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The paper presents a simulation and parameter-estimation approach for evaluating stochastic patterns of population growth and spread of an annual forest herb, Melampyrum pratense (Orobanchaceae). The survival of a species during large-scale changes in land use and climate will depend, to a considerable extent, on its dispersal and colonisation abilities. Predictions on species migration need a combination of field studies and modelling efforts. Our study on the ability of M. pratense to disperse into so far unoccupied areas was based on experiments in secondary woodland in NE Germany. Experiments started in 1997 at three sites where the species was not yet present, with 300 seeds sown within one square meter. Population development was then recorded until 2001 by mapping of individuals with a resolution of 5 cm. Additional observations considered density dependence of seed production. We designed a spatially explicit individual-based computer simulation model to explain the spatial patterns of population development and to predict future population spread. Besides primary drop of seeds (barochory) it assumed secondary seed transport by ants (myrmecochory) with an exponentially decreasing dispersal tail. An important feature of populationpattern explanation was the simultaneous estimation of both population-growth and dispersal parameters from consistent spatio-temporal data sets. As the simulation model produced stochastic time series and random spatially discrete distributions of individuals we estimated parameters by minimising the expectation of weighted sums of squares. These sums-ofsquares criteria considered population sizes, radial population distributions around the area of origin and distributions of individuals within squares of 25*25 cm, the range of density action. Optimal parameter values, together with the precision of the estimates, were obtained from calculating sums of squares in regular grids of parameter values. Our modelling results showed that transport of fractions of seeds by ants over distances of 1…2 m was indispensable for explaining the observed population spread that led to distances of at most 8 m from population origin within 3 years. Projections of population development over 4 additional years gave a diffusion-like increase of population area without any “outposts”. This prediction generated by the simulation model gave a hypothesis which should be revised by additional field observations. Some structural deviations between observations and model output already indicated that for full understanding of population spread the set of dispersal mechanisms assumed in the model may have to be extended by additional features of plant-animal mutualism.
In semi-arid savannah ecosystems, the vegetation structure and composition, i.e. the architecture of trees, shrubs, grass tussocks and herbaceous plants, offer a great variety of habitats and niches to sustain animal diversity. In the last decades intensive human land use practises like livestock farming have altered the vegetation in savannah ecosystems worldwide. Extensive grazing leads to a reduction of the perennial and herbaceous vegetation cover, which results in an increased availability of bare soil. Both, the missing competition with perennial grasses and the increase of bare soils favour shrub on open ground and lead to area-wide shrub encroachment. As a consequence of the altered vegetation structure and composition, the structural diversity declines. It has been shown that with decreasing structural diversity animal diversity decline across a variety of taxa. Knowledge on the effects of overgrazing on reptiles, which are an important part of the ecosystem, are missing. Furthermore, the impact of habitat degradation on factors of a species population dynamic and life history, e.g., birth rate, survival rate, predation risk, space requirements or behavioural adaptations are poorly known. Therefore, I investigated the impact of overgrazing on the reptile community in the southern Kalahari. Secondly I analysed population dynamics and the behaviour of the Spotted Sand Lizard, Pedioplanis l. lineoocellata. All four chapters clearly demonstrate that habitat degradation caused by overgrazing had a severe negative impact upon (i) the reptile community as a whole and (ii) on population parameters of Pedioplanis l. lineoocellata. Chapter one showed a significant decline of regional reptile diversity and abundance in degraded habitats. In chapter two I demonstrated that P. lineoocellata moves more frequently, spends more time moving and covers larger distances in degraded than in non-degraded habitats. In addition, home range size of the lizard species increases in degraded habitats as shown by chapter three. Finally, chapter four showed the negative impacts of overgrazing on several population parameters of P. lineoocellata. Absolute population size of adult and juvenile lizards, survival rate and birth rate are significantly lower in degraded habitats. Furthermore, the predation risk was greatly increased in degraded habitats. A combination of a variety of aspects can explain the negative impact of habitat degradation on reptiles. First, reduced prey availability negatively affects survival rate, the birth rate and overall abundance. Second, the loss of perennial plant cover leads to a loss of niches and to a reduction of opportunities to thermoregulate. Furthermore, a loss of cover and is associated with increased predation risk. A major finding of my thesis is that the lizard P. lineoocellata can alter its foraging strategy. Species that are able to adapt and change behaviour, such as P. lineoocellata can effectively buffer against changes in their environment. Furthermore, perennial grass cover can be seen as a crucial ecological component of the vegetation in the semi-arid savannah system of the southern Kalahari. If perennial grass cover is reduced to a certain degree reptile diversity will decline and most other aspects of reptile life history will be negatively influenced. Savannah systems are characterised by a mixture of trees, shrubs and perennial grasses. These three vegetation components determine the composition and structure of the vegetation and accordingly influence the faunal diversity. Trees are viewed as keystone structures and focal points of animal activity for a variety of species. Trees supply animals with shelter, shade and food and act as safe sites, nesting sites, observation posts and foraging sites. Recent research demonstrates a positive influence of shrub patches on animal diversity. Moreover, it would seem that intermediate shrub cover can also sustain viable populations in savannah landscapes as has been demonstrated for small carnivores and rodent species. The influence of perennial grasses on faunal diversity did not receive the same attention as the influence of trees and shrubs. In my thesis I didn’t explicitly measure the direct effects of perennial grasses but my results strongly imply that it has an important role. If the perennial grass cover is significantly depleted my results suggest it will negatively influence reptile diversity and abundance and on several populations parameters of P. lineoocellata. Perennial grass cover is associated with the highest prey abundance, reptile diversity and reptile abundance. It provides reptiles both a refuge from predators and opportunities to optimise thermoregulation. The relevance of each of the three vegetation structural elements is different for each taxa and species. In conclusion, I can all three major vegetation structures in the savannah system are important for faunal diversity.
The factors that determine the efficiency of energy transfer in aquatic food webs have been investigated for many decades. The plant-animal interface is the most variable and least predictable of all levels in the food web. In order to study determinants of food quality in a large lake and to test the recently proposed central importance of the long-chained eicosapentaenoic acid (EPA) at the pelagic producer-grazer interface, we tested the importance of polyunsaturated fatty acids (PUFAs) at the pelagic producerconsumer interface by correlating sestonic food parameters with somatic growth rates of a clone of Daphnia galeata. Daphnia growth rates were obtained from standardized laboratory experiments spanning one season with Daphnia feeding on natural seston from Lake Constance, a large pre-alpine lake. Somatic growth rates were fitted to sestonic parameters by using a saturation function. A moderate amount of variation was explained when the model included the elemental parameters carbon (r2 = 0.6) and nitrogen (r2 = 0.71). A tighter fit was obtained when sestonic phosphorus was incorporated (r2 = 0.86). The nonlinear regression with EPA was relatively weak (r2 = 0.77), whereas the highest degree of variance was explained by three C18-PUFAs. The best (r2 = 0.95), and only significant, correlation of Daphnia's growth was found with the C18-PUFA α-linolenic acid (α-LA; C18:3n-3). This correlation was weakest in late August when C:P values increased to 300, suggesting that mineral and PUFA-limitation of Daphnia's growth changed seasonally. Sestonic phosphorus and some PUFAs showed not only tight correlations with growth, but also with sestonic α-LA content. We computed Monte Carlo simulations to test whether the observed effects of α-LA on growth could be accounted for by EPA, phosphorus, or one of the two C18-PUFAs, stearidonic acid (C18:4n-3) and linoleic acid (C18:2n-6). With >99 % probability, the correlation of growth with α-LA could not be explained by any of these parameters. In order to test for EPA limitation of Daphnia's growth, in parallel with experiments on pure seston, growth was determined on seston supplemented with chemostat-grown, P-limited Stephanodiscus hantzschii, which is rich in EPA. Although supplementation increased the EPA content 80-800x, no significant changes in the nonlinear regression of the growth rates with α-LA were found, indicating that growth of Daphnia on pure seston was not EPA limited. This indicates that the two fatty acids, EPA and α-LA, were not mutually substitutable biochemical resources and points to different physiological functions of these two PUFAs. These results support the PUFA-limitation hypothesis for sestonic C:P < 300 but are contrary to the hypothesis of a general importance of EPA, since no evidence for EPA limitation was found. It is suggested that the resource ratios of EPA and α-LA rather than the absolute concentrations determine which of the two resources is limiting growth.
Significant seasonal variation in size at settlement has been observed in newly settled larvae of Dreissena polymorpha in Lake Constance. Diet quality, which varies temporally and spatially in freshwater habitats, has been suggested as a significant factor influencing life history and development of freshwater invertebrates. Accordingly, experiments were conducted with field-collected larvae to test the hypothesis that diet quality can determine planktonic larval growth rates, size at settlement and subsequent post-metamorphic growth rates. Larvae were fed one of two diets or starved. One diet was composed of cyanobacterial cells which are deficient in polyunsaturated fatty acids (PUFAs), and the other was a mixed diet rich in PUFAs. Freshly metamorphosed animals from the starvation treatment had a carbon content per individual 70% lower than that of larvae fed the mixed diet. This apparent exhaustion of larval internal reserves resulted in a 50% reduction of the postmetamorphic growth rates. Growth was also reduced in animals previously fed the cyanobacterial diet. Hence, low food quantity or low food quality during the larval stage of D. polymorpha lead to irreversible effects for postmetamorphic animals, and is related to inferior competitive abilities.
Poly(A) Polymerase 1 (PAPS1) influences organ size and pathogen response in Arabidopsis thaliana
(2014)
Polyadenylation of pre-mRNAs is critical for efficient nuclear export, stability, and translation of the mature mRNAs, and thus for gene expression. The bulk of pre-mRNAs are processed by canonical nuclear poly(A) polymerase (PAPS). Both vertebrate and higher-plant genomes encode more than one isoform of this enzyme, and these are coexpressed in different tissues. However, in neither case is it known whether the isoforms fulfill different functions or polyadenylate distinct subsets of pre-mRNAs. This thesis shows that the three canonical nuclear PAPS isoforms in Arabidopsis are functionally specialized owing to their evolutionarily divergent C-terminal domains. A moderate loss-of-function mutant in PAPS1 leads to increase in floral organ size, whereas leaf size is reduced. A strong loss-of-function mutation causes a male gametophytic defect, whereas a weak allele leads to reduced leaf growth. By contrast, plants lacking both PAPS2 and PAPS4 function are viable with wild-type leaf growth. Polyadenylation of SMALL AUXIN UP RNA (SAUR) mRNAs depends specifically on PAPS1 function. The resulting reduction in SAUR activity in paps1 mutants contributes to their reduced leaf growth, providing a causal link between polyadenylation of specific pre-mRNAs by a particular PAPS isoform and plant growth. Additionally, opposite effects of PAPS1 on leaf and flower growth reflect the different identities of these organs. The overgrowth of paps1 mutant petals is due to increased recruitment of founder cells into early organ primordia whereas the reduced leaf size is due to an ectopic pathogen response. This constitutive immune response leads to increased resistance to the biotrophic oomycete Hyaloperonospora arabidopsidis and reflects activation of the salicylic acid-independent signalling pathway downstream of ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)/PHYTOALEXIN DEFICIENT4 (PAD4). Immune responses are accompanied by intracellular redox changes. Consistent with this, the redox-status of the chloroplast is altered in paps1-1 mutants. The molecular effects of the paps1-1 mutation were analysed using an RNA sequencing approach that distinguishes between long- and short tailed mRNA. The results shown here suggest the existence of an additional layer of regulation in plants and possibly vertebrate gene expression, whereby the relative activities of canonical nuclear PAPS isoforms control de novo synthesized poly(A) tail length and hence expression of specific subsets of mRNAs.
The contractile vacuole (CV) is an osmoregulatory organelle found exclusively in algae and protists. In addition to expelling excessive water out of the cell, it also expels ions and other metabolites and thereby contributes to the cell's metabolic homeostasis. The interest in the CV reaches beyond its immediate cellular roles. The CV's function is tightly related to basic cellular processes such as membrane dynamics and vesicle budding and fusion; several physiological processes in animals, such as synaptic neurotransmission and blood filtration in the kidney, are related to the CV's function; and several pathogens, such as the causative agents of sleeping sickness, possess CVs, which may serve as pharmacological targets. The green alga Chlamydomonas reinhardtii has two CVs. They are the smallest known CVs in nature, and they remain relatively untouched in the CV-related literature. Many genes that have been shown to be related to the CV in other organisms have close homologues in C. reinhardtii. We attempted to silence some of these genes and observe the effect on the CV. One of our genes, VMP1, caused striking, severe phenotypes when silenced. Cells exhibited defective cytokinesis and aberrant morphologies. The CV, incidentally, remained unscathed. In addition, mutant cells showed some evidence of disrupted autophagy. Several important regulators of the cell cycle as well as autophagy were found to be underexpressed in the mutant. Lipidomic analysis revealed many meaningful changes between wild-type and mutant cells, reinforcing the compromised-autophagy observation. VMP1 is a singular protein, with homologues in numerous eukaryotic organisms (aside from fungi), but usually with no relatives in each particular genome. Since its first characterization in 2002 it has been associated with several cellular processes and functions, namely autophagy, programmed cell-death, secretion, cell adhesion, and organelle biogenesis. It has been implicated in several human diseases: pancreatitis, diabetes, and several types of cancer. Our results reiterate some of the observations in VMP1's six reported homologues, but, importantly, show for the first time an involvement of this protein in cell division. The mechanisms underlying this involvement in Chlamydomonas, as well as other key aspects, such as VMP1's subcellular localization and interaction partners, still await elucidation.
Mars is one of the best candidates among planetary bodies for supporting life. The presence of water in the form of ice and atmospheric vapour together with the availability of biogenic elements and energy are indicators of the possibility of hosting life as we know it. The occurrence of permanently frozen ground – permafrost, is a common phenomenon on Mars and it shows multiple morphological analogies with terrestrial permafrost. Despite the extreme inhospitable conditions, highly diverse microbial communities inhabit terrestrial permafrost in large numbers. Among these are methanogenic archaea, which are anaerobic chemotrophic microorganisms that meet many of the metabolic and physiological requirements for survival on the martian subsurface. Moreover, methanogens from Siberian permafrost are extremely resistant against different types of physiological stresses as well as simulated martian thermo-physical and subsurface conditions, making them promising model organisms for potential life on Mars. The main aims of this investigation are to assess the survival of methanogenic archaea under Mars conditions, focusing on methanogens from Siberian permafrost, and to characterize their biosignatures by means of Raman spectroscopy, a powerful technology for microbial identification that will be used in the ExoMars mission. For this purpose, methanogens from Siberian permafrost and non-permafrost habitats were subjected to simulated martian desiccation by exposure to an ultra-low subfreezing temperature (-80ºC) and to Mars regolith (S-MRS and P-MRS) and atmospheric analogues. They were also exposed to different concentrations of perchlorate, a strong oxidant found in martian soils. Moreover, the biosignatures of methanogens were characterized at the single-cell level using confocal Raman microspectroscopy (CRM). The results showed survival and methane production in all methanogenic strains under simulated martian desiccation. After exposure to subfreezing temperatures, Siberian permafrost strains had a faster metabolic recovery, whereas the membranes of non-permafrost methanogens remained intact to a greater extent. The strain Methanosarcina soligelidi SMA-21 from Siberian permafrost showed significantly higher methane production rates than all other strains after the exposure to martian soil and atmospheric analogues, and all strains survived the presence of perchlorate at the concentration on Mars. Furthermore, CRM analyses revealed remarkable differences in the overall chemical composition of permafrost and non-permafrost strains of methanogens, regardless of their phylogenetic relationship. The convergence of the chemical composition in non-sister permafrost strains may be the consequence of adaptations to the environment, and could explain their greater resistance compared to the non-permafrost strains. As part of this study, Raman spectroscopy was evaluated as an analytical technique for remote detection of methanogens embedded in a mineral matrix. This thesis contributes to the understanding of the survival limits of methanogenic archaea under simulated martian conditions to further assess the hypothetical existence of life similar to methanogens on the martian subsurface. In addition, the overall chemical composition of methanogens was characterized for the first time by means of confocal Raman microspectroscopy, with potential implications for astrobiological research.
In semi-arid savannas, unsustainable land use can lead to degradation of entire landscapes, e.g. in the form of shrub encroachment. This leads to habitat loss and is assumed to reduce species diversity. In BIOTA phase 1, we investigated the effects of land use on population dynamics on farm scale. In phase 2 we scale up to consider the whole regional landscape consisting of a diverse mosaic of farms with different historic and present land use intensities. This mosaic creates a heterogeneous, dynamic pattern of structural diversity at a large spatial scale. Understanding how the region-wide dynamic land use pattern affects the abundance of animal and plant species requires the integration of processes on large as well as on small spatial scales. In our multidisciplinary approach, we integrate information from remote sensing, genetic and ecological field studies as well as small scale process models in a dynamic region-wide simulation tool. <hr> Interdisziplinäres Zentrum für Musterdynamik und Angewandte Fernerkundung Workshop vom 9. - 10. Februar 2006.
Adenylates are metabolites with essential function in metabolism and signaling in all living organisms. As Cofactors, they enable thermodynamically unfavorable reactions to be catalyzed enzymatically within cells. Outside the cell, adenylates are involved in signalling processes in animals and emerging evidence suggests similar signaling mechanisms in the plants’ apoplast. Presumably, apoplastic apyrases are involved in this signaling by hydrolyzing the signal mediating molecules ATP and ADP to AMP. This PhD thesis focused on the role of adenylates on metabolism and development of potato (Solanum tuberosum) by using reverse genetics and biochemical approaches. To study the short and long term effect of cellular ATP and the adenylate energy charge on potato tuber metabolism, an apyrase from Escherichia coli targeted into the amyloplast was expressed inducibly and constitutively. Both approaches led to the identification of adaptations to reduced ATP/energy charge levels on the molecular and developmental level. These comprised a reduction of metabolites and pathway fluxes that require significant amounts of ATP, like amino acid or starch synthesis, and an activation of processes that produce ATP, like respiration and an immense increase in the surface-to-volume ratio. To identify extracellular enzymes involved in adenylate conversion, green fluorescent protein and activity localization studies in potato tissue were carried out. It was found that extracellular ATP is imported into the cell by an apoplastic enzyme complement consisting of apyrase, unspecific phosphatase, adenosine nucleosidase and an adenine transport system. By changing the expression of a potato specific apyrase via transgenic approaches, it was found that this enzyme has strong impact on plant and particular tuber development in potato. Whereas metabolite levels were hardly altered, transcript profiling of tubers with reduced apyrase activity revealed a significant upregulation of genes coding for extensins, which are associated with polar growth. The results are discussed in context of adaptive responses of plants to changes in the adenylate levels and the proposed role of apyrase in apoplastic purinergic signaling and ATP salvaging. In summary, this thesis provides insight into adenylate regulated processes within and outside non-photosynthetic plant cells.
Decisions for the conservation of biodiversity and sustainable management of natural resources are typically related to large scales, i.e. the landscape level. However, understanding and predicting the effects of land use and climate change on scales relevant for decision-making requires to include both, large scale vegetation dynamics and small scale processes, such as soil-plant interactions. Integrating the results of multiple BIOTA subprojects enabled us to include necessary data of soil science, botany, socio-economics and remote sensing into a high resolution, process-based and spatially-explicit model. Using an example from a sustainably-used research farm and a communally used and degraded farming area in semiarid southern Namibia we show the power of simulation models as a tool to integrate processes across disciplines and scales.
Background: Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae) in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H2S in sulfidic springs) drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence) were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration) before and after the flood. Results: Habitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave), but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre). By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre. Conclusions: The virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little affected by temporary perturbations, as adaptations to physico-chemical stressors may directly affect the survival probability in divergent habitat types.
The importance of cryptic diversity in rotifers is well understood regarding its ecological consequences, but there remains an in depth comprehension of the underlying molecular mechanisms and forces driving speciation. Temperature has been found several times to affect species spatio-temporal distribution and organisms’ performance, but we lack information on the mechanisms that provide thermal tolerance to rotifers. High cryptic diversity was found recently in the freshwater rotifer “Brachionus calyciflorus”, showing that the complex comprises at least four species: B. calyciflorus sensu stricto (s.s.), B. fernandoi, B. dorcas, and B. elevatus. The temporal succession among species which have been observed in sympatry led to the idea that temperature might play a crucial role in species differentiation.
The central aim of this study was to unravel differences in thermal tolerance between species of the former B. calyciflorus species complex by comparing phenotypic and gene expression responses. More specifically, I used the critical maximum temperature as a proxy for inter-species differences in heat-tolerance; this was modeled as a bi-dimensional phenotypic trait taking into consideration the intention and the duration of heat stress. Significant differences on heat-tolerance between species were detected, with B. calyciflorus s.s. being able to tolerate higher temperatures than B. fernandoi.
Based on evidence of within species neutral genetic variation, I further examined adaptive genetic variability within two different mtDNA lineages of the heat tolerant B. calyciflorus s.s. to identify SNPs and genes under selection that might reflect their adaptive history. These analyses did not reveal adaptive genetic variation related to heat, however, they show putatively adaptive genetic variation which may reflect local adaptation. Functional enrichment of putatively positively selected genes revealed signals of adaptation in genes related to “lipid metabolism”, “xenobiotics biodegradation and metabolism” and “sensory system”, comprising candidate genes which can be utilized in studies on local adaptation. An absence of genetically-based differences in thermal adaptation between the two mtDNA lineages, together with our knowledge that B. calyciflorus s.s. can withstand a broad range of temperatures, led to the idea to further investigate shared transcriptomic responses to long-term exposure to high and low temperatures regimes. With this, I identified candidate genes that are involved in the response to temperature imposed stress. Lastly, I used comparative transcriptomics to examine responses to imposed heat-stress in heat-tolerant and heat-sensitive Brachionus species. I found considerably different patterns of gene expression in the two species. Most striking are patterns of expression regarding the heat shock proteins (hsps) between the two species. In the heat-tolerant, B. calyciflorus s.s., significant up-regulation of hsps at low temperatures was indicative of a stress response at the cooler end of the temperature regimes tested here. In contrast, in the heat-sensitive B. fernandoi, hsps generally exhibited up-regulation of these genes along with rising temperatures. Overall, identification of differences in expression of genes suggests suppression of protein biosynthesis to be a mechanism to increase thermal tolerance. Observed patterns in population growth are correlated with the hsp gene expression differences, indicating that this physiological stress response is indeed related to phenotypic life history performance.
Recent advances in microscopy have led to an improved visualization of different cell processes. Yet, this also leads to a higher demand of tools which can process images in an automated and quantitative fashion. Here, we present two applications that were developed to quantify different processes in eukaryotic cells which rely on the organization and dynamics of the cytoskeleton.. In plant cells, microtubules and actin filaments form the backbone of the cytoskeleton. These structures support cytoplasmic streaming, cell wall organization and tracking of cellular material to and from the plasma membrane. To better understand the underlying mechanisms of cytoskeletal organization, dynamics and coordination, frameworks for the quantification are needed. While this is fairly well established for the microtubules, the actin cytoskeleton has remained difficult to study due to its highly dynamic behaviour. One aim of this thesis was therefore to provide an automated framework to quantify and describe actin organization and dynamics. We used the framework to represent actin structures as networks and examined the transport efficiency in Arabidopsis thaliana hypocotyl cells. Furthermore, we applied the framework to determine the growth mode of cotton fibers and compared the actin organization in wild-type and mutant cells of rice. Finally, we developed a graphical user interface for easy usage. Microtubules and the actin cytoskeleton also play a major role in the morphogenesis of epidermal leaf pavement cells. These cells have highly complex and interdigitated shapes which are hard to describe in a quantitative way. While the relationship between microtubules, the actin cytoskeleton and shape formation is the object of many studies, it is still not clear how and if the cytoskeletal components predefine indentations and protrusions in pavement cell shapes. To understand the underlying cell processes which coordinate cell morphogenesis, a quantitative shape descriptor is needed. Therefore, the second aim of this thesis was the development of a network-based shape descriptor which captures global and local shape features, facilitates shape comparison and can be used to evaluate shape complexity. We demonstrated that our framework can be used to describe and compare shapes from various domains. In addition, we showed that the framework accurately detects local shape features of pavement cells and outperform contending approaches. In the third part of the thesis, we extended the shape description framework to describe pavement cell shape features on tissue-level by proposing different network representations of the underlying imaging data.
Transcription factors (TFs) are ubiquitous gene expression regulators and play essential roles in almost all biological processes. This Ph.D. project is primarily focused on the functional characterisation of MYB112 - a member of the R2R3-MYB TF family from the model plant Arabidopsis thaliana. This gene was selected due to its increased expression during senescence based on previous qRT-PCR expression profiling experiments of 1880 TFs in Arabidopsis leaves at three developmental stages (15 mm leaf, 30 mm leaf and 20% yellowing leaf). MYB112 promoter GUS fusion lines were generated to further investigate the expression pattern of MYB112. Employing transgenic approaches in combination with metabolomics and transcriptomics we demonstrate that MYB112 exerts a major role in regulation of plant flavonoid metabolism. We report enhanced and impaired anthocyanin accumulation in MYB112 overexpressors and MYB112-deficient mutants, respectively. Expression profiling reveals that MYB112 acts as a positive regulator of the transcription factor PAP1 leading to increased anthocyanin biosynthesis, and as a negative regulator of MYB12 and MYB111, which both control flavonol biosynthesis. We also identify MYB112 early responsive genes using a combination of several approaches. These include gene expression profiling (Affymetrix ATH1 micro-arrays and qRT-PCR) and transactivation assays in leaf mesophyll cell protoplasts. We show that MYB112 binds to an 8-bp DNA fragment containing the core sequence (A/T/G)(A/C)CC(A/T)(A/G/T)(A/C)(T/C). By electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation coupled to qPCR (ChIP-qPCR) we demonstrate that MYB112 binds in vitro and in vivo to MYB7 and MYB32 promoters revealing them as direct downstream target genes. MYB TFs were previously reported to play an important role in controlling flavonoid biosynthesis in plants. Many factors acting upstream of the anthocyanin biosynthesis pathway show enhanced expression levels during nitrogen limitation, or elevated sucrose content. In addition to the mentioned conditions, other environmental parameters including salinity or high light stress may trigger anthocyanin accumulation. In contrast to several other MYB TFs affecting anthocyanin biosynthesis pathway genes, MYB112 expression is not controlled by nitrogen limitation, or carbon excess, but rather is stimulated by salinity and high light stress. Thus, MYB112 constitutes a previously uncharacterised regulatory factor that modifies anthocyanin accumulation under conditions of abiotic stress.
Nob1 (New Zealand obese 1) bezeichnet einen Adipositas-QTL auf Chr. 5 der Maus (LODBMI >3,3), der in einem Rückkreuzungsexperiment der Mausstämme NZO (adipös) und SJL (schlank) identifiziert wurde. Um Kandidatengene für Adipositas zu finden, wurden mehr als 300 Nob1-Transkripte mit Hilfe von Genexpressionsanalysen auf Unterschiede in stoffwechselrelevanten Geweben zwischen beiden Mausstämmen untersucht. Sieben Gene zeigten eine differentielle Expression: 2310045A20Rik, Tbc1d1, Ppp1cb, Mll5, Insig1, Abhd1 und Alox5ap. Die codierenden Bereiche dieser Gene wurden anschließend auf Sequenzunterschiede zwischen NZO und SJL untersucht. Nur im Gen Tbc1d1, das im Peak-Bereich des Nob1 lokalisiert ist, wurde eine SJL-spezifische Deletion von sieben Basen detektiert, die zu einer Leserasterverschiebung und einem vorzeitigen Abbruch des Proteins in der funktionellen Rab-GAP-Domäne führt (Loss-of-Function-Mutation). Interessanterweise wurde eine Variante von TBC1D1 (R125W) in Kopplungsanalysen mit Adipositas beim Menschen assoziiert (Stone et al., 2006). TBC1D1 zeigt eine hohe Homologie zu TBC1D4 (AS160), das im Insulinsignalweg eine wichtige Rolle spielt. In 17 weiteren Genen im Peak-Bereich des Nob1 wurde keine weitere SJL-spezifischen Mutation detektiert. Bei NZO-Tieren erfolgte die Tbc1d1-mRNA-Expression vorwiegend in glycolytischen Fasern des Skelettmuskels. Zudem wurden zwei gewebsspezifisch exprimierte Tbc1d1-Isoformen identifiziert, die sich durch alternatives Splicen der Exone 12 und 13 unterscheiden. Die im Rahmen dieser Arbeit gefundenen Ergebnisse machen Tbc1d1 zu einem plausiblen Kandidatengen für den Nob1-QTL. Welche Funktion Tbc1d1 im Glucose- und Fettstoffwechsel des Skelettmuskels hat, muss in weiteren Analysen untersucht werden.
Variation in nitrogen deposition and available soil nitrogen in a forest–grassland ecotone in Canada
(2004)
Regional variation in nitrogen (N) deposition increases plant productivity and decreases species diversity, but landscape- or local-scale influences on N deposition are less well-known. Using ion-exchange resin, we measured variation of N deposition and soil N availability within Elk Island National Park in the ecotone between grassland and boreal forest in western Canada. The park receives regionally high amounts of atmospheric N deposition (22 kg ha⁻¹ yr⁻¹). N deposition was on average higher ton clayrich luvisols than on brunisols, and areas burned 1 – 15 years previously received more atmospheric N than unburned sites. We suggest that the effects of previous fires and soil type on deposition rate act through differences in canopy structure. The magnitude of these effects varied with the presence of ungulate grazers (bison, moose, elk) and vegetation type (forest, shrubland, grassland). Available soil N (ammonium and nitrate) was higher in burned than unburned sites in the absence of grazing, suggesting an effect of deposition. On grazed sites, differences between fire treatments were small, presumably because the removal of biomass by grazers reduced the effect of fire. Aspen invades native grassland in this region, and our results suggest that fire without grazing might reinforce the expansion of forest into grassland facilitated by N deposition.
Germination rates and germination fractions of seeds can be predicted well by the hydrothermal time (HTT) model. Its four parameters hydrothermal time, minimum soil temperature, minimum soil moisture, and variation of minimum soil moisture, however, must be determined by lengthy germination experiments at combinations of several levels of soil temperature and moisture. For some applications of the HTT model it is more important to have approximate estimates for many species rather than exact values for only a few species. We suggest that minimum temperature and variation of minimum moisture can be estimated from literature data and expert knowledge. This allows to derive hydrothermal time and minimum moisture from existing data from germination experiments with one level of temperature and moisture. We applied our approach to a germination experiment comparing germination fractions of wild annual species along an aridity gradient in Israel. Using this simplified approach we estimated hydrothermal time and minimum moisture of 36 species. Comparison with exact data for three species shows that our method is a simple but effective method for obtaining parameters for the HTT model. Hydrothermal time and minimum moisture supposedly indicate climate related germination strategies. We tested whether these two parameters varied with the climate at the site where the seeds had been collected. We found no consistent variation with climate across species, suggesting that variation is more strongly controlled by site-specific factors.