector in LandSHIFT. The comparison indicates that the ‘Global Forest Products Model’ (GFPM) is most suitable for obtaining projections on future roundwood harvests for further study with the LandSHIFT forest sector. Accordingly, the GFPM is adapted and applied to simulate wood demands for the global forestry sector conditional on selected scenarios from the Millennium Ecosystem Assessment and the Global Environmental Outlook until 2050. Secondly, the Lund-Potsdam-Jena (LPJ) dynamic global vegetation model is utilized to simulate the change in potential vegetation carbon stocks for the forested locations in LandSHIFT. The LPJ data is used in collaboration with spatially explicit forest inventory data on aboveground biomass to allocate the demands for raw forest products and identify locations of deforestation. Using the previous results as an input, a methodology to simulate the spatial dynamics of forests based on wood extraction is developed within the LandSHIFT framework. The land-use allocation procedure specified in the module translates the country level demands for forest products into woody biomass requirements for forest areas, and allocates these on a five arc minute grid. In a first version, the model assumes only actual conditions through the entire study period and does not explicitly address forest age structure. Although the module is in a very preliminary stage of development, it already captures the effects of important drivers of land-use change like cropland and urban expansion. As a first plausibility test, the module performance is tested under three forest management scenarios. The module succeeds in responding to changing inputs in an expected and consistent manner. The entire methodology is applied in an exemplary scenario analysis for India. A couple of future research priorities need to be addressed, particularly the incorporation of plantation establishments; issue of age structure dynamics; as well as the implementation of a new technology change factor in the GFPM which can allow the specification of substituting raw wood products (especially fuelwood) by other non-wood products.

Smallholder group certification in Uganda - Analysis of internal control systems in two organic export companies

The organic agricultural sector of Uganda is among the most developed in Africa in terms of its professional institutional network and high growth rates of number of certified farmers and land area. Smallholder farmers are certified organic through contract production for export companies using a group certification scheme (internal control system - ICS). The ICS is a viable and well-accepted tool to certify small-scale producers in developing countries all over the world. Difficulties in certification are still stated to be among the main constraints for Uganda’s organic sector development. Therefore, this paper reports a qualitative case study comprising 34 expert interviews in two organic fresh-produce export companies in central Uganda, aiming to explore the challenges which underlie organic certification with ICS. The study shows that farmers cannot be labelled as ‘organic by default’ but deliberately engage in organic production as a marketing strategy. The small quantities purchased by the organic companies lead to a difficult marketing situation for the farmers, causing production and infiltration risks on the farm level. These risks require increased control that challenges the companies organizationally. The risks and control needs are a reason to involve farmers in ICS procedures and innovatively adapt the ICS by means of a bypass around formal perspective restrictions. The paper discusses different perspectives on risks, risk control and certification.

Semi-algebraic methods for symbolic analysis of complex reaction networks

The identification of chemical mechanism that can exhibit oscillatory phenomena in reaction networks are currently of intense interest. In particular, the parametric question of the existence of Hopf bifurcations has gained increasing popularity due to its relation to the oscillatory behavior around the fixed points. However, the detection of oscillations in high-dimensional systems and systems with constraints by the available symbolic methods has proven to be difficult. The development of new efficient methods are therefore required to tackle the complexity caused by the high-dimensionality and non-linearity of these systems. In this thesis, we mainly present efficient algorithmic methods to detect Hopf bifurcation fixed points in (bio)-chemical reaction networks with symbolic rate constants, thereby yielding information about their oscillatory behavior of the networks. The methods use the representations of the systems on convex coordinates that arise from stoichiometric network analysis. One of the methods called HoCoQ reduces the problem of determining the existence of Hopf bifurcation fixed points to a first-order formula over the ordered field of the reals that can then be solved using computational-logic packages. The second method called HoCaT uses ideas from tropical geometry to formulate a more efficient method that is incomplete in theory but worked very well for the attempted high-dimensional models involving more than 20 chemical species. The instability of reaction networks may lead to the oscillatory behaviour. Therefore, we investigate some criterions for their stability using convex coordinates and quantifier elimination techniques. We also study Muldowney's extension of the classical Bendixson-Dulac criterion for excluding periodic orbits to higher dimensions for polynomial vector fields and we discuss the use of simple conservation constraints and the use of parametric constraints for describing simple convex polytopes on which periodic orbits can be excluded by Muldowney's criteria. All developed algorithms have been integrated into a common software framework called PoCaB (platform to explore bio- chemical reaction networks by algebraic methods) allowing for automated computation workflows from the problem descriptions. PoCaB also contains a database for the algebraic entities computed from the models of chemical reaction networks.

Farmers’ perspectives with regard to arable crop production and deagrarianisation: an analysis of Nkonkobe Municipality, South Africa

This exploratory study evaluated biophysical, cultural and socio-economic factors affecting crop production and land utilisation in the Nkonkobe Municipality, South Africa. The study sought to establish what farmers in the area perceive as serious threats to crop production, drivers for land abandonment, and how best current agricultural production could be intensified. The farmers’ perspectives were assessed through interviews using semi-structured and open-ended questionnaires. The results of the study revealed declining crop productivity and increase in land abandonment in the Municipality. The biophysical drivers of land abandonment were low and erratic rainfall and land degradation while the socio-economic drivers were labour shortages due to old age and youth movement to cities, lack of farming equipment and security concerns. The most abandoned crops were maize, sorghum and wheat. This trend was attributed to the labour intensiveness of cereal production and a shift in dietary preference to purchased rice. These findings should be factored in any programmes that seek to increase land utilisation and crop productivity in the Municipality.

An analysis of household farm investment decisions under varying land tenure arrangements in Ghana

Land tenure insecurity is widely perceived as a disincentive for long-term land improvement investment hence the objective of this paper is to evaluate how tenure (in)security associated with different land use arrangements in Ghana influenced households’ plot level investment decisions and choices. The paper uses data from the Farmer-Based Organisations (FBO) survey. The FBO survey collected information from 2,928 households across three ecological zones of Ghana using multistaged cluster sampling. Probit and Tobit models tested the effects of land tenancy and ownership arrangements on households’ investment behaviour while controlling other factors. It was found that marginal farm size was inversely related to tenure insecurity while tenure insecurity correlate positively with value of farm land and not farm size. Individual ownership and documentation of land significantly reduced the probability of households losing uncultivated lands. Individual land ownership increased both the probability of investing and level of investments made in land improvement and irrigation probably due to increasing importance households place on land ownership. Two possible explanations for this finding are: First, that land markets and land relations have changed significantly over the last two decades with increasing money transaction and fixed agreements propelled by population growth and increasing value of land. Secondly, inclusion of irrigation investment as a long term investment in land raises the value of household investment and the time period required to reap the returns on the investments. Households take land ownership and duration of tenancy into consideration if the resource implications of land investments are relatively huge and the time dimension for harvesting returns to investments is relatively long.