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The natural abundance of Coiled Coil (CC) motifs in cytoskeleton and extracellular matrix proteins suggests that CCs play an important role as passive (structural) and active (regulatory) mechanical building blocks. CCs are self-assembled superhelical structures consisting of 2-7 α-helices. Self-assembly is driven by hydrophobic and ionic interactions, while the helix propensity of the individual helices contributes additional stability to the structure. As a direct result of this simple sequence-structure relationship, CCs serve as templates for protein design and sequences with a pre-defined thermodynamic stability have been synthesized de novo. Despite this quickly increasing knowledge and the vast number of possible CC applications, the mechanical function of CCs has been largely overlooked and little is known about how different CC design parameters determine the mechanical stability of CCs. Once available, this knowledge will open up new applications for CCs as nanomechanical building blocks, e.g. in biomaterials and nanobiotechnology.
With the goal of shedding light on the sequence-structure-mechanics relationship of CCs, a well-characterized heterodimeric CC was utilized as a model system. The sequence of this model system was systematically modified to investigate how different design parameters affect the CC response when the force is applied to opposing termini in a shear geometry or separated in a zipper-like fashion from the same termini (unzip geometry). The force was applied using an atomic force microscope set-up and dynamic single-molecule force spectroscopy was performed to determine the rupture forces and energy landscape properties of the CC heterodimers under study. Using force as a denaturant, CC chain separation is initiated by helix uncoiling from the force application points. In the shear geometry, this allows uncoiling-assisted sliding parallel to the force vector or dissociation perpendicular to the force vector. Both competing processes involve the opening of stabilizing hydrophobic (and ionic) interactions. Also in the unzip geometry, helix uncoiling precedes the rupture of hydrophobic contacts.
In a first series of experiments, the focus was placed on canonical modifications in the hydrophobic core and the helix propensity. Using the shear geometry, it was shown that both a reduced core packing and helix propensity lower the thermodynamic and mechanical stability of the CC; however, with different effects on the energy landscape of the system. A less tightly packed hydrophobic core increases the distance to the transition state, with only a small effect on the barrier height. This originates from a more dynamic and less tightly packed core, which provides more degrees of freedom to respond to the applied force in the direction of the force vector. In contrast, a reduced helix propensity decreases both the distance to the transition state and the barrier height. The helices are ‘easier’ to unfold and the remaining structure is less thermodynamically stable so that dissociation perpendicular to the force axis can occur at smaller deformations.
Having elucidated how canonical sequence modifications influence CC mechanics, the pulling geometry was investigated in the next step. Using one and the same sequence, the force application points were exchanged and two different shear and one unzipping geometry were compared. It was shown that the pulling geometry determines the mechanical stability of the CC. Different rupture forces were observed in the different shear as well as in the unzipping geometries, suggesting that chain separation follows different pathways on the energy landscape. Whereas the difference between CC shearing and unzipping was anticipated and has also been observed for other biological structures, the observed difference for the two shear geometries was less expected. It can be explained with the structural asymmetry of the CC heterodimer. It is proposed that the direction of the α-helices, the different local helix propensities and the position of a polar asparagine in the hydrophobic core are responsible for the observed difference in the chain separation pathways. In combination, these factors are considered to influence the interplay between processes parallel and perpendicular to the force axis.
To obtain more detailed insights into the role of helix stability, helical turns were reinforced locally using artificial constraints in the form of covalent and dynamic ‘staples’. A covalent staple bridges to adjacent helical turns, thus protecting them against uncoiling. The staple was inserted directly at the point of force application in one helix or in the same terminus of the other helix, which did not experience the force directly. It was shown that preventing helix uncoiling at the point of force application reduces the distance to the transition state while slightly increasing the barrier height. This confirms that helix uncoiling is critically important for CC chain separation. When inserted into the second helix, this stabilizing effect is transferred across the hydrophobic core and protects the force-loaded turns against uncoiling. If both helices were stapled, no additional increase in mechanical stability was observed. When replacing the covalent staple with a dynamic metal-coordination bond, a smaller decrease in the distance to the transition was observed, suggesting that the staple opens up while the CC is under load.
Using fluorinated amino acids as another type of non-natural modification, it was investigated how the enhanced hydrophobicity and the altered packing at the interface influences CC mechanics. The fluorinated amino acid was inserted into one central heptad of one or both α-helices. It was shown that this substitution destabilized the CC thermodynamically and mechanically. Specifically, the barrier height was decreased and the distance to the transition state increased. This suggests that a possible stabilizing effect of the increased hydrophobicity is overruled by a disturbed packing, which originates from a bad fit of the fluorinated amino acid into the local environment. This in turn increases the flexibility at the interface, as also observed for the hydrophobic core substitution described above. In combination, this confirms that the arrangement of the hydrophobic side chains is an additional crucial factor determining the mechanical stability of CCs.
In conclusion, this work shows that knowledge of the thermodynamic stability alone is not sufficient to predict the mechanical stability of CCs. It is the interplay between helix propensity and hydrophobic core packing that defines the sequence-structure-mechanics relationship. In combination, both parameters determine the relative contribution of processes parallel and perpendicular to the force axis, i.e. helix uncoiling and uncoiling-assisted sliding as well as dissociation. This new mechanistic knowledge provides insight into the mechanical function of CCs in tissues and opens up the road for designing CCs with pre-defined mechanical properties. The library of mechanically characterized CCs developed in this work is a powerful starting point for a wide spectrum of applications, ranging from molecular force sensors to mechanosensitive crosslinks in protein nanostructures and synthetic extracellular matrix mimics.
Starch is an insoluble polyglucan, comprises of two polymers, namely, the branched α-1,4: α-1,6-D-glucan amylopectin and the almost unbranched α-1,4-D-glucan amylose. The growth of all plants is directly dependent on the accumulation of transitory starch during the daytime when photosynthesis takes place and subsequently starch degradation during the night. Starch phosphorylation takes place by starch-related dikinases called α-glucan, water dikinase (GWD), and phosphoglucan, water dikinase (PWD), and is a very important step in starch degradation. The biochemical mechanisms of phosphorylation of starch are not properly understood. Recent studies have found that there are two starch binding proteins namely, Early Starvation1 (ESV1) and Like Early Starvation1 (LESV), which play an important role in starch metabolism. It has been shown that ESV1 and LESV proteins affect the starch phosphorylation activity of GWD and PWD enzymes, which control the rate of degradation of starch granules. In this thesis, various in vitro assays were performed to identify and understand the mechanism of recombinant proteins; ESV1 and LESV on the starch degradation. The starch degradation was performed by phosphorylation enzymes, GWD and PWD separately. In various enzymatic assays, the influence of the ESV1 and LESV on the actions of GWD and PWD on the surfaces of different native starch granules were analysed. Furthermore, ESV1 and LESV have specifically shown influences on the phosphorylation activities of GWD and PWD on the starch granule surfaces in an antagonistic pattern in such a way that, the GWD mediated phosphorylation were significantly reduced while PWD mediated phosphorylation were significantly increased respectively. In another set of experiments, ISA and BAM hydrolyzing enzymes were used to alter the structure of starch, and then determine the effect of both dikinases mediated phosphorylation in the presence of ESV1 and LESV on the altered starch granules surfaces. In these results, significant decreases in both GWD and PWD mediated phosphorylation were observed in all the treatments containing either ESV1 or LESV proteins only or both ESV1 and LESV. It was also found that LESV preferentially binds to both amylose and amylopectin, while ESV1 binds to highly ordered glucans such as maltodextrins and amylopectin, which are crystalline in structure. Both ESV1 or LESV proteins either individually or in combination have shown influence on the activity of GWD and PWD phosphate incorporation into the starch granules via reduction even though at different percentages depending on the sources of starch, therefore it is difficult to distinguish the specific function between them. The biochemical studies have shown that protein-glucan interaction specifically between ESV1 or LESV or in combination with different species of starch granules has very strong surface binding, or it might be possible that both the proteins not only bind to the surface of the starch granules but also have entered deep inside the glucan structure of the starch granules. However, the results also revealed that ESV1 and LESV did not alter the autophosphorylation of the dikinases. Also, the chain length distribution pattern of the released glucan chains after treatment of starch with ISA enzyme was evaluated with respect to the degree of polymerization (DP) of the different starch granules. Capillary electrophoresis was employed to study the effect of LESV and ESV1 on the chain length distribution. In summary, this study confirms that ESV1 and LESV play an important role in organizing and regulating the starch metabolism process. In the later half, studies were performed to monitor whether the metabolism of carbohydrates and partitioning, contribute to the higher salt tolerance of the facultative halophyte Hordeum marinum when compared to glycophyte Hordeum vulgare. Seedlings with the same size from both species were hydroponically grown at 0, 150, and 300 mM of NaCl for 3 weeks. H. marinum maintained a high relative growth rate, which was found concomitant in higher aptitude plants to maintain efficient shoot tissue hydration and integrity of membrane under salt conditions when compared to H. vulgare. Hence, our data suggested that the change in the starch storage, distribution of soluble sugar concentrations between source and sink organs, and also changes in the level of enzymes involved in the starch metabolism was significant to give insights into the importance of carbohydrate metabolism in barley species with regards to the salt tolerance. Although these results are still in their nascent state, it could be vital for other researchers to formulate future studies. The preliminary results which were studies about the carbohydrate metabolism and partitioning in salt responses in the halophyte H. marinum and the glycophyte H. vulgare revealed that salt tolerance in barley species is not due to osmotic adjustments, but due to other reasons that were not explored in the past studies. However, the activity of DPE2 in H. vulgare was not hampered by the presence of NaCl as observed. While Pho1 and Pho2, activities were highly increased in cultivated barley. These findings could be suggestive of a possible role of these enzymes in the responses of carbohydrate metabolism to salinity. When sea and cultivated barley species were compared, it was discovered that the former had more versatility in carbohydrate metabolism and distribution.
Proteostasis of the tonoplast : synthesis, sorting and turnover of the potassum channel AtTPK1
(2010)
Among the bloom-forming and potentially harmful cyanobacteria, the genus Microcystis represents a most diverse taxon, on the genomic as well as on morphological and secondary metabolite levels. Microcystis communities are composed of a variety of diversified strains. The focus of this study lies on potential interactions between Microcystis representatives and the roles of secondary metabolites in these interaction processes.
The role of secondary metabolites functioning as signaling molecules in the investigated interactions is demonstrated exemplary for the prevalent hepatotoxin microcystin. The extracellular and intracellular roles of microcystin are tested in microarray-based transcriptomic approaches. While an extracellular effect of microcystin on Microcystis transcription is confirmed and connected to a specific gene cluster of another secondary metabolite in this study, the intracellularly occurring microcystin is related with several pathways of the primary metabolism. A clear correlation of a microcystin knockout and the SigE-mediated regulation of carbon metabolism is found. According to the acquired transcriptional data, a model is proposed that postulates the regulating effect of microcystin on transcriptional regulators such as the alternative sigma factor SigE, which in return captures an essential role in sugar catabolism and redox-state regulation.
For the purpose of simulating community conditions as found in the field, Microcystis colonies are isolated from the eutrophic lakes near Potsdam, Germany and established as stably growing under laboratory conditions. In co-habitation simulations, the recently isolated field strain FS2 is shown to specifically induce nearly immediate aggregation reactions in the axenic lab strain Microcystis aeruginosa PCC 7806. In transcriptional studies via microarrays, the induced expression program in PCC 7806 after aggregation induction is shown to involve the reorganization of cell envelope structures, a highly altered nutrient uptake balance and the reorientation of the aggregating cells to a heterotrophic carbon utilization, e.g. via glycolysis. These transcriptional changes are discussed as mechanisms of niche adaptation and acclimation in order to prevent competition for resources.
Species are adapted to the environment they live in. Today, most environments are subjected to rapid global changes induced by human activity, most prominently land cover and climate changes. Such transformations can cause adjustments or disruptions in various eco-evolutionary processes. The repercussions of this can appear at the population level as shifted ranges and altered abundance patterns. This is where global change effects on species are usually detected first.
To understand how eco-evolutionary processes act and interact to generate patterns of range and abundance and how these processes themselves are influenced by environmental conditions, spatially-explicit models provide effective tools. They estimate a species’ niche as the set of environmental conditions in which it can persist. However, the currently most commonly used models rely on static correlative associations that are established between a set of spatial predictors and observed species distributions. For this, they assume stationary conditions and are therefore unsuitable in contexts of global change. Better equipped are process-based models that explicitly implement algorithmic representations of eco-evolutionary mechanisms and evaluate their joint dynamics. These models have long been regarded as difficult to parameterise, but an increased data availability and improved methods for data integration lessen this challenge. Hence, the goal of this thesis is to further develop process-based models, integrate them into a complete modelling workflow, and provide the tools and guidance for their successful application.
With my thesis, I presented an integrated platform for spatially-explicit eco-evolutionary modelling and provided a workflow for their inverse calibration to observational data. In the first chapter, I introduced RangeShiftR, a software tool that implements an individual-based modelling platform for the statistical programming language R. Its open-source licensing, extensive help pages and available tutorials make it accessible to a wide audience. In the second chapter, I demonstrated a comprehensive workflow for the specification, calibration and validation of RangeShiftR by the example of the red kite in Switzerland. The integration of heterogeneous data sources, such as literature and monitoring data, allowed to successfully calibrate the model. It was then used to make validated, spatio-temporal predictions of future red kite abundance. The presented workflow can be adopted to any study species if data is available. In the third chapter, I extended RangeShiftR to directly link demographic processes to climatic predictors. This allowed me to explore the climate-change responses of eight Swiss breeding birds in more detail. Specifically, the model could identify the most influential climatic predictors, delineate areas of projected demographic suitability, and attribute current population trends to contemporary climate change.
My work shows that the application of complex, process-based models in conservation-relevant contexts is feasible, utilising available tools and data. Such models can be successfully calibrated and outperform other currently used modelling approaches in terms of predictive accuracy. Their projections can be used to predict future abundances or to assess alternative conservation scenarios. They further improve our mechanistic understanding of niche and range dynamics under climate change. However, only fully mechanistic models, that include all relevant processes, allow to precisely disentangle the effects of single processes on observed abundances. In this respect, the RangeShiftR model still has potential for further extensions that implement missing influential processes, such as species interactions.
Dynamic, process-based models are needed to adequately model a dynamic reality. My work contributes towards the advancement, integration and dissemination of such models. This will facilitate numeric, model-based approaches for species assessments, generate ecological insights and strengthen the reliability of predictions on large spatial scales under changing conditions.
In the context of ecological risk assessment of chemicals, individual-based population models hold great potential to increase the ecological realism of current regulatory risk assessment procedures. However, developing and parameterizing such models is time-consuming and often ad hoc. Using standardized, tested submodels of individual organisms would make individual-based modelling more efficient and coherent. In this thesis, I explored whether Dynamic Energy Budget (DEB) theory is suitable for being used as a standard submodel in individual-based models, both for ecological risk assessment and theoretical population ecology. First, I developed a generic implementation of DEB theory in an individual-based modeling (IBM) context: DEB-IBM. Using the DEB-IBM framework I tested the ability of the DEB theory to predict population-level dynamics from the properties of individuals. We used Daphnia magna as a model species, where data at the individual level was available to parameterize the model, and population-level predictions were compared against independent data from controlled population experiments. We found that DEB theory successfully predicted population growth rates and peak densities of experimental Daphnia populations in multiple experimental settings, but failed to capture the decline phase, when the available food per Daphnia was low. Further assumptions on food-dependent mortality of juveniles were needed to capture the population dynamics after the initial population peak. The resulting model then predicted, without further calibration, characteristic switches between small- and large-amplitude cycles, which have been observed for Daphnia. We conclude that cross-level tests help detecting gaps in current individual-level theories and ultimately will lead to theory development and the establishment of a generic basis for individual-based models and ecology. In addition to theoretical explorations, we tested the potential of DEB theory combined with IBMs to extrapolate effects of chemical stress from the individual to population level. For this we used information at the individual level on the effect of 3,4-dichloroanailine on Daphnia. The individual data suggested direct effects on reproduction but no significant effects on growth. Assuming such direct effects on reproduction, the model was able to accurately predict the population response to increasing concentrations of 3,4-dichloroaniline. We conclude that DEB theory combined with IBMs holds great potential for standardized ecological risk assessment based on ecological models.
Ribosomes decode mRNA to synthesize proteins. Ribosomes, once considered static, executing machines, are now viewed as dynamic modulators of translation. Increasingly detailed analyses of structural ribosome heterogeneity led to a paradigm shift toward ribosome specialization for selective translation. As sessile organisms, plants cannot escape harmful environments and evolved strategies to withstand. Plant cytosolic ribosomes are in some respects more diverse than those of other metazoans. This diversity may contribute to plant stress acclimation. The goal of this thesis was to determine whether plants use ribosome heterogeneity to regulate protein synthesis through specialized translation. I focused on temperature acclimation, specifically on shifts to low temperatures. During cold acclimation, Arabidopsis ceases growth for seven days while establishing the responses required to resume growth. Earlier results indicate that ribosome biogenesis is essential for cold acclimation. REIL mutants (reil-dkos) lacking a 60S maturation factor do not acclimate successfully and do not resume growth. Using these genotypes, I ascribed cold-induced defects of ribosome biogenesis to the assembly of the polypeptide exit tunnel (PET) by performing spatial statistics of rProtein changes mapped onto the plant 80S structure. I discovered that growth cessation and PET remodeling also occurs in barley, suggesting a general cold response in plants. Cold triggered PET remodeling is consistent with the function of Rei-1, a REIL homolog of yeast, which performs PET quality control. Using seminal data of ribosome specialization, I show that yeast remodels the tRNA entry site of ribosomes upon change of carbon sources and demonstrate that spatially constrained remodeling of ribosomes in metazoans may modulate protein synthesis. I argue that regional remodeling may be a form of ribosome specialization and show that heterogeneous cytosolic polysomes accumulate after cold acclimation, leading to shifts in the translational output that differs between wild-type and reil-dkos. I found that heterogeneous complexes consist of newly synthesized and reused proteins. I propose that tailored ribosome complexes enable free 60S subunits to select specific 48S initiation complexes for translation. Cold acclimated ribosomes through ribosome remodeling synthesize a novel proteome consistent with known mechanisms of cold acclimation. The main hypothesis arising from my thesis is that heterogeneous/ specialized ribosomes alter translation preferences, adjust the proteome and thereby activate plant programs for successful cold acclimation.
Leaf senescence is an active process required for plant survival, and it is flexibly controlled, allowing plant adaptation to environmental conditions. Although senescence is largely an age-dependent process, it can be triggered by environmental signals and stresses. Leaf senescence coordinates the breakdown and turnover of many cellular components, allowing a massive remobilization and recycling of nutrients from senescing tissues to other organs (e.g., young leaves, roots, and seeds), thus enhancing the fitness of the plant. Such metabolic coordination requires a tight regulation of gene expression. One important mechanism for the regulation of gene expression is at the transcriptional level via transcription factors (TFs). The NAC TF family (NAM, ATAF, CUC) includes various members that show elevated expression during senescence, including ORE1 (ANAC092/AtNAC2) among others. ORE1 was first reported in a screen for mutants with delayed senescence (oresara1, 2, 3, and 11). It was named after the Korean word “oresara,” meaning “long-living,” and abbreviated to ORE1, 2, 3, and 11, respectively. Although the pivotal role of ORE1 in controlling leaf senescence has recently been demonstrated, the underlying molecular mechanisms and the pathways it regulates are still poorly understood. To unravel the signaling cascade through which ORE1 exerts its function, we analyzed particular features of regulatory pathways up-stream and down-stream of ORE1. We identified characteristic spatial and temporal expression patterns of ORE1 that are conserved in Arabidopsis thaliana and Nicotiana tabacum and that link ORE1 expression to senescence as well as to salt stress. We proved that ORE1 positively regulates natural and dark-induced senescence. Molecular characterization of the ORE1 promoter in silico and experimentally suggested a role of the 5’UTR in mediating ORE1 expression. ORE1 is a putative substrate of a calcium-dependent protein kinase named CKOR (unpublished data). Promising data revealed a positive regulation of putative ORE1 targets by CKOR, suggesting the phosphorylation of ORE1 as a requirement for its regulation. Additionally, as part of the ORE1 up-stream regulatory pathway, we identified the NAC TF ATAF1 which was able to transactivate the ORE1 promoter in vivo. Expression studies using chemically inducible ORE1 overexpression lines and transactivation assays employing leaf mesophyll cell protoplasts provided information on target genes whose expression was rapidly induced upon ORE1 induction. First, a set of target genes was established and referred to as early responding in the ORE1 regulatory network. The consensus binding site (BS) of ORE1 was characterized. Analysis of some putative targets revealed the presence of ORE1 BSs in their promoters and the in vitro and in vivo binding of ORE1 to their promoters. Among these putative target genes, BIFUNCTIONAL NUCLEASE I (BFN1) and VND-Interacting2 (VNI2) were further characterized. The expression of BFN1 was found to be dependent on the presence of ORE1. Our results provide convincing data which support a role for BFN1 as a direct target of ORE1. Characterization of VNI2 in age-dependent and stress-induced senescence revealed ORE1 as a key up-stream regulator since it can bind and activate VNI2 expression in vivo and in vitro. Furthermore, VNI2 was able to promote or delay senescence depending on the presence of an activation domain located in its C-terminal region. The plasticity of this gene might include alternative splicing (AS) to regulate its function in different organs and at different developmental stages, particularly during senescence. A model is proposed on the molecular mechanism governing the dual role of VNI2 during senescence.
The fragmentation of natural habitat caused by anthropogenic land use changes is one of the main drivers of the current rapid loss of biodiversity. In face of this threat, ecological research needs to provide predictions of communities' responses to fragmentation as a prerequisite for the effective mitigation of further biodiversity loss. However, predictions of communities' responses to fragmentation require a thorough understanding of ecological processes, such as species dispersal and persistence. Therefore, this thesis seeks an improved understanding of community dynamics in fragmented landscapes. In order to approach this overall aim, I identified key questions on the response of plant diversity and plant functional traits to variations in species' dispersal capability, habitat fragmentation and local environmental conditions. All questions were addressed using spatially explicit simulations or statistical models. In chapter 2, I addressed scale-dependent relationships between dispersal capability and species diversity using a grid-based neutral model. I found that the ratio of survey area to landscape size is an important determinant of scale-dependent dispersal-diversity relationships. With small ratios, the model predicted increasing dispersal-diversity relationships, while decreasing dispersal-diversity relationships emerged, when the ratio approached one, i.e. when the survey area approached the landscape size. For intermediate ratios, I found a U-shaped pattern that has not been reported before. With this study, I unified and extended previous work on dispersal-diversity relationships. In chapter 3, I assessed the type of regional plant community dynamics for the study area in the Southern Judean Lowlands (SJL). For this purpose, I parameterised a multi-species incidence-function model (IFM) with vegetation data using approximate Bayesian computation (ABC). I found that the type of regional plant community dynamics in the SJL is best characterized as a set of isolated “island communities” with very low connectivity between local communities. Model predictions indicated a significant extinction debt with 33% - 60% of all species going extinct within 1000 years. In general, this study introduces a novel approach for combining a spatially explicit simulation model with field data from species-rich communities. In chapter 4, I first analysed, if plant functional traits in the SJL indicate trait convergence by habitat filtering and trait divergence by interspecific competition, as predicted by community assembly theory. Second, I assessed the interactive effects of fragmentation and the south-north precipitation gradient in the SJL on community-mean plant traits. I found clear evidence for trait convergence, but the evidence for trait divergence fundamentally depended on the chosen null-model. All community-mean traits were significantly associated with the precipitation gradient in the SJL. The trait associations with fragmentation indices (patch size and connectivity) were generally weaker, but statistically significant for all traits. Specific leaf area (SLA) and plant height were consistently associated with fragmentation indices along the precipitation gradient. In contrast, seed mass and seed number were interactively influenced by fragmentation and precipitation. In general, this study provides the first analysis of the interactive effects of climate and fragmentation on plant functional traits. Overall, I conclude that the spatially explicit perspective adopted in this thesis is crucial for a thorough understanding of plant community dynamics in fragmented landscapes. The finding of contrasting responses of local diversity to variations in dispersal capability stresses the importance of considering the diversity and composition of the metacommunity, prior to implementing conservation measures that aim at increased habitat connectivity. The model predictions derived with the IFM highlight the importance of additional natural habitat for the mitigation of future species extinctions. In general, the approach of combining a spatially explicit IFM with extensive species occupancy data provides a novel and promising tool to assess the consequences of different management scenarios. The analysis of plant functional traits in the SJL points to important knowledge gaps in community assembly theory with respect to the simultaneous consequences of habitat filtering and competition. In particular, it demonstrates the importance of investigating the synergistic consequences of fragmentation, climate change and land use change on plant communities. I suggest that the integration of plant functional traits and of species interactions into spatially explicit, dynamic simulation models offers a promising approach, which will further improve our understanding of plant communities and our ability to predict their dynamics in fragmented and changing landscapes.
Cyanobacteria produce about 40 percent of the world’s primary biomass, but also a variety of often toxic peptides such as microcystin. Mass developments, so called blooms, can pose a real threat to the drinking water supply in many parts of the world. This study aimed at characterizing the biological function of microcystin production in one of the most common bloom-forming cyanobacterium Microcystis aeruginosa.
In a first attempt, the effect of elevated light intensity on microcystin production and its binding to cellular proteins was studied. Therefore, conventional microcystin quantification techniques were combined with protein-biochemical methods. RubisCO, the key enzyme for primary carbon fixation was a major microcystin interaction partner. High light exposition strongly stimulated microcystin-protein interactions. Up to 60 percent of the total cellular microcystin was detected bound to proteins, i.e. inaccessible for standard quantification procedures. Underestimation of total microcystin contents when neglecting the protein fraction was also demonstrated in field samples. Finally, an immuno-fluorescence based method was developed to identify microcystin producing cyanobacteria in mixed populations.
The high light induced microcystin interaction with proteins suggested an impact of the secondary metabolite on the primary metabolism of Microcystis by e.g. modulating the activity of enzymes. For addressing that question, a comprehensive GC/MS-based approach was conducted to compare the accumulation of metabolites in the wild-type of Microcystis aeruginosa PCC 7806 and the microcystin deficient ΔmcyB mutant. From all 501 detected non-redundant metabolites 85 (17 percent) accumulated significantly different in either of both genotypes upon high light exposition. Accumulation of compatible solutes in the ΔmcyB mutant suggests a role of microcystin in fine-tuning the metabolic flow to prevent stress related to excess light, high oxygen concentration and carbon limitation.
Co-analysis of the widely used model cyanobacterium Synechocystis PCC 6803 revealed profound metabolic differences between species of cyanobacteria. Whereas Microcystis channeled more resources towards carbohydrate synthesis, Synechocystis invested more in amino acids. These findings were supported by electron microscopy of high light treated cells and the quantification of storage compounds. While Microcystis accumulated mainly glycogen to about 8.5 percent of its fresh weight within three hours, Synechocystis produced higher amounts of cyanophycin. The results showed that the characterization of species-specific metabolic features should gain more attention with regard to the biotechnological use of cyanobacteria.
Predator-forager interactions are a major factor in evolutionary adaptation of many species, as predators need to gain energy by consuming prey species, and foragers needs to avoid the worst fate of mortality while still consuming resources for energetic gains. In this evolutionary arms race, the foragers have constantly evolved anti-predator behaviours (e.g. foraging activity changes). To describe all these complex changes, researchers developed the framework of the landscape of fear, that is, the spatio-temporal variation of perceived predation risk. This concept simplifies all the involved ecological processes into one framework, by integrating animal biology and distribution with habitat characteristics. Researchers can then evaluate the perception of predation risk in prey species, what are the behavioural responses of the prey and, therefore, understand the cascading effects of landscapes of fear at the resource levels (tri-trophic effects). Although tri-trophic effects are well studied at the predator-prey interaction level, little is known on how the forager-resource interactions are part of the overall cascading effects of landscapes of fear, despite the changes of forager feeding behaviour - that occur with perceived predation risk - affecting directly the level of the resources.
This thesis aimed to evaluate the cascading effects of the landscape of fear on biodiversity of resources, and how the feeding behaviour and movement of foragers shaped the final resource species composition (potential coexistence mechanisms). We studied the changes caused by landscapes of fear on wild and captive rodent communities and evaluated: the cascading effects of different landscapes of fear on a tri-trophic system (I), the effects of fear on a forager’s movement patterns and dietary preferences (II) and cascading effects of different types of predation risk (terrestrial versus avian, III).
In Chapter I, we applied a novel measure to evaluate the cascading effects of fear at the level of resources, by quantifying the diversity of resources left after the foragers gave-up on foraging (diversity at the giving-up density). We tested the measure at different spatial levels (local and regional) and observed that with decreased perceived predation risk, the density and biodiversity of resources also decreased. Foragers left a very dissimilar community of resources based on perceived risk and resources functional traits, and therefore acted as an equalising mechanism.
In Chapter II, we wanted to understand further the decision-making processes of rodents in different landscapes of fear, namely, in which resource species rodents decided to forage on (based on three functional traits: size, nutrients and shape) and how they moved depending on perceived predation risk. In safe landscapes, individuals increased their feeding activity and movements and despite the increased costs, they visited more often patches that were further away from their central-place. Despite a preference for the bigger resources regardless of risk, when perceived predation risk was low, individuals changed their preference to fat-rich resources.
In Chapter III, we evaluated the cascading effects of two different types of predation risk in rodents: terrestrial (raccoon) versus avian predation risk. Raccoon presence or absence did not alter the rodents feeding behaviour in different landscapes of fear. Rodent’s showed risk avoidance behaviours towards avian predators (spatial risk avoidance), but not towards raccoons (lack of temporal risk avoidance).
By analysing the effects of fear in tri-trophic systems, we were able to deepen the knowledge of how non-consumptive effects of predators affect the behaviour of foragers, and quantitatively measure the cascading effects at the level of resources with a novel measure. Foragers are at the core of the ecological processes and responses to the landscape of fear, acting as variable coexistence agents for resource species depending on perceived predation risk. This newly found measures and knowledge can be applied to more trophic chains, and inform researchers on biodiversity patterns originating from landscapes of fear.
The adaptive evolutionary potential of a species or population to cope with omnipresent environmental challenges is based on its genetic variation. Variability at immune genes, such as the major histocompatibility complex (MHC) genes, is assumed to be a very powerful and effective tool to keep pace with diverse and rapidly evolving pathogens. In my thesis, I studied natural levels of variation at the MHC genes, which have a key role in immune defence, and parasite burden in different small mammal species. I assessed the importance of MHC variation for parasite burden in small mammal populations in their natural environment. To understand the processes shaping different patterns of MHC variation I focused on evidence of selection through pathogens upon the host. Further, I addressed the issue of low MHC diversity in populations or species, which could potentially arise as a result from habitat fragmentation and isolation. Despite their key role in the mammalian evolution the marsupial MHC has been rarely investigated. Studies on primarily captive or laboratory bred individuals indicated very little or even no polymorphism at the marsupial MHC class II genes. However, natural levels of marsupial MHC diversity and selection are unknown to date as studies on wild populations are virtually absent. I investigated MHC II variation in two Neotropical marsupial species endemic to the threatened Brazilian Atlantic Forest (Gracilinanus microtarsus, Marmosops incanus) to test whether the predicted low marsupial MHC class II polymorphism proves to be true under natural conditions. For the first time in marsupials I confirmed characteristics of MHC selection that were so far only known from eutherian mammals, birds, and fish: Positive selection on specific codon sites, recombination, and trans-species polymorphism. Beyond that, the two marsupial species revealed considerable differences in their MHC class II diversity. Diversity was rather low in M. incanus but tenfold higher in G. microtarsus, disproving the predicted general low marsupial MHC class II variation. As pathogens are believed to be very powerful drivers of MHC diversity, I studied parasite burden in both host species to understand the reasons for the remarkable differences in MHC diversity. In both marsupial species specific MHC class II variants were associated to either high or low parasite load highlighting the importance of the marsupial MHC class II in pathogen defence. I developed two alternative scenarios with regard to MHC variation, parasite load, and parasite diversity. In the ‘evolutionary equilibrium’ scenario I assumed the species with low MHC diversity, M. incanus, to be under relaxed pathogenic selection and expected low parasite diversity. Alternatively, low MHC diversity could be the result of a recent loss of genetic variation by means of a genetic bottleneck event. Under this ‘unbalanced situation’ scenario, I assumed a high parasite burden in M. incanus due to a lack of resistance alleles. Parasitological results clearly reject the first scenario and point to the second scenario, as M. incanus is distinctly higher parasitised but parasite diversity is relatively equal compared to G. microtarsus. Hence, I suggest that the parasite load in M. incanus is rather the consequence than the cause for its low MHC diversity. MHC variation and its associations to parasite burden have been typically studied within single populations but MHC variation between populations was rarely taken into account. To gain scientific insight on this issue, I chose a common European rodent species. In the yellow necked mouse (Apodemus flavicollis), I investigated the effects of genetic diversity on parasite load not on the individual but on the population level. I included populations, which possess different levels of variation at the MHC as well as at neutrally evolving genetic markers (microsatellites). I was able to show that mouse populations with a high MHC allele diversity are better armed against high parasite burdens highlighting the significance of adaptive genetic diversity in the field of conservation genetics. An individual itself will not directly benefit from its population’s large MHC allele pool in terms of parasite resistance. But confronted with the multitude of pathogens present in the wild a population with a large MHC allele reservoir is more likely to possess individuals with resistance alleles. These results deepen our understanding of the complex causes and processes of evolutionary adaptations between hosts and pathogens.
Variation in traits permeates and affects all levels of biological organisation, from within individuals to between species. Yet, intraspecific trait variation (ITV) is not sufficiently represented in many ecological theories. Instead, species averages are often assumed. Especially ITV in behaviour has only recently attracted more attention as its pervasiveness and magnitude became evident. The surge in interest in ITV in behaviour was accompanied by a methodological and technological leap in the field of movement ecology. Many aspects of behaviour become visible via movement, allowing us to observe inter-individual differences in fundamental processes such as foraging, mate searching, predation or migration. ITV in movement behaviour may result from within-individual variability and consistent, repeatable among-individual differences. Yet, questions on why such among-individual differences occur in the first place and how they are integrated with life-history have remained open. Furthermore, consequences of ITV, especially of among-individual differences in movement behaviour, on populations and species communities are not sufficiently understood. In my thesis, I approach timely questions on the sources and consequences of ITV, particularly, in movement behaviour. After outlining fundamental concepts and the current state of knowledge, I approach these questions by using agent-based models to integrate concepts from behavioural and movement ecology and to develop novel perspectives.
Modern coexistence theory is a central pillar of community ecology, yet, insufficiently considers ITV in behaviour. In chapter 2, I model a competitive two-species system of ground-dwelling, central-place foragers to investigate the consequences of among-individual differences in movement behaviour on species coexistence. I show that the simulated among-individual differences, which matched with empirical data, reduce fitness differences betweem species, i.e. provide an equalising coexistence mechanism. Furthermore, I explain this result mechanistically and, thus, resolve an apparent ambiguity of the consequences of ITV on species coexistence described in previous studies.
In chapter 3, I turn the focus to sources of among-individual differences in movement behaviour and their potential integration with life-history. The pace-of-life syndrome (POLS) theory predicts that the covariation between among-individual differences in behaviour and life-history is mediated by a trade-off between early and late reproduction. This theory has generated attention but is also currently scrutinised. In chapter 3, I present a model which supports a recent conceptual development that suggests fluctuating density-dependent selection as a cause of the POLS. Yet, I also identified processes that may alter the association between movement behaviour and life-history across levels of biological organization.
ITV can buffer populations, i.e. reduce their extinction risk. For instance, among-individual differences can mediate portfolio effects or increase evolvability and, thereby, facilitate rapid evolution which can alleviate extinction risk. In chapter 4, I review ITV, environmental heterogeneity, and density-dependent processes which constitute local buffer mechanisms. In the light of habitat isolation, which reduces connectivity between populations, local buffer mechanisms may become more relevant compared to dispersal-related regional buffer mechanisms. In this chapter, I argue that capacities, latencies, and interactions of local buffer mechanisms should motivate more process-based and holistic integration of local buffer mechanisms in theoretical and empirical studies.
Recent perspectives propose to apply principles from movement and community ecology to study filamentous fungi. It is an open question whether and how the arrangement and geometry of microstructures select for certain movement traits, and, thus, facilitate coexistence-stabilising niche partitioning. As a coauthor of chapter 5, I developed an agent-based model of hyphal tips navigating in soil-like microstructures along a gradient of soil porosity. By measuring network properties, we identified changes in the optimal movement behaviours along the gradient. Our findings suggest that the soil architecture facilitates niche partitioning.
The core chapters are framed by a general introduction and discussion. In the general introduction, I outline fundamental concepts of movement ecology and describe theory and open questions on sources and consequences of ITV in movement behaviour. In the general discussion, I consolidate the findings of the core chapters and critically discuss their respective value and, if applicable, their impact. Furthermore, I emphasise promising avenues for further research.
Bioelectrochemical investigation of E. coli TMAO reductase and R. capsulatus formate dehydrogenase
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The Arctic region is especially impacted by global warming as temperatures in high latitude regions have increased and are predicted to further rise at levels above the global average. This is crucial to Arctic soils and the shallow shelves of the Arctic Ocean as they are underlain by permafrost. Perennially frozen ground is a habitat for a large number and great diversity of viable microorganisms, which can remain active even under freezing conditions. Warming and thawing of permafrost makes trapped soil organic carbon more accessible to microorganisms. They can transform it to the greenhouse gases carbon dioxide, methane and nitrous oxide. On the other hand, it is assumed that thawing of the frozen ground stimulates microbial activity and carbon turnover. This can lead to a positive feedback loop of warming and greenhouse gas release.
Submarine permafrost covers most areas of the Siberian Arctic Shelf and contains a large though unquantified carbon pool. However, submarine permafrost is not only affected by changes in the thermal regime but by drastic changes in the geochemical composition as it formed under terrestrial conditions and was inundated by Holocene sea level rise and coastal erosion. Seawater infiltration into permafrost sediments resulted in an increase of the pore water salinity and, thus, in thawing of permafrost in the upper sediment layers even at subzero temperatures. The permafrost below, which was not affected by seawater, remained ice-bonded, but warmed through seawater heat fluxes.
The objective of this thesis was to study microbial communities in submarine permafrost with a focus on their response to seawater influence and long-term warming using a combined approach of molecular biological and physicochemical analyses. The microbial abundance, community composition and structure as well as the diversity were investigated in drill cores from two locations in the Laptev Sea, which were subjected to submarine conditions for centuries to millennia. The microbial abundance was measured through total cell counts and copy numbers of the 16S rRNA gene and of functional genes. The latter comprised genes which are indicative for methane production (mcrA) and sulfate reduction (dsrB). The microbial community was characterized by high-throughput-sequencing of the 16S rRNA gene. Physicochemical analyses included the determination of the pore water geochemical and stable isotopic composition, which were used to describe the degree of seawater influence. One major outcome of the thesis is that the submarine permafrost stratified into different so-called pore water units centuries as well as millennia after inundation: (i) sediments that were mixed with seafloor sediments, (ii) sediments that were infiltrated with seawater, and (iii) sediments that were unaffected by seawater. This stratification was reflected in the submarine permafrost microbial community composition only millennia after inundation but not on time-scales of centuries.
Changes in the community composition as well as abundance were used as a measure for microbial activity and the microbial response to changing thermal and geochemical conditions. The results were discussed in the context of permafrost temperature, pore water composition, paleo-climatic proxies and sediment age. The combination of permafrost warming and increasing salinity as well as permafrost warming alone resulted in a disturbance of the microbial communities at least on time-scales of centuries. This was expressed by a loss of microbial abundance and bacterial diversity. At the same time, the bacterial community of seawater unaffected but warmed permafrost was mainly determined by environmental and climatic conditions at the time of sediment deposition. A stimulating effect of warming was observed only in seawater unaffected permafrost after millennia-scale inundation, visible through increased microbial abundance and reduced amounts of substrate.
Despite submarine exposure for centuries to millennia, the community of bacteria in submarine permafrost still generally resembled the community of terrestrial permafrost. It was dominated by phyla like Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes and Proteobacteria, which can be active under freezing conditions.
Moreover, the archaeal communities of both study sites were found to harbor high abundances of marine and terrestrial anaerobic methane oxidizing archaea (ANME). Results also suggested ANME populations to be active under in situ conditions at subzero temperatures. Modeling showed that potential anaerobic oxidation of methane (AOM) could mitigate the release of almost all stored or microbially produced methane from thawing submarine permafrost.
Based on the findings presented in this thesis, permafrost warming and thawing under submarine conditions as well as permafrost warming without thaw are supposed to have marginal effects on the microbial abundance and community composition, and therefore likely also on carbon mobilization and the formation of methane. Thawing under submarine conditions even stimulates AOM and thus mitigates the release of methane.
Bottom-up synthetic biology is used for the understanding of how a cell works. It is achieved through developing techniques to produce lipid-based vesicular structures as cellular mimics. The most common techniques used to produce cellular mimics or synthetic cells is through electroformation and swelling method. However, the abovementioned techniques cannot efficiently encapsulate macromolecules such as proteins, enzymes, DNA and even liposomes as synthetic organelles. This urges the need to develop new techniques that can circumvent this issue and make the artificial cell a reality where it is possible to imitate a eukaryotic cell through encapsulating macromolecules. In this thesis, the aim to construct a cell system using giant unilamellar vesicles (GUVs) to reconstitute the mitochondrial molybdenum cofactor biosynthetic pathway. This pathway is highly conserved among all life forms, and therefore is known for its biological significance in disorders induced through its malfunctioning. Furthermore, the pathway itself is a multi-step enzymatic reaction that takes place in different compartments. Initially, GTP in the mitochondrial matrix is converted to cPMP in the presence of cPMP synthase. Further, produced cPMP is transported across the membrane to the cytosol, to be converted by MPT synthase into MPT. This pathway provides a possibility to address the general challenges faced in the development of a synthetic cell, to encapsulate large biomolecules with good efficiency and greater control and to evaluate the enzymatic reactions involved in the process.
For this purpose, the emulsion-based technique was developed and optimised to allow rapid production of GUVs (~18 min) with high encapsulation efficiency (80%). This was made possible by optimizing various parameters such as density, type of oil, the impact of centrifugation speed/time, lipid concentration, pH, temperature, and emulsion droplet volume. Furthermore, the method was optimised in microtiter plates for direct experimentation and visualization after the GUV formation. Using this technique, the two steps - formation of cPMP from GTP and the formation of MPT from cPMP were encapsulated in different sets of GUVs to mimic the two compartments. Two independent fluorescence-based detection systems were established to confirm the successful encapsulation and conversion of the reactants. Alternatively, the enzymes produced using bacterial expression and measured. Following the successful encapsulation and evaluation of enzymatic reactions, cPMP transport across mitochondrial membrane has been mimicked using GUVs using a complex mitochondrial lipid composition. It was found that the cPMP interaction with the lipid bilayer results in transient pore-formation and leakage of internal contents.
Overall, it can be concluded that in this thesis a novel technique has been optimised for fast production of functional synthetic cells. The individual enzymatic steps of the Moco biosynthetic pathway have successfully implemented and quantified within these cellular mimics.
The plant cell wall plays several crucial roles during plant development with its integrity acting as key signalling component for growth regulation during biotic and abiotic stresses. Cellulose microfibrils, the principal load-bearing components is the major component of the primary cell wall, whose synthesis is mediated by microtubule-associated CELLULOSE SYNTHASE (CESA) COMPLEXES (CSC). Previous studies have shown that CSC interacting proteins COMPANION OF CELLULOSE SYNTHASE (CC) facilitate sustained cellulose synthesis during salt stress by promoting repolymerization of cortical microtubules. However, our understanding of cellulose synthesis during salt stress remains incomplete.
In this study, a pull-down of CC1 protein led to the identification of a novel interactor, termed LEA-like. Phylogenetic analysis revealed that LEA-like belongs to the LATE EMBRYOGENESIS ABUNDANT (LEA) protein family, specifically to the LEA_2 subgroup, showing a close relationship with the CC proteins. Roots of the double mutants lea-like and its closest homolog emb3135 exhibited hypersensitivity when grown on cellulose synthesis inhibitors. Further analysis of higher-order mutants of lea-like, emb3135, and cesa6 demonstrated a genetic interaction between them indicating a significant role in cellulose synthesis.
Live-cell imaging revealed that both LEA-like and EMB3135 migrated with the CSC at the plasma membrane along microtubule tracks in control and oryzalin-treated conditions which destabilize microtubules, suggesting a tight interaction. Investigation of fluorescently labeled lines of different domains of the LEA-like protein revealed that the N-terminal cytosolic domain of LEA-like colocalizes with microtubules, suggesting a physical association between the two.
Considering the established role of LEA proteins in abiotic stress tolerance, we performed phenotypic analysis of the mutant under various stresses. Growth of double mutants of lea-like and emb3135 on NaCl containing media resulted in swelling of root cell indicating a putative role in salt stress tolerance. Supportive of this the quadruple mutant, lacking LEA-like, EMB3135, CC1, and CC2 proteins, exhibited a severe root growth defect on NaCl media compared to control conditions. Live-cell imaging revealed that under salt stress, the LEA-like protein forms aggregates in the plasma membrane.
In conclusion, this study has unveiled two novel interactors of the CSC that act with the CC proteins that regulate plant growth in response to salt stress providing new insights into the intricate regulation of cellulose synthesis, particularly under such conditions.
Macrophages play an integral role for the innate immune system. It is critically important for basic research and therapeutic applications to find approaches to potentially modulate their function as the first line of defense. Transient genetic engineering via delivery of synthetic mRNA can serve for such purposes as a robust, reliable and safe technology to modulate macrophage functions. However, a major drawback particularly in the transfection of sensitive immune cells such as macrophages is the immunogenicity of exogenous IVT-mRNAs. Consequently, the direct modulation of human macrophage activity by mRNA-mediated genetic engineering was the aim of this work. The synthetic mRNA can instruct macrophages to synthesize specific target proteins, which can steer macrophage activity in a tailored fashion. Thus, the focus of this dissertation was to identify parameters triggering unwanted immune activation of macrophages, and to find approaches to minimize such effects. When comparing different carrier types as well as mRNA chemistries, the latter had unequivocally a more pronounced impact on activation of human macrophages and monocytes. Exploratory investigations revealed that the choice of nucleoside chemistry, particularly of modified uridine, plays a crucial role for IVT-mRNA-induced immune activation, in a dose-dependent fashion. Additionally, the contribution of the various 5’ cap structures tested was only minor. Moreover, to address the technical aspects of the delivery of multiple genes as often mandatory for advanced gene delivery studies, two different strategies of payload design were investigated, namely “bicistronic” delivery and “monocistronic” co-delivery. The side-by-side comparison of mRNA co-delivery via a bicistronic design (two genes, one mRNA) with a monocistronic design (two gene, two mRNAs) unexpectedly revealed that, despite the intrinsic equimolar nature of the bicistronic approach, it was outperformed by the monocistronic approach in terms of reliable co-expression when quantified on the single cell level. Overall, the incorporation of chemical modifications into IVT-mRNA by using respective building blocks, primarily with the aim to minimize immune activation as exemplified in this thesis, has the potential to facilitate the selection of the proper mRNA chemistry to address specific biological and clinical challenges. The technological aspects of gene delivery evaluated and validated by the quantitative methods allowed us to shed light on crucial process parameters and mRNA design criteria, required for reliable co-expression schemes of IVT-mRNA delivery.
Elucidating the molecular basis of enhanced growth in the Arabidopsis thaliana accession Bur-0
(2021)
The life cycle of flowering plants is a dynamic process that involves successful passing through several developmental phases and tremendous progress has been made to reveal cellular and molecular regulatory mechanisms underlying these phases, morphogenesis, and growth. Although several key regulators of plant growth or developmental phase transitions have been identified in Arabidopsis, little is known about factors that become active during embryogenesis, seed development and also during further postembryonic growth. Much less is known about accession-specific factors that determine plant architecture and organ size. Bur-0 has been reported as a natural Arabidopsis thaliana accession with exceptionally big seeds and a large rosette; its phenotype makes it an interesting candidate to study growth and developmental aspects in plants, however, the molecular basis underlying this big phenotype remains to be elucidated. Thus, the general aim of this PhD project was to investigate and unravel the molecular mechanisms underlying the big phenotype in Bur-0.
Several natural Arabidopsis accessions and late flowering mutant lines were analysed in this study, including Bur-0. Phenotypes were characterized by determining rosette size, seed size, flowering time, SAM size and growth in different photoperiods, during embryonic and postembryonic development. Our results demonstrate that Bur-0 stands out as an interesting accession with simultaneously larger rosettes, larger SAM, later flowering phenotype and larger seeds, but also larger embryos. Interestingly, inter-accession crosses (F1) resulted in bigger seeds than the parental self-crossed accessions, particularly when Bur-0 was used as the female parental genotype, suggesting parental effects on seed size that might be maternally controlled. Furthermore, developmental stage-based comparisons revealed that the large embryo size of Bur-0 is achieved during late embryogenesis and the large rosette size is achieved during late postembryonic growth. Interestingly, developmental phase progression analyses revealed that from germination onwards, the length of developmental phases during postembryonic growth is delayed in Bur-0, suggesting that in general, the mechanisms that regulate developmental phase progression are shared across developmental phases.
On the other hand, a detailed physiological characterization in different tissues at different developmental stages revealed accession-specific physiological and metabolic traits that underlie accession-specific phenotypes and in particular, more carbon resources during embryonic and postembryonic development were found in Bur-0, suggesting an important role of carbohydrates in determination of the bigger Bur-0 phenotype. Additionally, differences in the cellular organization, nuclei DNA content, as well as ploidy level were analyzed in different tissues/cell types and we found that the large organ size in Bur-0 can be mainly attributed to its larger cells and also to higher cell proliferation in the SAM, but not to a different ploidy level.
Furthermore, RNA-seq analysis of embryos at torpedo and mature stage, as well as SAMs at vegetative and floral transition stage from Bur-0 and Col-0 was conducted to identify accession-specific genetic determinants of plant phenotypes, shared across tissues and developmental stages during embryonic and postembryonic growth. Potential candidate genes were identified and further validation of transcriptome data by expression analyses of candidate genes as well as known key regulators of organ size and growth during embryonic and postembryonic development confirmed that the high confidence transcriptome datasets generated in this study are reliable for elucidation of molecular mechanisms regulating plant growth and accession-specific phenotypes in Arabidopsis.
Taken together, this PhD project contributes to the plant development research field providing a detailed analysis of mechanisms underlying plant growth and development at different levels of biological organization, focusing on Arabidopsis accessions with remarkable phenotypical differences. For this, the natural accession Bur-0 was an ideal outlier candidate and different mechanisms at organ and tissue level, cell level, metabolism, transcript and gene expression level were identified, providing a better understanding of different factors involved in plant growth regulation and mechanisms underlying different growth patterns in nature.
Import and decomposition of dissolved organic carbon in pre-dams of drinking water reservoirs
(2017)
Dissolved organic carbon (DOC) depicts a key component in the aquatic carbon cycle as well as for drinking water production from surface waters. DOC concentrations increased in water bodies of the northern hemisphere in the last decades, posing ecological consequences and water quality problems. Within the pelagic zone of lakes and reservoirs, the DOC pool is greatly affected by biological activity as DOC is simultaneously produced and decomposed. This thesis aimed for a conceptual understanding of organic carbon cycling and DOC quality changes under differing hydrological and trophic conditions. Further, the occurrence of aquatic priming was investigated, which has been proposed as a potential process facilitating the microbial decomposition of stable allochthonous DOC within the pelagic zone.
To study organic carbon cycling under different hydrological conditions, quantitative and qualitative investigations were carried out in three pre-dams of drinking water reservoirs exhibiting a gradient in DOC concentrations and trophic states. All pre-dams were mainly autotrophic in their epilimnia. Discharge and temperature were identified as the key factors regulating net production and respiration in the upper water layers of the pre-dams. Considerable high autochthonous production was observed during the summer season under higher trophic status and base flow conditions. Up to 30% of the total gained organic carbon was produced within the epilimnia. Consequently, this affected the DOC quality within the pre-dams over the year and enhanced characteristics of algae-derived DOC were observed during base flow in summer. Allochthonous derived DOC dominated at high discharges and oligotrophic conditions when production and respiration were low. These results underline that also small impoundments with typically low water residence times are hotspots of carbon cycling, significantly altering water quality in dependence of discharge conditions, temperature and trophic status. Further, it highlights that these factors need to be considered in future water management as increasing temperatures and altered precipitation patterns are predicted in the context of climate change.
Under base flow conditions, heterotrophic bacteria preferentially utilized older DOC components with a conventional radiocarbon age of 195-395 years before present (i.e. before 1950). In contrast, younger carbon components (modern, i.e. produced after 1950) were mineralized following a storm flow event. This highlights that age and recalcitrance of DOC are independent from each other. To assess the ages of the microbially consumed DOC, a simplified method was developed to recover the respired CO2 from heterotrophic bacterioplankton for carbon isotope analyses (13C, 14C). The advantages of the method comprise the operation of replicate incubations at in-situ temperatures using standard laboratory equipment and thus enabling an application in a broad range of conditions.
Aquatic priming was investigated in laboratory experiments during the microbial decomposition of two terrestrial DOC substrates (peat water and soil leachate). Thereby, natural phytoplankton served as a source of labile organic matter and the total DOC pool increased throughout the experiments due to exudation and cell lysis of the growing phytoplankton. A priming effect for both terrestrial DOC substrates was revealed via carbon isotope analysis and mixing models. Thereby, priming was more pronounced for the peat water than for the soil leachate. This indicates that the DOC source and the amount of the added labile organic matter might influence the magnitude of a priming effect. Additional analysis via high-resolution mass spectrometry revealed that oxidized, unsaturated compounds were more strongly decomposed under priming (i.e. in phytoplankton presence). Given the observed increase in DOC concentrations during the experiments, it can be concluded that aquatic priming is not easily detectable via net concentration changes alone and could be considered as a qualitative effect.
The knowledge gained from this thesis contributes to the understanding of aquatic carbon cycling and demonstrated how DOC dynamics in freshwaters vary with hydrological, seasonal and trophic conditions. It further demonstrated that aquatic priming contributes to the microbial transformation of organic carbon and the observed decay of allochthonous DOC during transport in inland waters.
The highly conserved protein complex containing the Target of Rapamycin (TOR) kinase is known to integrate intra- and extra-cellular stimuli controlling nutrient allocation and cellular growth. This thesis describes three studies aimed to understand how TOR signaling pathway influences carbon and nitrogen metabolism in Chlamydomonas reinhardtii. The first study presents a time-resolved analysis of the molecular and physiological features across the diurnal cycle. The inhibition of TOR leads to 50% reduction in growth followed by nonlinear delays in the cell cycle progression. The metabolomics analysis showed that the growth repression is mainly driven by differential carbon partitioning between anabolic and catabolic processes. Furthermore, the high accumulation of nitrogen-containing compounds indicated that TOR kinase controls the carbon to nitrogen balance of the cell, which is responsible for biomass accumulation, growth and cell cycle progression. In the second study the cause of the high accumulation of amino acids is explained. For this purpose, the effect of TOR inhibition on Chlamydomonas was examined under different growth regimes using stable 13C- and 15N-isotope labeling. The data clearly showed that an increased nitrogen uptake is induced within minutes after the inhibition of TOR. Interestingly, this increased N-influx is accompanied by increased activities of nitrogen assimilating enzymes. Accordingly, it was concluded that TOR inhibition induces de-novo amino acid synthesis in Chlamydomonas. The recognition of this novel process opened an array of questions regarding potential links between central metabolism and TOR signaling. Therefore a detailed phosphoproteomics study was conducted to identify the potential substrates of TOR pathway regulating central metabolism. Interestingly, some of the key enzymes involved in carbon metabolism as well as amino acid synthesis exhibited significant changes in the phosphosite intensities immediately after TOR inhibition. Altogether, these studies provide a) detailed insights to metabolic response of Chlamydomonas to TOR inhibition, b) identification of a novel process causing rapid upshifts in amino acid levels upon TOR inhibition and c) finally highlight potential targets of TOR signaling regulating changes in central metabolism. Further biochemical and molecular investigations could confirm these observations and advance the understanding of growth signaling in microalgae.
Daylength is one of several parameters controlling flowering time in many plant species. The day length is perceived in leaves, but how the floral signal is transduced to the shoot apex via the phloem to induce flowering remains to be elucidated. This study aimed at the identification of new candidates involved in the induction of flowering by employing three plant species, Arabidopsis thaliana, Sinapis alba and Brassica napus in combination with transcript profiling by Affymetrix chip hybridization, metabolite profiling by gas chromatography – mass spectrometry and targeted protein analysis using antibodies. All analyses were performed on tissue-specific samples and focused on phloem sap or phloem exudates. To find common transcript and metabolite candidates potentially associated with the floral transition, two independent induction systems in Arabidopsis were used: a photoextension system, whereby plants received fourteen additional hours of light, and a parallel dexamethasone-inducible system, which was centered on the induction of the known flowering gene CONSTANS (CO). Identification of signals preceding the CO cascade was possible using the light extension regime, while downstream events dependent on CO activation were compared in both systems. Altogether, a number of interesting transcript and metabolite candidates were identified in both systems with some degree of overlap. Sinapis alba was used to investigate the universality of the floral signals between species. Comparisons of metabolite data revealed a few common candidates that may prove interesting for further studies. In addition, a targeted approach was carried out to investigate the presence of the Flowering Locus T (FT) protein during different stages of flower development using an antibody. Interesting changes in the sizes of antigens from rape phloem were seen and appeared consistent in Arabidopsis and to a lesser extent in Sinapis. Overall, the broad surveying approaches for transcripts and metabolites used in this study revealed several new potential candidates involved in the induction and/or regulation of flowering. As far as the protein work, additional experiments will reveal the link between FT and floral induction as well as its role in maintaining the floral state using the abovementioned plant species.
Investigating novel potential regulators of phosphate stress responses in Arabidopsis thaliana
(2010)
It is well documented that transcriptionally coordinated genes tend to be functionally related, and that such relationships may be conserved across different species, and even kingdoms. (Ihmels et al., 2004). Such relationships was initially utilized to reveal functional gene modules in yeast and mammals (Ihmels et al., 2004), and to explore orthologous gene functions between different species and kingdoms (Stuart et al., 2003; Bergmann et al., 2004). Model organisms, such as Arabidopsis, are readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer the acquired knowledge from these model organisms to species that are of greater importance to our society. However, due to large gene families in plants, the identification of functional equivalents of well characterized Arabidopsis genes in other plants is a non-trivial task, which often returns erroneous or inconclusive results. In this thesis, concepts of utilizing co-expression networks to help infer (i) gene function, (ii) organization of biological processes and (iii) knowledge transfer between species are introduced. An often overlooked fact by bioinformaticians is that a bioinformatic method is as useful as its accessibility. Therefore, majority of the work presented in this thesis was directed on developing freely available, user-friendly web-tools accessible for any biologist.
Deoxyribonucleic acid (DNA) nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled according to the geometry of their desired target, resulting in optimized binding and/or signaling interactions.
This dissertation covers three main projects. All of them use variations of functionalized DNA nanostructures that act as platform for oligovalent presentation of ligands. The purpose of this work was to evaluate the ability of DNA nanostructures to precisely display different types of functional molecules and to consequently enhance their efficacy according to the concept of multivalency. Moreover, functionalized DNA structures were examined for their suitability in functional screening assays. The developed DNA-based compound ligands were used to target structures in different biological systems.
One part of this dissertation attempted to bind pathogens with small modified DNA nanostructures. Pathogens like viruses and bacteria are known for their multivalent attachment to host cells membranes. By blocking their receptors for recognition and/or fusion with their targeted host in an oligovalent manner, the objective was to impede their ability to adhere to and invade cells. For influenza A, only enhanced binding of oligovalent peptide-DNA constructs compared to the monovalent peptide could be observed, whereas in the case of respiratory syncytial virus (RSV), binding as well as blocking of the target receptors led to an increased inhibition of infection in vitro.
In the final part, the ability of chimeric DNA-peptide constructs to bind to and activate signaling receptors on the surface of cells was investigated. Specific binding of DNA trimers, conjugated with up to three peptides, to EphA2 receptor expressing cells was evaluated in flow cytometry experiments. Subsequently, their ability to activate these receptors via phosphorylation was assessed. EphA2 phosphorylation was significantly increased by DNA trimers carrying three peptides compared to monovalent peptide. As a result of activation, cells underwent characteristic morphological changes, where they "round up" and retract their periphery.
The results obtained in this work comprehensively prove the capability of DNA nanostructures to serve as stable, biocompatible, controllable platforms for the oligovalent presentation of functional ligands. Functionalized DNA nanostructures were used to enhance biological effects and as tool for functional screening of bio-activity. This work demonstrates that modified DNA structures have the potential to improve drug development and to unravel the activation of signaling pathways.
Human-induced alterations of the environment are causing biotic changes worldwide, including the extinction of species and a mixing of once disparate floras and faunas. One type of biological communities that is expected to be particularly affected by environmental alterations are herb layer plant communities of fragmented forests such as those in the west European lowlands. However, our knowledge about current changes in species diversity and composition in these communities is limited due to a lack of adequate long-term studies. In this thesis, I resurveyed the herb layer communities of ancient forest patches in the Weser-Elbe region (NW Germany) after two decades using 175 semi-permanent plots. The general objectives were (i) to quantify changes in plant species diversity considering also between-community (β) and functional diversity, (ii) to determine shifts in species composition in terms of species’ niche breadth and functional traits and (iii) to find indications on the most likely environmental drivers for the observed changes. These objectives were pursued with four independent research papers (Chapters 1-4) whose results were brought together in a General Discussion. Alpha diversity (species richness) increased by almost four species on average, whereas β diversity tended to decrease (Chapter 1). The latter is interpreted as a beginning floristic homogenization. The observed changes were primarily the result of a spread of native habitat generalists that are able to tolerate broad pH and moisture ranges. The changes in α and β diversity were only significant when species abundances were neglected (Chapters 1 and 2), demonstrating that the diversity changes resulted mainly from gains and losses of low-abundance species. This study is one of the first studies in temperate Europe that demonstrates floristic homogenization of forest plant communities at a larger than local scale. The diversity changes found at the taxonomic level did not result in similar changes at the functional level (Chapter 2). The likely reason is that these communities are functionally “buffered”. Single communities involve most of the functional diversity of the regional pool, i.e., they are already functionally rich, while they are functionally redundant among each other, i.e., they are already homogeneous. Independent of taxonomic homogenization, the abundance of 30 species decreased significantly (Chapter 4). These species included 12 ancient forest species (i.e., species closely tied to forest patches with a habitat continuity > 200 years) and seven species listed on the Red List of endangered plant species in NW Germany. If these decreases continue over the next decades, local extinctions may result. This biotic impoverishment would seriously conflict with regional conservation goals. Community assembly mechanisms changed at the local level particularly at sites that experienced disturbance by forest management activities between the sampling periods (Chapter 3). Disturbance altered community assembly mechanisms in two ways: (i) it relaxed environmental filters and allowed the coexistence of different reproduction strategies, as reflected by a higher diversity of reproductive traits at the time of the resurvey, and (ii) it enhanced light availability and tightened competitive filters. These limited the functional diversity with respect to canopy height and selected for taller species. Thirty-one winner and 30 loser species, which had significantly increased or decreased in abundance, respectively, were characterized by various functional traits and ecological performances to find indications on the most likely environmental drivers for the observed floristic changes (Chapter 4). Winner species had higher seed longevity, flowered later in the season and had more often an oceanic distribution compared to loser species. Loser species tended to have a higher specific leaf area, to be more susceptible to deer browsing and to have a performance optimum at higher soil pH values compared to winner species. Multiple logistic regression analyses indicated that disturbances due to forest management interventions were the primary cause of the species shifts. As one of the first European resurvey studies, this study provides indications that an enhanced browsing pressure due to increased deer densities and increasingly warmer winters are important drivers. The study failed to demonstrate that eutrophication and acidification due to atmospheric deposition substantially drive herb layer changes. The restriction of the sample to the most base-rich sites in the region is discussed as a likely reason. Furthermore, the decline of several ancient forest species is discussed as an indication that the forest patches are still paying off their “extinction debt”, i.e., exhibit a delayed response to forest fragmentation.
Transcription factor networks in the initial ohase of drouht stress in rice (Oryza sativa L.)
(2009)
Engineering hyaluronic acid / poly-L-lysine films as a platform for controlling cell behaviour
(2012)
Plant-derived Transcription Factors for Orthologous Regulation of Gene Expression in the Yeast Saccharomyces cerevisiae
Control of gene expression by transcription factors (TFs) is central in many synthetic biology projects where tailored expression of one or multiple genes is often needed. As TFs from evolutionary distant organisms are unlikely to affect gene expression in a host of choice, they represent excellent candidates for establishing orthogonal control systems. To establish orthogonal regulators for use in yeast (Saccharomyces cerevisiae), we chose TFs from the plant Arabidopsis thaliana. We established a library of 106 different combinations of chromosomally integrated TFs, activation domains (yeast GAL4 AD, herpes simplex virus VP64, and plant EDLL) and synthetic promoters harbouring cognate cis-regulatory motifs driving a yEGFP reporter. Transcriptional output of the different driver / reporter combinations varied over a wide spectrum, with EDLL being a considerably stronger transcription activation domain in yeast, than the GAL4 activation domain, in particular when fused to Arabidopsis NAC TFs. Notably, the strength of several NAC - EDLL fusions exceeded that of the strong yeast TDH3 promoter by 6- to 10-fold. We furthermore show that plant TFs can be used to build regulatory systems encoded by centromeric or episomal plasmids. Our library of TF – DNA-binding site combinations offers an excellent tool for diverse synthetic biology applications in yeast.
COMPASS: Rapid combinatorial optimization of biochemical pathways based on artificial transcription factors
We established a high-throughput cloning method, called COMPASS for COMbinatorial Pathway ASSembly, for the balanced expression of multiple genes in Saccharomyces cerevisiae. COMPASS employs orthogonal, plant-derived artificial transcription factors (ATFs) for controlling the expression of pathway genes, and homologous recombination-based cloning for the generation of thousands of individual DNA constructs in parallel. The method relies on a positive selection of correctly assembled pathway variants from both, in vivo and in vitro cloning procedures. To decrease the turnaround time in genomic engineering, we equipped COMPASS with multi-locus CRISPR/Cas9-mediated modification capacity. In its current realization, COMPASS allows combinatorial optimization of up to ten pathway genes, each transcriptionally controlled by nine different ATFs spanning a 10-fold difference in expression strength. The application of COMPASS was demonstrated by generating cell libraries producing beta-carotene and co-producing beta-ionone and biosensor-responsive naringenin. COMPASS will have many applications in other synthetic biology projects that require gene expression balancing.
CaPRedit: Genome editing using CRISPR-Cas9 and plant-derived transcriptional regulators for the redirection of flux through the FPP branch-point in yeast. Technologies developed over the past decade have made Saccharomyces cerevisiae a promising platform for production of different natural products. We developed CRISPR/Ca9- and plant derived regulator-mediated genome editing approach (CaPRedit) to greatly accelerate strain modification and to facilitate very low to very high expression of key enzymes using inducible regulators. CaPRedit can be implemented to enhance the production of yeast endogenous or heterologous metabolites in the yeast S. cerevisiae. The CaPRedit system aims to faciltiate modification of multiple targets within a complex metabolic pathway through providing new tools for increased expression of genes encoding rate-limiting enzymes, decreased expression of essential genes, and removed expression of competing pathways. This approach is based on CRISPR/Cas9-mediated one-step double-strand breaks to integrate modules containing IPTG-inducible plant-derived artificial transcription factor and promoter pair(s) in a desired locus or loci. Here, we used CaPRedit to redirect the yeast endogenous metabolic flux toward production of farnesyl diphosphate (FPP), a central precursor of nearly all yeast isoprenoid products, by overexpression of the enzymes lead to produce FPP from glutamate. We found significantly higher beta-carotene accumulation in the CaPRedit-mediated modified strain than in the wild type (WT) strain. More specifically, CaPRedit_FPP 1.0 strain was generated, in which three genes involved in FPP synthesis, tHMG1, ERG20, and GDH2, were inducibly overexpressed under the control of strong plant-derived ATFPs. The beta–carotene accumulated in CaPRedit_FPP 1.0 strain to a level 1.3-fold higher than the previously reported optimized strain that carries the same overexpressed genes (as well as additional genetic modifications to redirect yeast endogenous metabolism toward FPP production). Furthermore, the genetic modifications implemented in CaPRedit_FPP 1.0 strain resulted in only a very small growth defect (growth rate relative to the WT is ~ -0.03).
Weakly electric mormyrid fish comprise about 200 species. 15 species of the genus Campylomormyrus have been described. These are very diverse concerning the trunk-like snout and the shape and duration of the electric organ discharge (EOD) and the anatomy of the electric organ. In this dissertation data on the reproduction in captivity of four species and on the ontogeny of the EOD and the EO of three species are presented.
Reproduction of the four species C. compressirostris, C. rhynchophorus, C. tshokwe and C. numenius: Cyclical reproduction was provoked by changing only water conductivity (C): decreasing C led to gonadal recrudescence, an increase induced gonad regression. Data on the reproduction and development of three species are presented (in C. numenius gonad development could only be achieved in males). Agonistic behavior in the C. tshokwe pair forced us to divide the breeding tank; therefore, only ovipositions occurred. However, injection of an artificial GnRH hormone allowed us to obtain ripe eggs and sperm and to perform successful artificial reproduction. All three species (C. compressirostris, C. rhynchophorus, C. tshokwe) are indeterminate fractional spawners. Spawnings/ovipositions occurred during the second half of the night; no parental care was observed; no special spawning substrates were necessary. C. compressirostris successfully spawned in breeding groups, C. rhynchophorus as pair. Spawning intervals ranged from 6 to 66 days in C. rhynchophorus, 10–75 days in C. tshokwe, and 18 days in C. compressirostris (calculated values). Fecundities (eggs per fractional spawning) ranged from 70 to 1570 eggs in C. rhynchophorus, 100–1192 in C. tshokwe, and 38–246 in C. compressirostris. All three species produce yolky, slightly sticky eggs. Egg diameter ranges from 2.3–3.0 mm. Hatching occurred on day 3, feeding started on day 11. Transition from larval to juvenile stage occurred at around 20 mm total length (TL). At this size C. rhynchophorus developed a higher body than the two other species and differences between the species in the melanin pigmentation of the unpaired fins occurred. Between 32 and 35 mm TL the upper and lower jaws developed.
C. compressirostris and C. tamandua are similar in morphology and both produce short EODs of ca. 150-200 μs duration. Both species reproduce easily in captivity. We tried to obtain natural hybrids in two breeding groups, 1) four males of C. compressirostris and three females of C. tamandua and 2) six females of C. compressirostris and four males of C. tamandua. In both combinations several times oviposition occurred, however, we never found fertilized eggs. In subsequent experiments, not described here, we obtained hybrids between these two species by means of artificial reproduction.
Ontogeny of the EOD and the EO: The Campylomormyrus species are very diverse both concerning the shape and the duration of their EODs. There are species with very short EODs, e.g. C. compressirostris duration, a species with an EOD length of about 4-8 ms duration (C. tshokwe) and species with very long EODs of about 25 ms duration (e.g. C. rhynchophorus). Due to the successful breeding of the three species in captivity, we were able to investigate in detail the ontogeny of the EOD. Larvae of the three species C. compressirostris, C. tshokwe and C. rhynchophorus first produce a biphasic larval EOD typical for these small larvae. The first activity of the adult electric organ in the caudal peduncle is a biphasic juvenile EOD. Juvenile C. compressirostris and C. tshokwe start out with a short biphasic EOD of about 160 – 200 μs duration at sizes between 25 mm (C. compressirostris) and 37 mm (C. tshokwe). Adult C. compressirostris show an EOD identical to that of the juvenile. In C. tshokwe, the juvenile EOD changes continuously during development both concerning duration, amplitude increase and shape. 18 cm long C. tshokwe still do not yet produce an EOD typical for the adult fish. Juveniles of C. rhynchophorus produce at 33 mm total length a juvenile biphasic EOD, however, of longer duration (about 640 μs) than the two species mentioned above. This juvenile EOD changes continuously both in form, amplitude increase and duration with growth until the adult EOD waveform appears at about 15 cm body length. In juveniles about seven cm long the triphasic feature of the EOD starts to develop due to the appearance of a second head positive phase. Specific EOD stages are produced in relation to size and not to age. Individual differences in the EOD both concerning shape and duration are very small. The basic anatomy of the electrocytes is very similar in all three species: the main stalk which receives the innervation, is located at the caudal face of the electrocyte. Membrane penetrations of the stalks do not occur. However, there are differences in the fine structure of the electrocytes in the three species. Papillae, proliferations of the membrane, which increase the surface area of the electrocyte and are thought to incrase the EOD-duration, are only found in C. tshokwe and C. rhynchophorus. In these two species in addition, holes develop in the electrocytes during ontogeny. This might also have an impact on EOD duration.
The Annamites mountain range of Southeast Asia which runs along the border of Viet Nam and Laos is an important biodiversity hotspot with high levels of endemism. However, that biodiversity is threatened by unsustainable hunting, and many protected areas across the region have been emptied of their wildlife. To better protect the unique species in the Annamites, it is crucial to have a better understanding of their ecology and distribution. Additionally, basic genetic information is needed to provide conservation stakeholders with essential information to facilitate conservation breeding and counteract the illegal wildlife trade. To date, this baseline information is lacking for many Annamites species.
This thesis aims to assess the effectiveness of using non-invasive collection methods, i.e. camera-trap surveys and leech-derived wildlife host DNA, in order to improve and enhance our understanding of ecology, distribution, and genetic diversity of the Annamites terrestrial mammals.
In chapter 1, we analysed data from a systematic landscape camera-trap survey using single-species occupancy models to assess the ecology and distribution of two little-known Annamite endemics, the Annamite dark muntjac (Muntiacus rooseveltorum / truongsonensis) and Annamite striped rabbit (Nesolagus timminsi), in multiple protected areas across the Annamites. This chapter provided the first in-depth information on their ecology, as well as distribution patterns at large spatial scales. Most notably, we found that the Annamite dark muntjac was predominantly found at higher elevations, while responses to elevation varied among study areas for the Annamite striped rabbit. We estimated occupancy probabilities for both endemics by using their responses to environmental and anthropogenic influences and used this information to make recommendations for targeted conservation actions. We discuss how the approach we used for these two Annamites endemics can be expanded for other little-known and threatened species in other tropical regions.
As is the case with ecology and distribution, very little is known about the genetic diversity of the Annamite striped rabbit and other mammals of the Annamites. This poor understanding is mainly attributed to the lack of a comprehensive DNA sample collection that covers the species’ entire distribution range, which is believed to be a consequence of the low density of mammals or the remoteness of species’ habitat. In order to overcome the difficulties when trying to collect DNA samples from elusive mammals, we applied invertebrate-derived DNA (iDNA) sampling via hematophagous leeches to indirectly obtain genetic materials of their terrestrial host mammals.
In chapter 2, leech-derived DNA was used to study the genetic diversity of the Annamite striped rabbit population. By analysing the DNA extracted from leech samples collected at multiple study areas of the central Annamites, we found a genetic variation with five haplotypes among nine obtained sequences. Despite this diversity, we found no clear phylogeographic pattern among the lagomorph’s populations in central Annamites. The findings have direct conservation implications for the species, as local stakeholders are currently establishing a conservation rescue and breeding facility for Annamite endemic species. Thus our results suggested that Annamite striped rabbits from multiple protected areas in central Annamites can be used as founders for the breeding program.
In chapter 3, the genetic material of six mammals, which are frequently found in Indochina's illegal wildlife trade, was extracted from leeches collected at six study sites across the Anamites. Species-specific genetic markers were used to obtain DNA fragments that were analysed together with Genbank reference sequences from other parts of the species’ distribution range. Our results showed that invertebrate-derived DNA can be used to fill the sampling gaps and provide genetic reference data that is needed for conservation breeding programmes or to counteract the illegal wildlife trade.
Overal, this dissertation provides the first insights in the ecology, distribution, and genetics of rare and threatened species of the Annamites by utilising camera traps and leech-derived DNA as two non-invasive collection methods. This information is essential for improving conservation efforts of local stakeholders and managers, especially for the Annamite endemics. Results in this dissertation also show the effectiveness of both non-invasive methods for studying terrestrial mammals at a landscape level. By expanding the application of these methods to other protected areas across the Annamites, we will further our understanding of ecology, distribution, and genetics of Annamite endemics. With such landscape-scale surveys, we are able to provide stakeholders with an overview of the current status of wildlife in the Annamites which supports efforts to protect these secretive species from illegal hunting and thus their extinction.
Pectic polysaccharides, a class of plant cell wall polymers, form one of the most complex networks known in nature. Despite their complex structure and their importance in plant biology, little is known about the molecular mechanism of their biosynthesis, modification, and turnover, particularly their structure-function relationship. One way to gain insight into pectin metabolism is the identification of mutants with an altered pectin structure. Those were obtained by a recently developed pectinase-based genetic screen. Arabidopsis thaliana seedlings grown in liquid medium containing pectinase solutions exhibited particular phenotypes: they were dwarfed and slightly chlorotic. However, when genetically different A. thaliana seed populations (random T-DNA insertional populations as well as EMS-mutagenized populations and natural variations) were subjected to this treatment, individuals were identified that exhibit a different visible phenotype compared to wild type or other ecotypes and may thus contain a different pectin structure (pec-mutants). After confirming that the altered phenotype occurs only when the pectinase is present, the EMS mutants were subjected to a detailed cell wall analysis with particular emphasis on pectins. This suite of mutants identified in this study is a valuable resource for further analysis on how the pectin network is regulated, synthesized and modified. Flanking sequences of some of the T-DNA lines have pointed toward several interesting genes, one of which is PEC100. This gene encodes a putative sugar transporter gene, which, based on our data, is implicated in rhamnogalacturonan-I synthesis. The subcellular localization of PEC100 was studied by GFP fusion and this protein was found to be localized to the Golgi apparatus, the organelle where pectin biosynthesis occurs. Arabidopsis ecotype C24 was identified as a susceptible one when grown with pectinases in liquid culture and had a different oligogalacturonide mass profile when compared to ecotype Col-0. Pectic oligosaccharides have been postulated to be signal molecules involved in plant pathogen defense mechanisms. Indeed, C24 showed elevated accumulation of reactive oxygen species upon pectinase elicitation and had altered response to the pathogen Alternaria brassicicola in comparison to Col-0. Using a recombinant inbred line population three major QTLs were identified to be responsible for the susceptibility of C24 to pectinases. In a reverse genetic approach members of the qua2 (putative pectin methyltransferase) family were tested for potential target genes that affect pectin methyl-esterification. The list of these genes was determined by in silico study of the pattern of expression and co-expression of all 34 members of this family resulting in 6 candidate genes. For only for one of the 6 analyzed genes a difference in the oligogalacturonide mass profile was observed in the corresponding knock-out lines, confirming the hypothesis that the methyl-esterification pattern of pectin is fine tuned by members of this gene family. This study of pectic polysaccharides through forward and reverse genetic screens gave new insight into how pectin structure is regulated and modified, and how these modifications could influence pectin mediated signalling and pathogenicity.
Arabidopsis thaliana trichomes exhibit strong birefringence under polarized light, a characteristic of cell walls containing large amounts of highly ordered cellulose microfibrils. The tbr1 mutant of Arabidopsis lacks trichome birefringence and is deficient in secondary cell wall cellulose synthesis (Potikha and Delmer, 1995). The TBR gene was identified by recombinational mapping, candidate gene sequencing and molecular complementation using genomic cosmid clones, as well as a p35S:TBR genomic DNA construct, fully rescuing the mutant phenotype in both cases. The only mutant allele available (tbr-1) carries a substitution (G to E) in a conserved aminoacid domain of the protein. TBR gene structure was proved to have a longer size than the one found to be annotated at the time of identification in the data-base. A full cDNA clone containing the full transcript was available and also complementation experiments using different gene fragments (annotated and suggested) leaded to the result that TBR gene is indeed, longer. TBR encodes a novel plant-specific protein with predicted plasma membrane localization, therefore being consistent with idea that is required for-, or is a novel component of a functional cellulose synthase complex. TBR is part of an Arabidopsis gene/protein family, (TBL-trichome birefringence like) which, depending on homology, comprises up to 20 members, none of which has a biological or biochemical function attributed. T-DNA insertion lines in TBR gene and two close homologues have been screened by PCR, but no homozygous were found and no trichomes phenotype was identified. Promoter-GUS lines were produced for TBR, as well as for its two closest homologues (one being a segmentally duplicated gene on chromosome III), using 1.6-2 kb of promoter sequence upstream of the annotated start codons. The TBR promoter was the only one of the three that yielded trichome expression, this probably explaining the phenotype of the TBR mutant. Moreover, TBR is expressed in leaves, in growing lateral roots, and in vascular tissues of young Arabidopsis seedlings and plantlets. Later on, the expression appears in inflorescens, stems, flowers and green siliques. This expression pattern is largely overlapping with those of the two analyzed homologues and it corresponds with data of RT-PCR expression profiling performed for TBR and the two analyzed homologues in different tissues, at different developmental stages. Biochemical analysis of cell wall (leaves and trichomes), as GC and MALDI-TOF, were performed, but revealed no major differences between tbr1 and wild type plants. Scanning electron microscopy analysis and cell wall polysaccharides antibody labeling showed a clear difference in the trichomes cell wall structure between mutant plant and wild type.
Functional metabolism of storage carbohydrates is vital to plants and animals. The water-soluble glycogen in animal cells and the amylopectin which is the major component of water-insoluble starch granules residing in plant plastids are chemically similar as they consist of α-1,6 branched α-1,4 glucan chains. Synthesis and degradation of transitory starch and of glycogen are accomplished by a set of enzymatic activities that to some extend are also similar in plants and animals. Chain elongation, branching, and debranching are achieved by synthases, branching enzymes, and debranching enzymes, respectively. Similarly, both types of polyglucans contain low amounts of phosphate esters whose abundance varies depending on species and organs. Starch is selectively phosphorylated by at least two dikinases (GWD and PWD) at the glucosyl carbons C6 and C3 and dephosphorylated by the phosphatase SEX4 and SEX4-like enzymes. In Arabidopsis insufficiency in starch phosphorylation or dephosphorylation results in largely impaired starch turnover, starch accumulation, and often in retardation of growth. In humans the progressive neurodegenerative epilepsy, Lafora disease, is the result of a defective enzyme (laforin) that is functional equivalent to the starch phosphatase SEX4 and capable of glycogen dephosphorylation. Patients lacking laforin progressively accumulate unphysiologically structured insoluble glycogen-derived particles (Lafora bodies) in many tissues including brain. Previous results concerning the carbon position of glycogen phosphate are contradictory. Currently it is believed that glycogen is esterified exclusively at the carbon positions C2 and C3 and that the monophosphate esters, being incorporated via a side reaction of glycogen synthase (GS), lack any specific function but are rather an enzymatic error that needs to be corrected. In this study a versatile and highly sensitive enzymatic cycling assay was established that enables quantification of very small G6P amounts in the presence of high concentrations of non-target compounds as present in hydrolysates of polysaccharides, such as starch, glycogen, or cytosolic heteroglycans in plants. Following validation of the G6P determination by analyzing previously characterized starches G6P was quantified in hydrolysates of various glycogen samples and in plant heteroglycans. Interestingly, glucosyl C6 phosphate is present in all glycogen preparations examined, the abundance varying between glycogens of different sources. Additionally, it was shown that carbon C6 is severely hyperphosphorylated in glycogen of Lafora disease mouse model and that laforin is capable of removing C6 phosphate from glycogen. After enrichment of phosphoglucans from amylolytically degraded glycogen, several techniques of two-dimensional NMR were applied that independently proved the existence of 6-phosphoglucosyl residues in glycogen and confirmed the recently described phosphorylation sites C2 and C3. C6 phosphate is neither Lafora disease- nor species-, or organ-specific as it was demonstrated in liver glycogen from laforin-deficient mice and in that of wild type rabbit skeletal muscle. The distribution of 6-phosphoglucosyl residues was analyzed in glycogen molecules and has been found to be uneven. Gradual degradation experiments revealed that C6 phosphate is more abundant in central parts of the glycogen molecules and in molecules possessing longer glucan chains. Glycogen of Lafora disease mice consistently contains a higher proportion of longer chains while most short chains were reduced as compared to wild type. Together with results recently published (Nitschke et al., 2013) the findings of this work completely unhinge the hypothesis of GS-mediated phosphate incorporation as the respective reaction mechanism excludes phosphorylation of this glucosyl carbon, and as it is difficult to explain an uneven distribution of C6 phosphate by a stochastic event. Indeed the results rather point to a specific function of 6-phosphoglucosyl residues in the metabolism of polysaccharides as they are present in starch, glycogen, and, as described in this study, in heteroglycans of Arabidopsis. In the latter the function of phosphate remains unclear but this study provides evidence that in starch and glycogen it is related to branching. Moreover a role of C6 phosphate in the early stages of glycogen synthesis is suggested. By rejecting the current view on glycogen phosphate to be a stochastic biochemical error the results permit a wider view on putative roles of glycogen phosphate and on alternative biochemical ways of glycogen phosphorylation which for many reasons are likely to be mediated by distinct phosphorylating enzymes as it is realized in starch metabolism of plants. Better understanding of the enzymology underlying glycogen phosphorylation implies new possibilities of Lafora disease treatment.
Plants possess cell wall, a polysaccharide exoskeleton which encompasses all plant cells. Cell wall gives plant cells mechanical support, defines their shape, enables growth and water transport through a plant. It also has important role in communication with the external environment. Regulation of plant cell wall biosynthesis and cell and organ morphogenesis depends on cell’s ability to detect mechanical signals originating both from the external environment and from internal plant tissues. Thanks to the presence of the cell wall, all living plant cells develop constant internal pressure generated by the active water uptake, known as turgor pressure, which enables them to grow. Thus, actively growing cells in the tissue are exerting mechanical stress to each other. In order to properly coordinate cell growth, tissue morphogenesis and maintain cell-to-cell adhesion, plant cell have to detect these mechanical signals. That is performed by a group of still not well enough characterized plant mechanosensitive proteins. Mechanosensors are proteins capable of detecting changes in mechanical stress patterns and translating them into physiological and developmental outputs. One of plant mechanosensitive proteins, DEFECTIVE KERNEL1 (DEK1) has shown to be a very important in proper plant development. DEK1 bears similarity with animal cysteine proteases of Calpain superfamily. DEK1 is very important for plant development since all null alleles are embryo lethal. During the last 20 years of DEK1 studies, this protein has proven to be a very difficult for different molecular and biochemical manipulations. As a consequence, very little is known about its direct target proteins. Wang and co-workers (2003) and Johnson and co-workers (2008) have given a valuable contribution to biochemical understanding of DEK1 by determining that it functions as Cys-protease in similar way as animal calpains. However, a lot of indirect knowledge was gathered about the effects of disruption and modulation of DEK1 activity. DEK1 is important for proper organ development, epidermal specification, and maintenance. However, some studies have inferred that DEK1 affects expression of different cell wall related genes, and it regulates cell-to-cell adhesion in epidermal cells. This led to two extensive studies (Amanda et al., 2016, 2017) which demonstrated importance of DEK1 in regulation leaf epidermal cell walls in A. thaliana mature leaves and inflorescence stems. These studies demonstrated that DEK1 also influences cell wall thickness and cell-to-cell adhesion and that it could potentially regulate cell growth and expansion. Building up on this research, we decided to try to further characterize molecular and biomechanical aspects of DEK1 mediated cell wall regulation, with special emphasis on regulation of cellulose synthesis. We used two mutant lines, with modulated DEK1 activity, a constitutive overexpressor for DEK1 CALPAIN domain and a point mutant in CALPAIN domain, dek1-4. In Chapter 3 we demonstrated that DEK1 regulates dynamics of Cellulose Synthase Complexes (CSCs). Both lines showed decreased crystalline cellulose contents. This led us to investigate if velocity of CSCs in cotyledons, was affected, since it is known that changes in cellulose contents are often caused by defects in CSC. We found that bothDEK1 modulated lines we used have significantly decreased velocity of CSCs. We have also examined plasma membrane turnover rates of CSCs and found out that after photo-bleaching OE CALPAIN has much faster recovery rates compared to Col-0 wild type, while dek1-4 has lower exocytotic rates of CSCs, and much longer life-time of CSCs inserted into the plasma membrane. These results suggested that DEK1 regulates different aspects of CSC dynamics, possibly through interaction with different regulatory proteins. Decrease in cellulose contents we observed in DEK1 modulated lines, prompted us to investigate how this reflects biomechanics and structural properties of epidermal cotyledon cell walls of DEK1 modulated lines, which is described in Chapter 4. To achieve this, we developed a novel microdissection method for isolation and mechanical and structural characterization of native epidermal cell wall monolayers using atomic force microscopy (AFM). AFM force spectroscopy assays showed that both DEK1 modulated lines had stiffer cell walls compared to Col-0. This was awkward since we initially detected decrease in crystalline cellulose which implied decrease in cell wall stiffness. However, subsequent high-resolution AFM imaging has revealed that DEK1 modulate lines cells walls have their cellulose microfibrils organized in thicker bundles than Col-0. Also, polysaccharide composition analysis has revealed that DEK1 modulated lines have increased abundance of pectins, which could also be responsible for the observed increase in cell wall stiffness. Previous work has shown that different dek1 mutants and modulated lines have defects in cell-to-cell adhesion. This implied that DEK1 may be involved in sensing and/or maintaining cell wall integrity (CWI). We performed several growth assays to determine role of DEK1 in CWI, which is described in Chapter 5. We performed cellulose synthesis perturbation assays with cellulose synthesis inhibitor Isoxaben and obtained very interesting results. While OE CALPAIN plants were hypersensitive to Isoxaben, dek1-4 has shown complete insensitivity. Furthermore, a regular CWI maintenance response, reported in A. thaliana as result of compromised CWI, ectopic lignification in seedlings’ roots was absent in both DEK1 modulated lines we examined. We detected interesting growth response of DEK1 lines to NaCl and mannitol treatments as well. Although these findings are pointing out that DEK1 could be part of CWI signalling pathways, more experiments are necessary to fully elucidate possible role of DEK1 in CWI sensing and/or maintenance pathways, especially to check if DEK1 is interacting with Catharanthus roseus Receptor Like Kinase group of CWI sensors. Studies on 4-month old short day grown DEK1 modulated lines, have shown defects in branching, with development of fasciated stem branches in a DEK1 modulated line overexpressing CALPAIN domain (Amanda et al., 2017). This result pointed out to a possibility that DEK1 may regulate organ morphogenesis and patterning at the level of shoot apical meristem (SAM). Work towards elucidating role of DEK1 in SAM maintenance and organ patterning is detailed in Chapter 6. We determined that OE CALPAIN had significantly larger central zone of SAM as well as larger individual SAM cells in central zone, as well as higher distribution of cell sizes, implying possible cell expansion defects. dek1-4 did not exhibited changes in SAM central zone size or individual stem cell size, but it seemed that it had increased number of stem cells in SAM central zone. Both DEK1 lines had perturbation of phyllotaxis on SAM level, with disturbed divergence angles between floral primordia. Disturbed phyllotaxis was also observed between siliques, in mature plants. In addition to this, OE CALPAIN has exhibited occurrence of multiple (up to four) siliques growing from a single stem node. All this is pointing out that DEK1 might participate in hormone-signalling in the SAM.. DEK1 is a highly intriguing protein. However, since it is a unigene, and in addition to that, a regulatory protease, it probably participates in multiple signalling pathways, which makes understanding its function much more complicated.
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.
Water is essential to life and thus, an essential resource. However, freshwater resources are limited and their maintenance is crucial. Pollution with chemicals and pathogens through urbanization and a growing population impair the quality of freshwater. Furthermore, water can serve as vector for the transmission of pathogens resulting in water-borne illness.
The Interdisciplinary Research Group III – "Water" of the Leibniz alliance project INFECTIONS‘21 investigated water as a hub for pathogens focusing on Clostridioides difficile and avian influenza A viruses that may be shed into the water. Another aim of this study was to characterize the bacterial communities in a wastewater treatment plant (WWTP) of the capital Berlin, Germany to further assess potential health risks associated with wastewater management practices.
Bacterial communities of WWTP inflow and effluent differed significantly. The proportion of fecal/enteric bacteria was relatively low and OTUs related to potential enteric pathogens were largely removed from inflow to effluent. However, a health risk might exist as an increased relative abundance of potential pathogenic Legionella spp. such as L. lytica was observed. Three Clostridioides difficile isolates from wastewater inflow and an urban bathing lake in Berlin (‗Weisser See‘) were obtained and sequenced. The two isolates from the wastewater did not carry toxin genes, whereas the isolate from the lake was positive for the toxin genes. All three isolates were closely related to human strains. This indicates a potential, but rather sporadic health risk. Avian influenza A viruses were detected in 38.8% of sediment samples by PCR, but virus isolation failed. An experiment with inoculated freshwater and sediment samples showed that virus isolation from sediment requires relatively high virus concentrations and worked much better in Madin-Darby Canine Kidney (MDCK) cell cultures than in embryonated chicken eggs, but low titre of influenza contamination in freshwater samples was sufficient to recover virus.
In conclusion, this work revealed potential health risks coming from bacterial groups with pathogenic potential such as Legionella spp. whose relative abundance is higher in the released effluent than in the inflow of the investigated WWTP. It further indicates that water bodies such as wastewater and lake sediments can serve as reservoir and vector, even for non-typical water-borne or water-transmitted pathogens such as C. difficile.
Climate change and human-driven eutrophication promote the spread of harmful cyanobacteria blooms in lakes worldwide, which affects water quality and impairs the aquatic food chain. In recent times, sedimentary ancient DNA-based (sedaDNA) studies were used to probe how centuries of climate and environmental changes have affected cyanobacterial assemblages in temperate lakes. However, there is a lack of information on the consistency between sediment-deposited cyanobacteria communities versus those of the water column, and on the individual role of natural climatic changes versus human pressure on cyanobacteria community dynamics over multi-millennia time scales.
Therefore, this thesis uses sedimentary ancient DNA of Lake Tiefer See in northeastern Germany to trace the deposition of cyanobacteria along the water column into the sediment, and to reconstruct cyanobacteria communities spanning the last 11,000 years using a set of molecular techniques including quantitative PCR, biomarkers, metabarcoding, and metagenome sequence analyses.
The results of this thesis proved that cyanobacterial composition and species richness did not significantly differ among different water depths, sediment traps, and surface sediments. This means that the cyanobacterial community composition from the sediments reflects the water column communities. However, there is a skewed sediment deposition of different cyanobacteria groups because of DNA alteration and/or deterioration during transport along the water column to the sediment. Specifically, single filament taxa, such as Planktothrix, are poorly represented in sediments despite being abundant in the water column as shown by an additional study of the thesis on cyanobacteria seasonality. In contrast, aggregate-forming taxa, like Aphanizomenon, are relatively overrepresented in sediment although they are not abundant in the water column. These different deposition patterns of cyanobacteria taxa should be considered in future DNA-based paleolimnological investigations. The thesis also reveals a substantial increase in total cyanobacteria abundance during the Bronze Age which is not apparent in prior phases of the early to middle Holocene and is suggested to be caused by human farming, deforestation, and excessive nutrient addition to the lake. Not only cyanobacterial abundance was influenced by human activity but also cyanobacteria community composition differed significantly between phases of no, moderate, and intense human impact.
The data presented in this thesis are the first on sedimentary cyanobacteria DNA since the early Holocene in a temperate lake. The results bring together archaeological, historical climatic, and limnological data with deep DNA-sequencing and paleoecology to reveal a legacy impact of human pressure on lake cyanobacteria populations dating back to approximately 4000 years.
Plants can be primed to survive the exposure to a severe heat stress (HS) by prior exposure to a mild HS. The information about the priming stimulus is maintained by the plant for several days. This maintenance of acquired thermotolerance, or HS memory, is genetically separable from the acquisition of thermotolerance itself and several specific regulatory factors have been identified in recent years.
On the molecular level, HS memory correlates with two types of transcriptional memory, type I and type II, that characterize a partially overlapping subset of HS-inducible genes. Type I transcriptional memory or sustained induction refers to the sustained transcriptional induction above non-stressed expression levels of a gene for a prolonged time period after the end of the stress exposure. Type II transcriptional memory refers to an altered transcriptional response of a gene after repeated exposure to a stress of similar duration and intensity. In particular, enhanced re-induction refers to a transcriptional pattern in which a gene is induced to a significantly higher degree after the second stress exposure than after the first.
This thesis describes the functional characterization of a novel positive transcriptional regulator of type I transcriptional memory, the heat shock transcription factor HSFA3, and compares it to HSFA2, a known positive regulator of type I and type II transcriptional memory. It investigates type I transcriptional memory and its dependence on HSFA2 and HSFA3 for the first time on a genome-wide level, and gives insight on the formation of heteromeric HSF complexes in response to HS. This thesis confirms the tight correlation between transcriptional memory and H3K4 hyper-methylation, reported here in a case study that aimed to reduce H3K4 hyper-methylation of the type II transcriptional memory gene APX2 by CRISPR/dCas9-mediated epigenome editing. Finally, this thesis gives insight into the requirements for a heat shock transcription factor to function as a positive regulator of transcriptional memory, both in terms of its expression profile and protein abundance after HS and the contribution of individual functional domains.
In summary, this thesis contributes to a more detailed understanding of the molecular processes underlying transcriptional memory and therefore HS memory, in Arabidopsis thaliana.
Chloroplasts as bioreactors : high-yield production of active bacteriolytic protein antibiotics
(2008)
Plants, more precisely their chloroplasts with their bacterial-like expression machinery inherited from their cyanobacterial ancestors, can potentially offer a cheap expression system for proteinaceous pharmaceuticals. This system would be easily scalable and provides appropriate safety due to chloroplasts maternal inheritance. In this work, it was shown that three phage lytic enzymes (Pal, Cpl-1 and PlyGBS) could be successfully expressed at very high levels and with high stability in tobacco chloroplasts. PlyGBS expression reached an amount of foreign protein accumulation (> 70% TSP) that has never been obtained before. Although the high expression levels of PlyGBS caused a pale green phenotype with retarded growth, presumably due to exhaustion of plastid protein synthesis capacity, development and seed production were not impaired under greenhouse conditions. Since Pal and Cpl-1 showed toxic effects when expressed in E. coli, a special plastid transformation vector (pTox) was constructed to allow DNA amplification in bacteria. The construction of the pTox transformation vector allowing a recombinase-mediated deletion of an E. coli transcription block in the chloroplast, leading to an increase of foreign protein accumulation to up to 40% of TSP for Pal and 20% of TSP for Cpl-1. High dose-dependent bactericidal efficiency was shown for all three plant-derived lytic enzymes using their pathogenic target bacteria S. pyogenes and S. pneumoniae. Confirmation of specificity was obtained for the endotoxic proteins Pal and Cpl-1 by application to E. coli cultures. These results establish tobacco chloroplasts as a new cost-efficient and convenient production platform for phage lytic enzymes and address the greatest obstacle for clinical application. The present study is the first report of lysin production in a non-bacterial system. The properties of chloroplast-produced lysins described in this work, their stability, high accumulation rate and biological activity make them highly attractive candidates for future antibiotics.
Uncovering the interplay between nutrient availability and cellulose biosynthesis inhibitor activity
(2022)
All plant cells are surrounded by a dynamic, carbohydrate-rich extracellular matrix known as the cell wall. Nutrient availability affects cell wall composition via uncharacterized regulatory mechanisms, and cellulose deficient mutants develop a hypersensitive root response to growth on high concentrations of nitrate. Since cell walls account for the bulk of plant biomass, it is important to understand how nutrients regulate cell walls. This could provide important knowledge for directing fertilizer treatments and engineering plants with higher nutrient use efficiency. The direct effect of nitrate on cell wall synthesis was investigated through growth assays on varying concentrations of nitrate, measuring cellulose content of roots and shoots, and assessing cellulose synthase activity (CESA) using live cell imaging with spinning disk confocal microscopy. A forward genetic screen was developed to isolate mutants impaired in nutrient-mediated cell wall regulation, revealing that cellulose biosynthesis inhibitor (CBI) activity is modulated by nutrient availability. Various non-CESA mutants were isolated that displayed CBI resistance, with the majority of mutations causing perturbation of mitochondria-localized proteins. To investigate mitochondrial involvement, the CBI mechanism of action was investigated using a reverse genetic screen, a targeted pharmacological screen, and -omics approaches. The results generated suggest that CBI-induced cellulose inhibition is due to off-target effects. This provides the groundwork to investigate uncharacterized processes of CESA regulation and adds valuable knowledge to the understanding of CBI activity, which could be harnessed to develop new and improved herbicides.
Sulfur is essential for the functionality of some important biomolecules in humans. Biomolecules like the Iron-sulfur clusters, tRNAs, Molybdenum cofactor, and some vitamins. The trafficking of sulfur involves proteins collectively called sulfurtransferase. Among these are TUM1, MOCS3, and NFS1.
This research investigated the role of TUM1 for molybdenum cofactor biosynthesis and cytosolic tRNA thiolation in humans. The rhodanese-like protein MOCS3 and the L-cysteine desulfurase (NFS1) have been previously demonstrated to interact with TUM1. These interactions suggested a dual function of TUM1 in sulfur transfer for Moco biosynthesis and cytosolic tRNA thiolation. TUM1 deficiency has been implicated to be responsible for a rare inheritable disorder known as mercaptolactate cysteine disulfiduria (MCDU), which is associated with a mental disorder. This mental disorder is similar to the symptoms of sulfite oxidase deficiency which is characterised by neurological disorders. Therefore, the role of TUM1 as a sulfurtransferase in humans was investigated, in CRISPR/Cas9 generated TUM1 knockout HEK 293T cell lines.
For the first time, TUM1 was implicated in Moco biosynthesis in humans by quantifying the intermediate product cPMP and Moco using HPLC. Comparing the TUM1 knockout cell lines to the wild-type, accumulation and reduction of cPMP and Moco were observed respectively. The effect of TUM1 knockout on the activity of a Moco-dependent enzyme, Sulfite oxidase, was also investigated. Sulfite oxidase is essential for the detoxification of sulfite to sulfate. Sulfite oxidase activity and protein abundance were reduced due to less availability of Moco. This shows that TUM1 is essential for efficient sulfur transfer for Moco biosynthesis. Reduction in cystathionin -lyase in TUM1 knockout cells was quantified, a possible coping mechanism of the cell against sulfite production through cysteine catabolism.
Secondly, the involvement of TUM1 in tRNA thio-modification at the wobble Uridine-34 was reported by quantifying the amount of mcm5s2U and mcm5U via HPLC. The reduction and accumulation of mcm5s2U and mcm5U in TUM1 knockout cells were observed in the nucleoside analysis. Herein, exogenous treatment with NaHS, a hydrogen sulfide donor, rescued the Moco biosynthesis, cytosolic tRNA thiolation, and cell proliferation deficits in TUM1 knockout cells.
Further, TUM1 was shown to impact mitochondria bioenergetics through the measurement of the oxygen consumption rate and extracellular acidification rate (ECAR) via the seahorse cell Mito stress analyzer. Reduction in total ATP production was also measured. This reveals how important TUM1 is for H2S biosynthesis in the mitochondria of HEK 293T.
Finally, the inhibition of NFS1 in HEK 293T and purified NFS1 protein by 2-methylene 3-quinuclidinone was demonstrated via spectrophotometric and radioactivity quantification. Inhibition of NFS1 by MQ further affected the iron-sulfur cluster-dependent enzyme aconitase activity.
Magnetite nanoparticles and their assembly comprise a new area of development for new technologies. The magnetic particles can interact and assemble in chains or networks. Magnetotactic bacteria are one of the most interesting microorganisms, in which the assembly of nanoparticles occurs. These microorganisms are a heterogeneous group of gram negative prokaryotes, which all show the production of special magnetic organelles called magnetosomes, consisting of a magnetic nanoparticle, either magnetite (Fe3O4) or greigite (Fe3S4), embedded in a membrane. The chain is assembled along an actin-like scaffold made of MamK protein, which makes the magnetosomes to arrange in mechanically stable chains. The chains work as a compass needle in order to allow cells to orient and swim along the magnetic field of the Earth.
The formation of magnetosomes is known to be controlled at the molecular level. The physico–chemical conditions of the surrounding environment also influence biomineralization. The work presented in this manuscript aims to understand how such external conditions, in particular the extracellular oxidation reduction potential (ORP) influence magnetite formation in the strain Magnetospirillum magneticum AMB-1. A controlled cultivation of the microorganism was developed in a bioreactor and the formation of magnetosomes was characterized.
Different techniques have been applied in order to characterize the amount of iron taken up by the bacteria and in consequence the size of magnetosomes produced at different ORP conditions. By comparison of iron uptake, morphology of bacteria, size and amount of magnetosomes per cell at different ORP, the formation of magnetosomes was inhibited at ORP 0 mV, whereas reduced conditions, ORP – 500 mV facilitate biomineralization process.
Self-assembly of magnetosomes occurring in magnetotactic bacteria became an inspiration to learn from nature and to construct nanoparticles assemblies by using the bacteriophage M13 as a template. The M13 bacteriophage is an 800 nm long filament with encapsulated single-stranded DNA that has been recently used as a scaffold for nanoparticle assembly. I constructed two types of assemblies based on bacteriophages and magnetic nanoparticles. A chain – like assembly was first formed where magnetite nanoparticles are attached along the phage filament. A sperm – like construct was also built with a magnetic head and a tail formed by phage filament.
The controlled assembly of magnetite nanoparticles on the phage template was possible due to two different mechanism of nanoparticle assembly. The first one was based on the electrostatic interactions between positively charged polyethylenimine coated magnetite nanoparticles and negatively charged phages. The second phage –nanoparticle assembly was achieved by bioengineered recognition sites. A mCherry protein is displayed on the phage and is was used as a linker to a red binding nanobody (RBP) that is fused to the one of the proteins surrounding the magnetite crystal of a magnetosome.
Both assemblies were actuated in water by an external magnetic field showing their swimming behavior and potentially enabling further usage of such structures for medical applications. The speed of the phage - nanoparticles assemblies are relatively slow when compared to those of microswimmers previously published. However, only the largest phage-magnetite assemblies could be imaged and it is therefore still unclear how fast these structures can be in their smaller version.
Inferring gene regulatory networks and cellular phases from time-resolved transcriptomics data
(2014)
Novel algorithms for prediction of protein complexes from protein-protein interacton networks
(2022)
During this PhD project three technical platforms were either improved or newly established in order to identify interesting genes involved in SNF, validate their expression and functionally characterise them. An existing 5.6K cDNA array (Colebatch et al., 2004) was extended to produce the 9.6K LjNEST array, while a second array, the 11.6K LjKDRI array, was also produced. Furthermore, the protocol for array hybridisation was substantially improved (Ott et al., in press). After functional classification of all clones according to the MIPS database and annotation of their corresponding tentative consensus sequence (TIGR) these cDNA arrays were used by several international collaborators and by our group (Krusell et al., 2005; in press). To confirm results obtained from the cDNA array analysis different sets of cDNA pools were generated that facilitate rapid qRT-PCR analysis of candidate gene expression. As stable transformation of Lotus japonicus takes several months, an Agrobacterium rhizogenes transformation system was established in the lab and growth conditions for screening transformants for symbiotic phenotypes were improved. These platforms enable us to identify genes, validate their expression and functionally characterise them in the minimum of time. The resources that I helped to establish, were used in collaboration with other people to characterise several genes like the potassium transporter LjKup and the sulphate transporter LjSst1, that were transcriptionally induced in nodules compared to uninfected roots, in more detail (Desbrosses et al., 2004; Krusell et al., 2005). Another gene that was studied in detail was LjAox1. This gene was identified during cDNA array experiments and detailed expression analysis revealed a strong and early induction of the gene during nodulation with high expression in young nodules which declines with the age of the nodule. Therefore, LjAox1 is an early nodulin. Promoter:gus fusions revealed an LjAox1 expression around the nodule endodermis. The physiological role of LjAox1 is currently being persued via RNAi. Using RNA interference, the synthesis of all symbiotic leghemoglobins was silenced simultaneously in Lotus japonicus. As a result, growth of LbRNAi lines was severely inhibited compared to wild-type plants when plants were grown under symbiotic conditions in the absence of mineral nitrogen. The nodules of these plants were arrested in growth 14 post inoculation and lacked the characteristic pinkish colour. Growing these transgenic plants in conditions where reduced nitrogen is available for the plant led to normal plant growth and development. This demonstrates that leghemoglobins are not required for plant development per se, and proves for the first time that leghemoglobins are indispensable for symbiotic nitrogen fixation. Absence of leghemoglobins in LbRNAi nodules led to significant increases in free-oxygen concentrations throughout the nodules, a decrease in energy status as reflected by the ATP/ADP ratio, and an absence of the bacterial nitrogenase protein. The bacterial population within nodules of LbRNAi plants was slightly reduced. Alterations of plant nitrogen and carbon metabolism in LbRNAi nodules was reflected in changes in amino acid composition and starch deposition (Ott et al., 2005). These data provide strong evidence that nodule leghemoglobins function as oxygen transporters that facilitate high flux rates of oxygen to the sites of respiration at low free oxygen concentrations within the infected cells.
Application of hybridisation capture to investigate complete mitogenomes from ancient samples
(2015)
Heat stress (HS) is one of the most common abiotic stresses, frequently affecting plant growth and crop production. With its fluctuating nature, HS episodes are frequently interspersed by stress-free intervals. Plants can be primed by HS, allowing them to survive better a recurrent stress episode. A memory of this priming can be maintained during stress-free intervals and this memory is closely correlated with transcriptional memory at several HS-inducible loci. This transcriptional memory is evident from hyper-induction of a locus upon a recurrent HS. ASCORBATE PEROXIDASE 2 (APX2) shows such hyper-induction upon recurring HS, however, the molecular basis of this transcriptional memory is not understood. Previous research showed that the HSinduced transcriptional memory at APX2 can last for up to seven days, and that it is controlled by cis-regulatory elements within the APX2 promoter.
To identify regulators involved in HS transcriptional memory, an unbiased forward genetic screening using EMS mutated seeds of pAPX2::LUC was performed from this screen. Two EMS mutants with affected transcriptional memory of LUC were identified. I confirmed that both two EMS mutants resulted from the gene mutations of HISTONE ACETYLTRANSFERASE 1 (HAC1). Besides pAPX2::LUC, the HS-induced transcription of other HS memory genes were also affected in hac1 mutants. Moreover, HAC1 may promote HS transcriptional memory by acetylating promoters of HS memory genes.
On the other hand, to identify cis-regulatory elements that are required for transcriptional memory of APX2, I performed promoter analysis of the four conserved HSEs identified within a functional APX2 promoter. I found out that one of the HSEs (HSE1) is necessary for both HS-induced APX2 transcription and transcriptional memory, while another one of HSEs (HSE2) is important for HS-induced APX2 transcriptional memory. I also found out that the HSE1 itself (with 10 bp of flanking sequence) is sufficient to confer HS-induced APX2 transcriptional memory, and HSE1 is also necessary for HSFA2 to bind on APX2 promoter and activate APX2 transcription. The findings will provide important clues for the molecular mechanism of transcriptional memory and will enable engineering of enhanced stress tolerance in crops.
The development of seeds in angiosperms starts with a complex process of double fertilization, involving the fusion of the maternal egg cell and central cell with two paternal sperm cells. This gives rise to the embryo and the nourishing endosperm, which are then enclosed by the seed coat, derived from the maternal integuments. The growth of the seed coat in Arabidopsis thaliana (Arabidopsis) is actively inhibited before fertilization by epigenetic regulators known as Polycomb Group (PcG) proteins. These proteins deposit a repressive histone mark called H3K27me3, which must be removed to enable seed coat formation. In this thesis, I explored the mechanism of removal of H3K27me3 marks from the integument cells following fertilization, which allows for seed coat formation. We hypothesized that this removal should be primarily facilitated by histone demethylases from the JMJ family and potentially influenced by the plant hormones Brassinosteroids (BRs). This hypothesis was supported by the expression patterns of the JMJ protein REF6 and of BR related genes, which are specifically expressed in the integuments and in the seed coat. Moreover, mutations in both these pathways lead to developmental defects, such as reduced ovule viability and delayed seed coat growth. Our research provides evidence suggesting that BR signalling is likely involved in recruiting JMJ-type histone demethylases to target loci responsible for seed coat growth. Moreover, we have discovered an additional pathway through which BRs regulate seed coat development, independent of their influence on H3K27me3 marks. This finding emphasizes the diverse roles of BRs in coordinating seed development, extending beyond their well-known involvement in plant growth and development. Furthermore, I explored the role of another epigenetic mark, DNA methylation, in fertilization-independent (or autonomous) seed formation in Arabidopsis. For this, we utilized epigenetic Recombinant Inbred Lines (epiRILs) and thus identified an epigenetic Quantitative Trait Locus (epiQTL) on chromosome II, potentially responsible for the larger autonomous seed size observed in DNA methylation mutants. Overall, this thesis significantly enhances our comprehension of the intricate relationship between epigenetic modifications, hormonal signaling, and plant reproductive processes. It offers valuable insights into the genetic mechanisms governing both sexual and asexual seed formation, while also presenting potential avenues for the engineer of advantageous traits in agricultural crops.
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.