TY - THES A1 - Jing, Yue T1 - Characterization of Serine Carboxypeptidase-like (SCPL) gene family in Brassicaceae Y1 - 2020 ER - TY - JOUR A1 - Ryo, Masahiro A1 - Jeschke, Jonathan M. A1 - Rillig, Matthias C. A1 - Heger, Tina T1 - Machine learning with the hierarchy-of-hypotheses (HoH) approach discovers novel pattern in studies on biological invasions JF - Research synthesis methods N2 - Research synthesis on simple yet general hypotheses and ideas is challenging in scientific disciplines studying highly context-dependent systems such as medical, social, and biological sciences. This study shows that machine learning, equation-free statistical modeling of artificial intelligence, is a promising synthesis tool for discovering novel patterns and the source of controversy in a general hypothesis. We apply a decision tree algorithm, assuming that evidence from various contexts can be adequately integrated in a hierarchically nested structure. As a case study, we analyzed 163 articles that studied a prominent hypothesis in invasion biology, the enemy release hypothesis. We explored if any of the nine attributes that classify each study can differentiate conclusions as classification problem. Results corroborated that machine learning can be useful for research synthesis, as the algorithm could detect patterns that had been already focused in previous narrative reviews. Compared with the previous synthesis study that assessed the same evidence collection based on experts' judgement, the algorithm has newly proposed that the studies focusing on Asian regions mostly supported the hypothesis, suggesting that more detailed investigations in these regions can enhance our understanding of the hypothesis. We suggest that machine learning algorithms can be a promising synthesis tool especially where studies (a) reformulate a general hypothesis from different perspectives, (b) use different methods or variables, or (c) report insufficient information for conducting meta-analyses. KW - artificial intelligence KW - hierarchy-of-hypotheses approach KW - machine learning KW - meta-analysis KW - synthesis KW - systematic review Y1 - 2019 U6 - https://doi.org/10.1002/jrsm.1363 SN - 1759-2879 SN - 1759-2887 VL - 11 IS - 1 SP - 66 EP - 73 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Schaub, Tonio A1 - Klaassen, Raymond H. G. A1 - Bouten, Willem A1 - Schlaich, Almut E. A1 - Koks, Ben J. T1 - Collision risk of Montagu’s Harriers Circus pygargus with wind turbines derived from high-resolution GPS tracking JF - Ibis : the international journal of avian science ; the journal of the British Ornithologists' Union N2 - Flight behaviour characteristics such as flight altitude and avoidance behaviour determine the species-specific collision risk of birds with wind turbines. However, traditional observational methods exhibit limited positional accuracy. High-resolution GPS telemetry represents a promising method to overcome this drawback. In this study, we used three-dimensional GPS tracking data including high-accuracy tracks recorded at 3-s intervals to investigate the collision risk of breeding male Montagu's Harriers Circus pygargus in the Dutch–German border region. Avoidance of wind turbines was quantified by a novel approach comparing observed flights to a null model of random flight behaviour. On average, Montagu's Harriers spent as much as 8.2 h per day in flight. Most flights were at low altitude, with only 7.1% within the average rotor height range (RHR; 45–125 m). Montagu's Harriers showed significant avoidance behaviour, approaching turbines less often than expected, particularly when flying within the RHR (avoidance rate of 93.5%). For the present state, with wind farms situated on the fringes of the regional nesting range, collision risk models based on our new insights on flight behaviour indicated 0.6–2.0 yearly collisions of adult males (as compared with a population size of c. 40 pairs). However, the erection of a new wind farm inside the core breeding area could markedly increase mortality (up to 9.7 yearly collisions). If repowering of the wind farms was carried out using low-reaching modern turbines (RHR 36–150 m), mortality would more than double, whereas it would stay approximately constant if higher turbines (RHR 86–200 m) were used. Our study demonstrates the great potential of high-resolution GPS tracking for collision risk assessments. The resulting information on collision-related flight behaviour allows for performing detailed scenario analyses on wind farm siting and turbine design, in contrast to current environmental assessment practices. With regard to Montagu's Harriers, we conclude that although the deployment of higher wind turbines represents an opportunity to reduce collision risk for this species, precluding wind energy developments in core breeding areas remains the most important mitigation measure. KW - avoidance rate KW - environmental impact KW - flight height KW - human-wildlife conflict KW - mitigation KW - raptors KW - renewable energy KW - wind energy Y1 - 2019 U6 - https://doi.org/10.1111/ibi.12788 SN - 0019-1019 SN - 1474-919X VL - 162 IS - 2 SP - 520 EP - 534 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Voigt, Christian A1 - Scholl, Julia M. A1 - Bauer, Juliane A1 - Teige, Tobias A1 - Yovel, Yossi A1 - Kramer-Schadt, Stephanie A1 - Gras, Pierre T1 - Movement responses of common noctule bats to the illuminated urban landscape JF - Landscape ecology N2 - Context Cities are a challenging habitat for obligate nocturnal mammals because of the ubiquitous use of artificial light at night (ALAN). How nocturnal animals move in an urban landscape, particularly in response to ALAN is largely unknown. Objectives We studied the movement responses, foraging and commuting, of common noctules (Nyctalus noctula) to urban landscape features in general and ALAN in particular. Methods We equipped 20 bats with miniaturized GPS loggers in the Berlin metropolitan area and related spatial positions of bats to anthropogenic and natural landscape features and levels of ALAN. Results Common noctules foraged close to ALAN only next to bodies of water or well vegetated areas, probably to exploit swarms of insects lured by street lights. In contrast, they avoided illuminated roads, irrespective of vegetation cover nearby. Predictive maps identified most of the metropolitan area as non-favoured by this species because of high levels of impervious surfaces and ALAN. Dark corridors were used by common noctules for commuting and thus likely improved the permeability of the city landscape. Conclusions We conclude that the spatial use of common noctules, previously considered to be more tolerant to light than other bats, is largely constrained by ALAN. Our study is the first individual-based GPS tracking study to show sensitive responses of nocturnal wildlife to light pollution. Approaches to protect urban biodiversity need to include ALAN to safeguard the larger network of dark habitats for bats and other nocturnal species in cities. KW - Urbanization KW - GPS tracking KW - Artificial light at night KW - ALAN KW - Habitat use KW - Preference KW - Movement KW - Common noctule bat Y1 - 2019 U6 - https://doi.org/10.1007/s10980-019-00942-4 SN - 0921-2973 SN - 1572-9761 VL - 35 IS - 1 SP - 189 EP - 201 PB - Springer CY - Dordrecht ER - TY - THES A1 - Moratti, Fabio Giulio T1 - Structural analysis of DYW proteins and identification of the mitochondrial DNA-binding proteome of Arabidopsis thaliana Y1 - 2020 ER - TY - THES A1 - Wenk, Sebastian T1 - Engineering formatotrophic growth in Escherichia coli N2 - To meet the demands of a growing world population while reducing carbon dioxide (CO2) emissions, it is necessary to capture CO2 and convert it into value-added compounds. In recent years, metabolic engineering of microbes has gained strong momentum as a strategy for the production of valuable chemicals. As common microbial feedstocks like glucose directly compete with human consumption, the one carbon (C1) compound formate was suggested as an alternative feedstock. Formate can be easily produced by various means including electrochemical reduction of CO2 and could serve as a feedstock for microbial production, hence presenting a novel entry point for CO2 to the biosphere and a storage option for excess electricity. Compared to the gaseous molecule CO2, formate is a highly soluble compound that can be easily handled and stored. It can serve as a carbon and energy source for natural formatotrophs, but these microbes are difficult to cultivate and engineer. In this work, I present the results of several projects that aim to establish efficient formatotrophic growth of E. coli – which cannot naturally grow on formate – via synthetic formate assimilation pathways. In the first study, I establish a workflow for growth-coupled metabolic engineering of E. coli. I demonstrate this approach by presenting an engineering scheme for the PFL-threonine cycle, a synthetic pathway for anaerobic formate assimilation in E. coli. The described methods are intended to create a standardized toolbox for engineers that aim to establish novel metabolic routes in E. coli and related organisms. The second chapter presents a study on the catalytic efficiency of C1-oxidizing enzymes in vivo. As formatotrophic growth requires generation of both energy and biomass from formate, the engineered E. coli strains need to be equipped with a highly efficient formate dehydrogenase, which provides reduction equivalents and ATP for formate assimilation. I engineered a strain that cannot generate reducing power and energy for cellular growth, when fed on acetate. Under this condition, the strain depends on the introduction of an enzymatic system for NADH regeneration, which could further produce ATP via oxidative phosphorylation. I show that the strain presents a valuable testing platform for C1-oxidizing enzymes by testing different NAD-dependent formate and methanol dehydrogenases in the energy auxotroph strain. Using this platform, several candidate enzymes with high in vivo activity, were identified and characterized as potential energy-generating systems for synthetic formatotrophic or methylotrophic growth in E. coli.   In the third chapter, I present the establishment of the serine threonine cycle (STC) – a synthetic formate assimilation pathway – in E. coli. In this pathway, formate is assimilated via formate tetrahydrofolate ligase (FtfL) from Methylobacterium extorquens (M. extorquens). The carbon from formate is attached to glycine to produce serine, which is converted into pyruvate entering central metabolism. Via the natural threonine synthesis and cleavage route, glycine is regenerated and acetyl-CoA is produced as the pathway product. I engineered several selection strains that depend on different STC modules for growth and determined key enzymes that enable high flux through threonine synthesis and cleavage. I could show that expression of an auxiliary formate dehydrogenase was required to achieve growth via threonine synthesis and cleavage on pyruvate. By overexpressing most of the pathway enzymes from the genome, and applying adaptive laboratory evolution, growth on glycine and formate was achieved, indicating the activity of the complete cycle. The fourth chapter shows the establishment of the reductive glycine pathway (rGP) – a short, linear formate assimilation route – in E. coli. As in the STC, formate is assimilated via M. extorquens FtfL. The C1 from formate is condensed with CO2 via the reverse reaction of the glycine cleavage system to produce glycine. Another carbon from formate is attached to glycine to form serine, which is assimilated into central metabolism via pyruvate. The engineered E. coli strain, expressing most of the pathway genes from the genome, can grow via the rGP with formate or methanol as a sole carbon and energy source. N2 - Um den steigenden Bedarf einer wachsenden Weltbevölkerung zu decken und gleichzeitig die CO2-Emissionen zu reduzieren, ist es notwendig, CO2 aufzufangen und zu recyceln. Durch gentechnische Veränderungen von Mikroorganismen ist es möglich diese zur Produktion wertvoller organischer Verbindungen zu nutzen. Da mikrobielle Kulturen primär mit Glucose gefüttert werden und somit mit menschlicher Nahrungsversorgung konkurrieren, wurde die C1-Verbindung Formiat als alternativer bakterieller Nährstoff vorgeschlagen.. Formiat kann durch unterschiedliche Verfahren hergestellt werden, unter anderem durch elektrochemische Reduktion von CO2. Dieses Verfahren ermöglicht das Recycling von CO2 und weiterhin eine Speichermöglichkeit für überschüssige Elektrizität. Formiat ist im Vergleich zum gasförmigen CO2 gut wasserlöslich, was den Transport und die Verwendung als mikrobiellen Nährstoff erleichtert. Natürlich vorkommende formatotrophe Mikroorganismen nutzen Formiat als Kohlenstoff- und Energiequelle. Diese lassen sich allerdings meist schwierig kultivieren und genetisch verändern. In dieser Arbeit stelle ich die Ergebnisse verschiedener Projekte vor, die gemeinsam darauf abzielen, effizientes formatotrophes Wachstum von E. coli – welches natürlicherweise nicht auf Formiat wachsen kann – mittels synthetischer Formiat-Assimilierungswege zu ermöglichen. In der ersten Studie stelle ich eine Strategie für wachstumsgekoppeltes Stoffwechsel-Engineering in E. coli vor. Ich erläutere diese Strategie anhand eines Beispiels, der schrittweisen Etablierung eines synthetischen Formiat- Assimilierungswegs, des PFL-Threonin-Zyklus. Die in diesem Kapitel beschriebenen Methoden sollen einen Leitfaden für Ingenieure bereitstellen, die neue Stoffwechselwege in E. coli und verwandten Organismen etablieren wollen. Im zweiten Kapitel stelle ich eine Studie über die katalytische Effizienz von C1-oxidierenden Enzymen vor. Da formatotrophes Wachstum sowohl die Erzeugung von Energie als auch von Biomasse aus Formiat erfordert, müssen synthetisch formatotrophe E. coli Stämme mit einer hocheffizienten Formiat-Dehydrogenase ausgestattet werden, welche Reduktionsäquivalente und ATP für die Assimilierung von Formiat liefert. Um die Effizienz verschiedener Enzyme testen und vergleichen zu können, entwickelte ich einen E. coli Stamm, der aus Acetat weder Reduktionsäquivalente noch Energie für das Zellwachstum erzeugen kann. Dieser „energie-auxotrophe“ Stamm benötigt eines zusätzlichen enzymatischen Systems zur NADH-Regenerierung, um auf Acetat wachsen zu können. Ich testete verschiedene NAD-abhängige Formiat- und Methanol-Dehydrogenasen in diesem Stamm und konnte zeigen, dass Wachstum auf Acetat durch Zugabe von Formiat oder Methanol ermöglicht wurde. Dies zeigt, dass der Stamm eine zuverlässige Testplattform für C1-oxidierende Enzyme darstellt. Unter Verwendung dieser Plattform wurden mehrere Kandidatenenzyme mit hoher in vivo-Aktivität identifiziert und als Kandidatenenzyme für synthetisches formatotrophes oder methylotrophes Wachstum in E. coli charakterisiert.   Im dritten Kapitel stelle ich die Etablierung des Serin-Threonin-Zyklus (STZ) – eines synthetischen Formiat-Assimilationswegs – in E. coli vor. In diesem Stoffwechselweg wird Formiat über die Formiat-Tetrahydrofolat-Ligase (FtfL) aus Methylobacterium extorquens (M. extorquens) assimiliert. Der Kohlenstoff aus Formiat wird an Glycin gebunden, um Serin zu produzieren, welches im nächsten Schritt in Pyruvat umgewandelt wird und so in den zentralen Kohlenstoffmetabolismus gelangt. Über den natürlichen Threonin-Synthese- und Spaltweg wird Glycin regeneriert und Acetyl-CoA als Produkt des Stoffwechselwegs generiert. Ich entwickelte mehrere E. coli Selektionsstämme, deren Wachstum von verschiedenen STZ-Modulen abhängt, und konnte Schlüsselenzyme bestimmen, die einen hohen Reaktionsfluss durch die Threonin-Synthese und -Spaltung ermöglichen. Ich konnte zeigen, dass die Expression einer Formiat-Dehydrogenase erforderlich ist, um Wachstum auf Pyruvat über Threonin zu erreichen. Durch Integration und Überexpression der meisten Enzyme des STZ auf Genomebene und Anwendung adaptiver Laborevolution wurde Wachstum auf Glycin und Formiat erreicht, was bedeutet, dass der gesamte Serin-Threonin-Zyklus in E. coli aktiv ist. Das vierte Kapitel zeigt die Etablierung des reduktiven Glycinwegs (rGW) – eines kurzen, linearen Formiat-Assimilierungswegs – in E. coli. Wie im STZ wird Formiat über M. extorquens FtfL assimiliert. Dabei wird das Kohlenstoffatom aus Formiat mit CO2 über die umgekehrte Reaktion des Glycin-Spaltungssystems zu Glycin kondensiert. Ein weiteres Kohlenstoffatom aus Formiat wird an Glycin gebunden, um Serin zu bilden, welches über Pyruvat in den Zentralstoffwechsel gelangt. Durch Expression der rGW Enzyme auf Genomebene und adaptive Laborevolution wurde ein E. coli Stamm erzeugt welcher über den rGW auf Formiat oder Methanol als einziger Kohlenstoff- und Energiequelle wachsen kann. KW - metabolic engineering KW - E. coli KW - formate assimilation KW - methanol assimilation KW - energy metabolism Y1 - 2020 ER - TY - THES A1 - Kubis, Armin T1 - Synthetic carbon neutral photorespiration bypasses BT - implementation and testing in Escherichia coli N2 - With populations growing worldwide and climate change threatening food production there is an urgent need to find ways to ensure food security. Increasing carbon fixation rate in plants is a promising approach to boost crop yields. The carbon-fixing enzyme Rubisco catalyzes, beside the carboxylation reaction, also an oxygenation reaction that generates glycolate-2P, which needs to be recycled via a metabolic route termed photorespiration. Photorespiration dissipates energy and most importantly releases previously fixed CO2, thus significantly lowering carbon fixation rate and yield. Engineering plants to omit photorespiratory CO2 release is the goal of the FutureAgriculture consortium and this thesis is part of this collaboration. The consortium aims to establish alternative glycolate-2P recycling routes that do not release CO2. Ultimately, they are expected to increase carbon fixation rates and crop yields. Natural and novel reactions, which require enzyme engineering, were considered in the pathway design process. Here I describe the engineering of two pathways, the arabinose-5P and the erythrulose shunt. They were designed to recycle glycolate-2P via glycolaldehyde into a sugar phosphate and thereby reassimilate glycolate-2P to the Calvin cycle. I used Escherichia coli gene deletion strains to validate and characterize the activity of both synthetic shunts. The strains’ auxotrophies can be alleviated by the activity of the synthetic route, thus providing a direct way to select for pathway activity. I introduced all pathway components to these dedicated selection strains and discovered inhibitions, limitations and metabolic cross talk interfering with pathway activity. After resolving these issues, I was able to show the in vivo activity of all pathway components and combine them into functional modules.. Specifically, I demonstrate the activity of a new-to-nature module of glycolate reduction to glycolaldehyde. Also, I successfully show a new glycolaldehyde assimilation route via arabinose-5P to ribulose-5P. In addition, all necessary enzymes for glycolaldehyde assimilation via L-erythrulose were shown to be active and an L-threitol assimilation route via L-erythrulose was established in E. coli. On their own, these findings demonstrate the power of using an easily engineerable microbe to test novel pathways; combined, they will form the basis for implementing photorespiration bypasses in plants. KW - Synthetic Biology KW - Photorespiration KW - Metabolic Engineering KW - Escherichia coli Y1 - 2020 ER - TY - JOUR A1 - Werger, Luise A1 - Bergmann, Joana A1 - Weber, Ewald A1 - Heinze, Johannes T1 - Wind intensity affects fine root morphological traits with consequences for plant-soil feedback effects JF - Annals of Botany Plants N2 - Wind influences the development, architecture and morphology of plant roots and may modify subsequent interactions between plants and soil (plant–soil feedbacks—PSFs). However, information on wind effects on fine root morphology is scarce and the extent to which wind changes plant–soil interactions remains unclear. Therefore, we investigated the effects of two wind intensity levels by manipulating surrounding vegetation height in a grassland PSF field experiment. We grew four common plant species (two grasses and two non-leguminous forbs) with soil biota either previously conditioned by these or other species and tested the effect of wind on root:shoot ratio, fine root morphological traits as well as the outcome for PSFs. Wind intensity did not affect biomass allocation (i.e. root:shoot ratio) in any species. However, fine-root morphology of all species changed under high wind intensity. High wind intensity increased specific root length and surface area and decreased root tissue density, especially in the two grasses. Similarly, the direction of PSFs changed under high wind intensity in all four species, but differences in biomass production on the different soils between high and low wind intensity were marginal and most pronounced when comparing grasses with forbs. Because soils did not differ in plant-available nor total nutrient content, the results suggest that wind-induced changes in root morphology have the potential to influence plant–soil interactions. Linking wind-induced changes in fine-root morphology to effects on PSF improves our understanding of plant–soil interactions under changing environmental conditions. KW - Wind KW - root traits KW - root morphology KW - specific root length KW - plant–soil feedback Y1 - 2020 U6 - https://doi.org/10.1093/aobpla/plaa050 SN - 2041-2851 VL - 12 IS - 5 PB - Oxford University Press CY - Oxford ER - TY - THES A1 - Kožul, Danijela T1 - Systematic identification of loci determining chloroplast and nuclear genome incompatibility in the evening primrose (Oenothera) Y1 - 2020 ER - TY - JOUR A1 - He, Hai A1 - Höper, Rune A1 - Dodenhöft, Moritz A1 - Marlière, Philippe A1 - Bar-Even, Arren T1 - An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli JF - Metabolic Engineering N2 - Engineering biotechnological microorganisms to use methanol as a feedstock for bioproduction is a major goal for the synthetic metabolism community. Here, we aim to redesign the natural serine cycle for implementation in E. coli. We propose the homoserine cycle, relying on two promiscuous formaldehyde aldolase reactions, as a superior pathway design. The homoserine cycle is expected to outperform the serine cycle and its variants with respect to biomass yield, thermodynamic favorability, and integration with host endogenous metabolism. Even as compared to the RuMP cycle, the most efficient naturally occurring methanol assimilation route, the homoserine cycle is expected to support higher yields of a wide array of products. We test the in vivo feasibility of the homoserine cycle by constructing several E. coli gene deletion strains whose growth is coupled to the activity of different pathway segments. Using this approach, we demonstrate that all required promiscuous enzymes are active enough to enable growth of the auxotrophic strains. Our findings thus identify a novel metabolic solution that opens the way to an optimized methylotrophic platform. KW - Pathway design KW - Promiscuous enzymes KW - Formaldehyde assimilation KW - Serine cycle KW - Growth selection Y1 - 2020 U6 - https://doi.org/10.1016/j.ymben.2020.03.002 SN - 1096-7176 SN - 1096-7184 VL - 60 SP - 1 EP - 13 PB - Elsevier CY - Amsterdam [u.a.] ER -