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Publication
Social and economic analysis of the organic sector in Bhutan
(2024) Tshotsho; Lippert, Christian
As in some other low-income countries, organic agriculture (OA) has been introduced in Bhutan and is increasingly being promoted by the state with a top-down approach. While the potential of OA to provide ecosystem services and empower smallholder farmers through market participation is well known, it is also widely recognized that smallholder farmers face many challenges. This thesis discusses the challenges of OA in the case of Bhutanese smallholder farmers and assesses the potential of the farmers' social network to address some of these challenges. What challenges do smallholder farmers face in a top-down approach to OA? What types of social networks are still practiced among smallholder farmers? What potential do social networks have in overcoming the challenges of OA that pose difficulties in implementation? Answering these questions is important because organic farmers report serious challenges that are often neglected by the government in low-income countries. Because farmers are part of a community and embedded in the social structure, a change at the community level can have a huge impact on individual members. The actions of each individual can also have an impact on others, which in turn can affect the overall outcome for the community. Farmers in low-income countries rely on informal network relationships of various kinds as a substitute for the missing or inadequate formal institutions. To assess the potential of farmers' social networks in addressing the challenges of OA, this thesis identifies specific social networks that are characteristic of the farming community and relevant to addressing the challenges of OA for smallholder farmers. This study is based on three main chapters that reflect the main objectives of the overall work: 1) To describe the large-scale conversion of the OA sector in Bhutan and discuss the challenges related to institutional capacity, management and farming practices, nutrient balances and yield gaps, 2) examining informal labor exchanges in farming villages with successful adoption of labor-intensive farming practices and determining the nature of social enforcement mechanisms used, and 3) outlining and testing how two conceptually distinct social mechanisms fit the observed reality of adoption of improved seeds in Bhutanese remote villages. The first chapter takes a descriptive approach, while the second chapter presents an empirical study. The last chapter has a primarily methodological focus. In addition to these three chapters, the relevance of social network in the case of OA and the aims of the thesis are presented in the introductory chapter, and a final chapter contains the major conclusions, limitations and policy implications of the findings. The second chapter, which deals with the first objective, analyzes the feasibility of large- scale conversion to OA in Bhutan. It illustrates that organic farmers must comply with the Bhutan Organic Standard (BOS) and that the number of certified farmers under the Local Organic Assurance System (LOAS) is increasing. The results also show that organic farmers are struggling with low yields, nutrient imbalances in nitrogen, lack of funds to implement organic programs, lack of extension services for OA, and other related institutional inadequacies. The chapter argues that analyzing and understanding the challenges of conversion to OA in Bhutan can lead to transferable findings to similar contexts characterized by smallholder farming systems. The third chapter, which deals with the second objective, examines informal labor exchanges in Bhutanese farming villages that have successfully adopted labor-intensive agricultural practices such as OA. It then tests the existence of social enforcement mechanisms described in the literature by relating the observed network pattern of labor exchange to farmers supposed cooperative behavior. The results show that labor exchange networks in organic farming villages are characterized by a high prevalence of completely connected structures (i.e. triad closure) that seem to constitute the main enforcement mechanism. It discusses how this social network (well-functioning labor exchange) can be used to select further villages for OA implementation in the future. The fourth chapter addresses the third objective and examines how two different forms of social network mechanisms–social contagion (direct communication) and structural equivalence (social standing)–can benefit the dissemination of improved seeds in a wider agricultural community. This study was formulated against the assumption that farmers do not make decisions in isolation and that technology diffusion models with social network considerations provide better explanations and policy guidance. The results provide evidence that an interventionist agricultural policy should not only favor farmers with multiple connections in the hope that their behavior will influence their multiple network partners, but also farmers in different social positions, including peripheral network positions, who can inspire other, less well-connected farmers to adopt. The thesis concludes that considering the potential of farmers’ social networks in solving some of the challenges of OA in low-income countries like Bhutan can open up new avenues of research. The thesis also concludes that a large-scale conversion to OA in Bhutan may be more difficult to accomplish than previously thought, given the evidence of important challenges that are currently neglected. Given the evidence on the role of social networks and how they are still functioning in some remote villages in Bhutan, a bottom-up initiative with additional government support is preferable to the current top-down approach.
Publication
The low mutational flexibility of the EPSP synthase in Bacillus subtilis is due to a higher demand for shikimate pathway intermediates
(2023) Schwedt, Inge; Schöne, Kerstin; Eckert, Maike; Pizzinato, Manon; Winkler, Laura; Knotkova, Barbora; Richts, Björn; Hau, Jann-Louis; Steuber, Julia; Mireles, Raul; Noda‐Garcia, Lianet; Fritz, Günter; Mittelstädt, Carolin; Hertel, Robert; Commichau, Fabian M.
Glyphosate (GS) inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase that is required for aromatic amino acid, folate and quinone biosynthesis in Bacillus subtilis and Escherichia coli. The inhibition of the EPSP synthase by GS depletes the cell of these metabolites, resulting in cell death. Here, we show that like the laboratory B. subtilis strains also environmental and undomesticated isolates adapt to GS by reducing herbicide uptake. Although B. subtilis possesses a GS-insensitive EPSP synthase, the enzyme is strongly inhibited by GS in the native environment. Moreover, the B. subtilis EPSP synthase mutant was only viable in rich medium containing menaquinone, indicating that the bacteria require a catalytically efficient EPSP synthase under nutrient-poor conditions. The dependency of B. subtilis on the EPSP synthase probably limits its evolvability. In contrast, E. coli rapidly acquires GS resistance by target modification. However, the evolution of a GS-resistant EPSP synthase under non-selective growth conditions indicates that GS resistance causes fitness costs. Therefore, in both model organisms, the proper function of the EPSP synthase is critical for the cellular viability. This study also revealed that the uptake systems for folate precursors, phenylalanine and tyrosine need to be identified and characterized in B. subtilis.
Publication
Recombinant production and characterization of metalloproteins from bacterial pathogens and the innate immune response
(2024) Göbel, Katharina; Fritz, Günter
The challenges and potential solutions of drug development are highlighted by discussing the identification, production and characterization of potential new drug targets in this study. The successful development of new and specific pharmaceuticals requires that the target for the respective new drug is available as a pure and homogenous molecule in its native state. Typically, the target molecule is a protein. E.g. antibacterial drugs target proteins from a bacterial pathogen or in human diseases pharmaceuticals predominantly target proteins of signaling pathways or receptors. These proteins are usually not available directly from the organism itself and have to be produced in an expression host and purified to homogeneity. Despite the advances in the field of recombinant protein expression and purification many proteins are very difficult to produce and thus represent the major bottleneck in the development of new pharmaceuticals. In particular demanding is the expression of metalloproteins, which make up to 30% of all proteins coded in the human genome and represent a major challenge in recombinant protein production. Metalloproteins are a diverse class of proteins that is crucial for various biological processes. They play an important role in the regulation, catalysis, and maintenance of biomolecular structure. Alone, 10% of all human proteins contain zinc ions and 2% contain iron, and both metal ions are often inserted by specific but so far unknown chaperones impeding the recombinant production of correctly folded and active proteins. The challenges in studying these metalloproteins arise from their complex structures and the difficulty of their expression and isolation. To overcome these problems new approaches and solutions are highlighted and exemplified by the production and characterization of potential new drug targets in this study. The focus lies particularly on metalloproteins that play a role in infectious diseases. Global health challenges include the persistent threat of infectious diseases despite advances in healthcare, hygiene and therapeutics. The COVID-19 pandemic and rising antibiotic resistance are prime examples of the ongoing risks. This research focuses on three different proteins: (1) the maturation factor NqrM from the bacterial pathogen Vibrio cholerae, (2) the human regulator of the interferon response ubiquitin-specific protease 18 (USP18) and its interaction partners, as well as (3) the viral Papain-like protease (PLpro) from the pathogenic virus SARS-CoV-2. All three proteins belong to the class of metalloproteins and bind either iron as in the case of NqrM or zinc as for USP18 and PLpro. New methods and strategies were developed to produce, isolate and investigate these metalloproteins and since all three proteins represent potential drug targets the results presented here provide the basis for future drug development. The production of proteins requires the selection of appropriate expression host systems such as bacteria, yeast, mammalian cells, etc., depending on the desired application. The study emphasizes the versatility of expression host E. coli due to its well-studied genetics, rapid growth kinetics and ease of handling. However, challenges such as the lack of post-translational modifications can lead to the production of non-functional proteins. Optimization of expression strategies is crucial, and the study describes various factors affecting protein production, including protein engineering, growth conditions, media composition and induction parameters expanding and enhancing the well-established E.coli expression system also for very challenging target proteins. The successful isolation of the proteins formed the fundamental basis for a detailed functional and structural characterization of the proteins. The research presented here takes a forward approach and encompasses the new strategies in cloning, recombinant expression and purification of proteins from bacteria, viruses and humans, emphasizing the advantages and disadvantages of homo- and heterologous recombinant expression. The results obtained highlight also the need for extensive experimental testing to establish optimal conditions, particularly for challenging proteins such as the metalloproteins studied here.
Publication
Automatic classification of submerged macrophytes at Lake Constance using laser bathymetry point clouds
(2024) Wagner, Nike; Franke, Gunnar; Schmieder, Klaus; Mandlburger, Gottfried; Wagner, Nike; Department of Geodesy and Geoinformation, TU Wien, Wiedner Hauptstr. 8-10, 1040 Vienna, Austria;; Franke, Gunnar; Institute of Landscape and Plant Ecology (320), University of Hohenheim, Ottilie-Zeller-Weg 2, 70599 Stuttgart, Germany; (G.F.); (K.S.); Schmieder, Klaus; Institute of Landscape and Plant Ecology (320), University of Hohenheim, Ottilie-Zeller-Weg 2, 70599 Stuttgart, Germany; (G.F.); (K.S.); Mandlburger, Gottfried; Department of Geodesy and Geoinformation, TU Wien, Wiedner Hauptstr. 8-10, 1040 Vienna, Austria;; Stateczny, Andrzej
Submerged aquatic vegetation, also referred to as submerged macrophytes, provides important habitats and serves as a significant ecological indicator for assessing the condition of water bodies and for gaining insights into the impacts of climate change. In this study, we introduce a novel approach for the classification of submerged vegetation captured with bathymetric LiDAR (Light Detection And Ranging) as a basis for monitoring their state and change, and we validated the results against established monitoring techniques. Employing full-waveform airborne laser scanning, which is routinely used for topographic mapping and forestry applications on dry land, we extended its application to the detection of underwater vegetation in Lake Constance. The primary focus of this research lies in the automatic classification of bathymetric 3D LiDAR point clouds using a decision-based approach, distinguishing the three vegetation classes, (i) Low Vegetation, (ii) High Vegetation, and (iii) Vegetation Canopy, based on their height and other properties like local point density. The results reveal detailed 3D representations of submerged vegetation, enabling the identification of vegetation structures and the inference of vegetation types with reference to pre-existing knowledge. While the results within the training areas demonstrate high precision and alignment with the comparison data, the findings in independent test areas exhibit certain deficiencies that are likely addressable through corrective measures in the future.
Publication
Studies of phytate degradation and associated mineral utilization in growing pigs
(2024) Klein, Nicolas; Rodehutscord, Markus
Phosphorus (P) is primarily stored in plant seeds as phytate, which is any salt of phytic acid (myo-inositol hexakisphosphate; InsP6). The enzymatic capacity of pigs and the microorganisms present in their digestive tract allows for only partial and incomplete prececal degradation of InsP6. To address this limitation, the addition of exogenous phytases to feed has been state-of-the-art for more than three decades. Phytases, found in various organisms like bacteria, fungi, plants, and animals, initiate the breakdown of InsP6 and inorganic phosphate, thereby making the liberated phosphate available for digestion. Substantial scientific research and practical field applications have shown that adding exogenous phytases to the diet of non-ruminants leads to an improvement in P digestibility and a reduction in P excretion. Over time, phytases with enhanced thermal profiles and higher activity at physiological pH milieus have been engineered. Additionally, advancements in plant breeding have increased intrinsic phytase activity in feed ingredients relevant to animal nutrition. Thus, this thesis aimed to deepen the understanding of inositol phosphate (InsP) degradation in ileal-cannulated pigs, focusing on how dietary variables can influence this process along the digestive tract. In the first study (Manuscript 1), diets based on wheat with variable intrinsic phytase activity and the addition of an exogenous phytase on InsP degradation in pigs were investigated. Although wheat intrinsic phytase contributed to increased InsP degradation and P digestibility in pigs, variation in intrinsic phytase activity by crossbreeding wheat, as achieved in this study, was not reflected in InsP degradation and P digestibility data. This discrepancy may be attributed to an inadequate proteolytic resistance of wheat phytase in the gastric compartment of the pig. A marked increase in prececal InsP degradation and P digestibility was achieved by adding a microbial phytase to the wheat-based feed. While exogenous phytase increases the digestibility of InsP-P, other dietary components may impair its hydrolytic activity. In the second study (Manuscript 2), the single and interactive effects of dietary Ca concentration and exogenous phytase in pigs were investigated. The study assessed the effects of dietary Ca and exogenous phytase on InsP degradation and nutrient digestibility in growing pigs. Additional dietary Ca decreased prececal InsP6 disappearance, but only with exogenous phytase. Concentrations of lower InsP isomers and myo-inositol in the ileal digesta and prececal P digestibility were greater with exogenous phytase, but not affected by dietary Ca concentration. In contrast, fecal InsP6 disappearance was lower and the concentration of InsP4-5 isomers in feces was greater with additional dietary Ca. The study revealed that dietary Ca concentration is relevant for InsP disappearance in the hindgut, but not in the ileum. However, when exogenous phytase is used, the dietary Ca concentration is important because prececal InsP degradation is affected by the Ca level in the diet. The third study (Manuscript 3) aimed to investigate the effects of dietary Ca sources, exogenous phytase, and formic acid on InsP degradation and nutrient digestibility in growing pigs. Replacing limestone with Ca formate reduced prececal InsP6 disappearance and prececal P digestibility. However, adding formic acid to a diet containing limestone and phytase enhanced prececal InsP6 disappearance and increased InsP2 and myo-inositol concentrations in the distal ileal digesta. Accordingly, prececal P digestibility was increased when formic acid was added to the diet containing limestone and exogenous phytase. This suggested that Ca formate is not a suitable alternative Ca source to limestone for optimizing prececal P release from InsP in growing pigs. The release of P from InsP by exogenous phytase in limestone diets can still be further increased by adding formic acid. In conclusion, the degradation of InsP in growing pigs is a complex process affected by dietary Ca concentration, dietary Ca source, and the presence of phytase. However, investigated dietary traits mainly affected InsP6, with lesser effects on lower InsP isomers, highlighting the importance of prececal hydrolytic breakdown of InsP6 to InsP5. This directly affected P digestibility of growing pigs. Intrinsic phytase activity in feed ingredients, such as wheat, can contribute to prececal InsP degradation but may be neglected when exogenous phytase is present in the feed. Exogenous phytase addition notably increased prececal InsP degradation and P digestibility in plant-based diets, and complete dephosphorylation of InsP in the prececal tract was implied by the increase of the final degradation product myo-inositol in the ileum content, urine, and blood. However, some P remained bound to InsP at the end of the ileum of growing pigs and was therefore not available for digestion. Nevertheless, some diets with exogenous phytase tested in this thesis met the recommended digestible P concentration. This suggests that diets formulated with adequate InsP-containing ingredients and exogenous phytase may obviate the need for mineral P addition, reducing the reliance on finite P sources in growing pig nutrition.