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Climate change, driven by increasing atmospheric levels of carbon dioxide (CO2), presents a significant societal challenge for the 21st century. Biotechnological approaches for microbial production of commodity chemicals and fuels offer possible solutions to re-fix CO2 from the atmosphere, thereby mitigating carbon emissions and contributing to a sustainable carbon-economy in the future. Biological CO2 fixation is also at the heart of agricultural productivity, where photosynthesis and the Calvin-Benson-Bassham cycle present promising biotechnological targets for crop improvement.
Synthetic biology allows testing metabolic solutions not known to exist in nature, which may exceed their natural counterparts in terms of efficiency. In this thesis, I explore the design of such new-to-nature metabolic pathways for biological CO2 utilization and their implementation in living cells (in vivo).
In the first chapter, I describe the development of a metabolic pathway that enables intracellular conversion of CO2 to formate, giving access to highly efficient carbon fixation routes. In nature, CO2-reduction remains restricted to anaerobic organisms and low redox potentials. Here, we introduce the “CORE cycle”, a synthetic metabolic pathway that converts CO2 to formate under fully aerobic conditions and ambient CO2 levels, using only NADPH as a reductant. We leverage this synthetic, ATP-energized pathway to overcome the thermodynamic and kinetic barriers associated with CO2-reduction. Applying rational metabolic engineering and adaptive evolution, this work demonstrates that Escherichia coli can utilize ambient CO2 as the sole source of one-carbon units and serine, achieving a first step towards novel modes of synthetic autotrophy. We further apply computational modeling to showcase the potential of the CORE cycle as a photorespiratory bypass for enhancing photosynthesis.
In the second chapter, I describe the development of the “LCM module”, a novel metabolic route for CO2-incorporating conversion of acetyl-CoA to pyruvate. This route relies on the newly uncovered, promiscuous activity of an adenosylcobalamin (B12)-dependent enzyme, which we significantly optimize through targeted hypermutation and in vivo selection strategies. The LCM module provides a shorter and more efficient pathway for acetyl-CoA assimilation compared to natural routes, offering novel opportunities for synthetic CO2 fixation.
Overall, through theoretical pathway analysis, enzyme bioprospecting, and modular metabolic engineering in E. coli, this thesis expands the solution space for biological CO2 fixation.
The order of destruction
(2024)
This book studies sugarcane monoculture, the dominant form of cultivation in the colonial Caribbean, in the later 1600s and 1700s up to the Haitian Revolution. Researching travel literature, plantation manuals, Georgic poetry, letters, and political proclamations, this book interprets texts by Richard Ligon, Henry Drax, James Grainger, Janet Schaw, and Toussaint Louverture. As the first extended investigation into its topic, this book reads colonial Caribbean monoculture as the conjunction of racial capitalism and agrarian capitalism in the tropics. Its eco-Marxist perspective highlights the dual exploitation of the soil and of enslaved agricultural producers under the plantation regime, thereby extending Marxist analysis to the early colonial Caribbean. By focusing on textual form (in literary and non-literary texts alike), this study discloses the bearing of monoculture on contemporary writers' thoughts. In the process, it emphasizes the significance of a literary tradition that, despite its ideological importance, is frequently neglected in (postcolonial) literary studies and the environmental humanities. Located at a crossroads of disciplines and perspectives, this study will be of interest to literary critics and historians working in the early Americas, to students and scholars of agriculture, colonialism, and (racial) capitalism, to those working in the environmental humanities, and to Marxist academics. It will be of great interest to scholars and researchers of language and literature, post-colonial studies, cultural studies, diaspora studies, and the Global South studies
Carbohydrates play a vital role in all living organisms; serving as a cornerstone in primary metabolism through the release of energy from their hydrolysis and subsequent re-utilization (Apriyanto et al., 2022). Starch is the principal carbohydrate reserve in plants, providing essential energy for plant growth. Furthermore, starch serves as a significant carbohydrate source in the human diet. Beyond its nutritional value, starch has extensive industrial application associated with many aspects of human society, such as feed, pharmacy, textiles, and the production of biodegradable plastics. Understanding the mechanisms underlying starch metabolism in plants carries multifaceted benefits. Not only does it contribute to increasing crop yield and refining grain quality, but also can improve the efficiency of industrial applications.
Starch in plants is categorized into two classes based on their location and function: transitory starch and storage starch. Transitory starch is produced in chloroplasts of autotrophic tissues/organs, such as leaves. It is synthesized during the day and degraded during the night. Storage starch is synthesized in heterotrophic tissues/organs, such as endosperm, roots and tubers, which is utilized for plant reproduction and industrial application in human life. Most studies aiming to comprehend starch metabolism of Arabidopsis thaliana primarily focus on transitory starch.
Starch is stored as granular form in chloroplast and amyloplast. The parameters of starch granules, including size, morphology, and quantity per chloroplast serve as indicators of starch metabolism status. However, the understanding of their regulatory mechanism is still incomplete. In this research, I initially employed a simple and adapted method based on laser confocal scanning microscopy (LCSM) to observe size, morphology and quantity of starch granules within chloroplasts in Arabidopsis thaliana in vivo. This method facilitated a rapid and versatile analysis of starch granule parameters across numerous samples. Utilizing this approach, I compared starch granule number per chloroplast between mesophyll cells and guard cells in both wild type plants (Col-0) and several starch related mutants. The results revealed that the granule number is distinct between mesophyll cells and guard cells, even within the same genetic background, suggesting that guard cells operate a unique regulatory mechanism of starch granule number.
Subsequently, I redirected my attention toward examining starch morphology. Through microscopy analyses, I observed a gradual alteration in starch granule morphology in certain mutants during leaf aging. Specifically, in mutants such as sex1-8 and dpe2phs1ss4, there was a progressive alteration in starch granule morphology over time. Conversely, in Col-0 and ss4 mutant, these morphological alterations were not evident. This discovery suggests a new perspective to understand the development of starch morphology.
Further investigation revealed that mutants lacking either Disproportionating enzyme 2 (DPE2) or MALTOSE-EXCESS 1 (MEX1) exhibited gradual alterations in starch morphology with leaf aging. Notably, the most severe effects on starch morphology occurred in double mutants lacking either DPE2 or MEX1 in conjunction with a lack of starch synthase 4 (SS4). In these mutations, a transformation of the starch granule morphology from the typical discoid morphology to oval and eventually to a spherical shape.
To investigate the changes in the internal structure of starch during this alteration, I analyzed the chain length distribution (CLD) of the amylopectin of young, intermediate and old leaves of the mutants. Throughout starch granule development, I found an increased presence of short glucan chains within the granules, particularly evident in dpe2ss4 and mex1ss4 mutants, as well as their parental single mutants. Notably, the single mutant ss4 also showed an affected granule morphology, albeit not influenced by leaf aging..
The CLD pattern of the amylopectin reflects an integrative regulation involving several participants in starch synthesis, including starch synthases (SSs), starch branching/debranching enzymes (SBEs/DBEs). Therefore, I further detected the expression of related genes on transcription level and the enzymatic activity of their respective proteins. Results indicated altered gene expression of several regulators in these mutants, particularly demonstrating dramatic alterations in dpe2 and dpe2ss4 with leaf aging. These changes corresponded with the observed alterations in starch granule morphology.
Taken together, I have identified and characterized a progressive alteration in starch granule morphology primarily resulting from the deficiencies in DPE2 and MEX1. Furthermore, I have associated the CLD pattern with the granule morphogenesis, as well as the gene expression and enzymatic activity of proteins involved in starch synthesis. Unlike SS4, which is implicated in starch initiation, MEX1 and DPE2 are involved into starch degradation. MEX1 is located in chloroplast envelope and DPE2 is situated in the cytosol. Considering the locations and known functions of DPE2/MEX1 and SS4, I infer that there might be two pathways influencing starch morphology: an initiation-affected pathway via SS4 and a degradation-affected pathway via DPE2/MEX1.
Phobic cosmopolitanism
(2024)
The inclusion of exotic germplasm serves as a crucial means to enhance allelic and
consequently phenotypic diversity in inbred crop species. Such species have experienced a reduction in diversity due to artificial selection focused on a limited set of traits. The natural biodiversity within ecosystems presents an opportunity to explore various traits influencing plant survival, reproductive fitness and yield potential. In agricultural research, the study of wild species closely related to cultivated plants serves as a means to comprehend the genetic foundations of past domestication events and the polymorphisms essential for future breeding efforts to develop superior varieties. In order to examine the metabolic composition, pinpoint quantitative trait loci (QTL) and facilitate their resolution an extensive large-scale analysis of metabolic QTL (mQTL) was conducted on tomato backcross inbred lines (BILs) derived from a cross between the wild species S. pennellii (5240) incorporated into the background of S. lycopersicum cv. LEA determinate inbred which can be grown in open fields and cv. TOP indeterminate which can be grown in greenhouse conditions. A large number of mQTL associated with primary secondary and lipid metabolism in fruit were identified across the two BIL populations. Epistasis, the interactions between genes at different loci, has been an interest in molecular and quantitative genetics for many decades. The study of epistasis requires the analysis of very large populations with multiple independent genotypes that carry specific genomic regions. In order to understand the genetic basis of tomato fruit metabolism, I extended the work to investigate epistatic interactions of the genomic regions. In addition, two candidate genes were identified through quantitative trait loci underlying fruit-specific sucrose and jasmonic acid derivatives. Finally, in this study, I assessed the genetic framework of fruit metabolic traits with a high level of detail, utilizing the newly created Solanum pennellii (5240) backcrossed introgression lines (n=3000). This investigation resulted in the discovery of promising candidate loci associated with significant fruit quality traits, including those to the abundance of glutamic acid and aspartic acid crucial elements contributing to the development of acidity and flavors.
Wars and the world
(2024)
This book offers a descriptive analysis of the Soviet/Russian wars in Afghanistan, Chechnya, and Georgia, as well as an in-depth exploration of the ways in which these wars are framed in the collective consciousness created by global popular culture. Russian and Western modalities of remembrance have been, and remain, engaged in a world war that takes place (not exclusively, but intensively) on the level of popular culture. The action/reaction dynamic, confrontational narratives and othering between the two "camps" never ceased. The Cold War, in many ways and contrary to the views of many others who hoped for the end of history, never really ended.
The trace elements copper, iron, manganese, selenium and zinc are essential micronutrients involved in various cellular processes, all with different responsibilities. Based on that importance, their concentrations are tightly regulated in mammalian organisms. The maintenance of those levels is termed trace element homeostasis and mediated by a combination of processes regulating absorption, cellular and systemic transport mechanisms, storage and effector proteins as well as excretion. Due to their chemical properties, some functions of trace elements overlap, as seen in antioxidative defence, for example, comprising an expansive spectrum of antioxidative proteins and molecules. Simultaneously, the same is true for regulatory mechanisms, causing trace elements to influence each other’s homeostases. To mimic physiological conditions, trace elements should therefore not be evaluated separately but considered in parallel. While many of these homeostatic mechanisms are well-studied, for some elements new pathways are still discovered. Additionally, the connections between dietary trace element intake, trace element status and health are not fully unraveled, yet. With current demographic developments, also the influence of ageing as well as of certain pathological conditions is of increasing interest. Here, the TraceAge research unit was initiated, aiming to elucidate the homeostases of and interactions between essential trace elements in healthy and diseased elderly. While human cohort studies can offer insights into trace element profiles, also in vivo model organisms are used to identify underlying molecular mechanisms. This is achieved by a set of feeding studies including mice of various age groups receiving diets of reduced trace element content. To account for cognitive deterioration observed with ageing, neurodegenerative diseases, as well as genetic mutations triggering imbalances in cerebral trace element concentrations, one TraceAge work package focuses on trace elements in the murine brain, specifically the cerebellum. In that context, concentrations of the five essential trace elements of interest, copper, iron, manganese, selenium and zinc, were quantified via inductively coupled plasma-tandem mass spectrometry, revealing differences in priority of trace element homeostases between brain and liver. Upon moderate reduction of dietary trace element supply, cerebellar concentrations of copper and manganese deviated from those in adequately supplied animals. By further reduction of dietary trace element contents, also concentrations of cerebellar iron and selenium were affected, but not as strong as observed in liver tissue. In contrast, zinc concentrations remained stable. Investigation of aged mice revealed cerebellar accumulation of copper and iron, possibly contributing to oxidative stress on account of their redox properties. Oxidative stress affects a multitude of cellular components and processes, among them, next to proteins and lipids, also the DNA. Direct insults impairing its integrity are of relevance here, but also indirect effects, mediated by the machinery ensuring genomic stability and its functionality. The system includes the DNA damage response, comprising detection of endogenous and exogenous DNA lesions, decision on subsequent cell fate and enabling DNA repair, which presents another pillar of genomic stability maintenance. Also in proteins of this machinery, trace elements act as cofactors, shaping the hypothesis of impaired genomic stability maintenance under conditions of disturbed trace element homeostasis. To investigate this hypothesis, a variety of approaches was used, applying OECD guidelines Organisation for Economic Co-operation and Development, adapting existing protocols for use in cerebellum tissue and establishing new methods. In order to assess the impact of age and dietary trace element depletion on selected endpoints estimating genomic instability, DNA damage and DNA repair were investigated. DNA damage analysis, in particular of DNA strand breaks and oxidatively modified DNA bases, revealed stable physiological levels which were neither affected by age nor trace element supply. To examine whether this is a result of increased repair rates, two steps characteristic for base excision repair, namely DNA incision and ligation activity, were studied. DNA glycosylases and DNA ligases were not reduced in their activity by age or trace element depletion, either. Also on the level of gene expression, major proteins involved in genomic stability maintenance were analysed, mirroring results obtained from protein studies. To conclude, the present work describes homeostatic regulation of trace elements in the brain, which, in absence of genetic mutations, is able to retain physiological levels even under conditions of reduced trace element supply to a certain extent. This is reflected by functionality of genomic stability maintenance mechanisms, illuminating the prioritization of the brain as vital organ.
Ada (Fishman) Maimon
(2023)
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.
Leaves exhibit cells with varying degrees of shape complexity along the proximodistal axis. Heterogeneities in growth directions within individual cells bring about such complexity in cell shape. Highly complex and interconnected gene regulatory networks and signaling pathways have been identified to govern these processes. In addition, the organization of cytoskeletal networks and cell wall mechanical properties greatly influences the regulation of cell shape. Research has shown that microtubules are involved in regulating cellulose deposition and direc-tion of cell growth. However, comprehensive analysis of the regulation of the actin cytoskele-ton in cell shape regulation has not been well studied.
This thesis provides evidence that actin regulates aspects of cell growth, division, and direction-al expansion that impacts morphogenesis of developing leaves. The jigsaw puzzle piece mor-phology of epidermal pavement cells further serves as an ideal system to investigate the com-plex process of morphogenetic processes occurring at the cellular level. Here we have em-ployed live cell based imaging studies to track the development of pavement cells in actin com-promised conditions. Genetic perturbation of two predominantly expressed vegetative actin genes ACTIN2 and ACTIN7 results in delayed emergence of the cellular protrusions in pave-ment cells. Perturbation of actin also impacted the organization of microtubule in these cells that is known to promote emergence of cellular protrusions. Further, live-cell imaging of actin or-ganization revealed a correlation with cell shape, suggesting that actin plays a role in influencing pavement cell morphogenesis.
In addition, disruption of actin leads to an increase in cell size along the leaf midrib, with cells being highly anisotropic due to reduced cell division. The reduction of cell division further im-pacted the morphology of the entire leaf, with the mutant leaves being more curved. These re-sults suggests that actin plays a pivotal role in regulating morphogenesis at the cellular and tis-sue scales thereby providing valuable insights into the role of the actin cytoskeleton in plant morphogenesis.
How do the rights of same-sex couples have to be ensured by states, and which kind of environmental obligations are induced by the right to life and to personal integrity? Questions as diverse and far-reaching as these are regularly dealt with by the Inter-American Court of Human Rights in its advisory function. This book is the first comprehensive, non-Spanish-written treatise on the advisory function of this Court. It analyzes the scope of the Court's advisory jurisdiction and its procedural practice in comparison with that of other international courts. Moreover, the legal effects of the Court’s advisory opinions and the question when the Court should better reject a request for an advisory opinion are examined.
Diglossic translanguaging
(2024)
This book examines how German-speaking Jews living in Berlin make sense and make use of their multilingual repertoire. With a focus on lexical variation, the book demonstrates how speakers integrate Yiddish and Hebrew elements into German for indexing belonging and for positioning themselves within the Jewish community. Linguistic choices are shaped by language ideologies (e.g., authenticity, prescriptivism, nostalgia). Speakers translanguage when using their multilingual repertoire, but do so in a diglossic way, using elements from different languages for specific domains
Aging is associated with bone loss, which can lead to osteoporosis and high fracture risk. This coincides with the enhanced formation of bone marrow adipose tissue (BMAT), suggesting a negative effect of bone marrow adipocytes on skeletal health. Increased BMAT formation is also observed in pathologies such as obesity, type 2 diabetes and osteoporosis. However, a subset of bone marrow adipocytes forming the constitutive BMAT (cBMAT), arise early in life in the distal skeleton, contain high levels of unsaturated fatty acids and are thought to provide a physiological function. Regulated BMAT (rBMAT) forms during aging and obesity in proximal regions of the bone and contain a large proportion of saturated fatty acids. Paradoxically, BMAT accumulation is also enhanced during caloric restriction (CR), a life-span extending dietary intervention. This indicates, that different types of BMAT can form in response to opposing nutritional stimuli with potentially different functions.
To this end, two types of nutritional interventions, CR and high fat diet (HFD), that are both described to induce BMAT accumulation were carried out. CR markedly increased BMAT formation in the proximal tibia and led to a higher proportion of unsaturated fatty acids, making it similar to the physiological cBMAT. Additionally, proximal and diaphyseal tibia regions displayed higher adiponectin expression. In aged mice, CR was associated with an improved trabecular bone structure. Taken together, these findings demonstrate, that the type of BMAT that forms during CR might provide beneficial effects for local bone stem/progenitor cells and metabolic health. The HFD intervention performed in this thesis showed no effect on BMAT accumulation and bone microstructure. RNA Seq analysis revealed alterations in the composition of the collagen-containing extracellular matrix (ECM).
In order to investigate the effects of glucose homeostasis on osteogenesis, differentiation capacity of immortalized multipotent mesenchymal stromal cells (MSCs) and osteochondrogenic progenitor cells (OPCs) was analyzed. Insulin improved differentiation in both cell types, however, combination of with a high glucose concentration led to an impaired mineralization of the ECM. In the MSCs, this was accompanied by the formation of adipocytes, indicating negative effects of the adipocytes formed during hyperglycemic conditions on mineralization processes. However, the altered mineralization pattern and structure of the ECM was also observed in OPCs, which did not form any adipocytes, suggesting further negative effects of a hyperglycemic environment on osteogenic differentiation.
In summary, the work provided in this thesis demonstrated that differentiation commitment of bone-resident stem cells can be altered through nutrient availability, specifically glucose. Surprisingly, both high nutrient supply, e.g. the hyperglycemic cell culture conditions, and low nutrient supply, e.g. CR, can induce adipogenic differentiation. However, while CR-induced adipocyte formation was associated with improved trabecular bone structure, adipocyte formation in a hyperglycemic cell-culture environment hampered mineralization. This thesis provides further evidence for the existence of different types of BMAT with specific functions.