TY - CHAP A1 - Inäbnit, Thomas A1 - Dennis, Alice B. T1 - The mitochondrial genome of Melampus bidentatus (Panpulmonata, Ellobioidea) T2 - Integrative and comparative biology / Society of Integrative and Comparative Biology Y1 - 2021 SN - 1540-7063 SN - 1557-7023 VL - 61 IS - Supplement 1 SP - E405 EP - E405 PB - Oxford University Press CY - Oxford ER - TY - JOUR A1 - Smith, Sarah R. A1 - Dupont, Chris L. A1 - McCarthy, James K. A1 - Broddrick, Jared T. A1 - Obornik, Miroslav A1 - Horak, Ales A1 - Füssy, Zoltán A1 - Cihlar, Jaromir A1 - Kleessen, Sabrina A1 - Zheng, Hong A1 - McCrow, John P. A1 - Hixson, Kim K. A1 - Araujo, Wagner L. A1 - Nunes-Nesi, Adriano A1 - Fernie, Alisdair A1 - Nikoloski, Zoran A1 - Palsson, Bernhard O. A1 - Allen, Andrew E. T1 - Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom JF - Nature Communications N2 - Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa. KW - Biochemistry KW - Computational biology and bioinformatics KW - Evolution KW - Microbiology KW - Molecular biology Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-12407-y SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Ma, Xuemin A1 - Zhang, Youjun A1 - Tureckova, Veronika A1 - Xue, Gang-Ping A1 - Fernie, Alisdair A1 - Mueller-Röber, Bernd A1 - Balazadeh, Salma T1 - The NAC Transcription Factor SlNAP2 Regulates Leaf Senescence and Fruit Yield in Tomato JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Leaf senescence is an essential physiological process in plants that supports the recycling of nitrogen and other nutrients to support the growth of developing organs, including young leaves, seeds, and fruits. Thus, the regulation of senescence is crucial for evolutionary success in wild populations and for increasing yield in crops. Here, we describe the influence of a NAC transcription factor, SlNAP2 (Solanum lycopersicum NAC-like, activated by Apetala3/Pistillata), that controls both leaf senescence and fruit yield in tomato (S. lycopersicum). SlNAP2 expression increases during age-dependent and dark-induced leaf senescence. We demonstrate that SlNAP2 activates SlSAG113 (S. lycopersicum SENESCENCE-ASSOCIATED GENE113), a homolog of Arabidopsis (Arabidopsis thaliana) SAG113, chlorophyll degradation genes such as SlSGR1 (S. lycopersicum senescence-inducible chloroplast stay-green protein 1) and SlPAO (S. lycopersicum pheide a oxygenase), and other downstream targets by directly binding to their promoters, thereby promoting leaf senescence. Furthermore, SlNAP2 directly controls the expression of genes important for abscisic acid (ABA) biosynthesis, S. lycopersicum 9-cis-epoxycarotenoid dioxygenase 1 (SlNCED1); transport, S. lycopersicum ABC transporter G family member 40 (SlABCG40); and degradation, S. lycopersicum ABA 8′-hydroxylase (SlCYP707A2), indicating that SlNAP2 has a complex role in establishing ABA homeostasis during leaf senescence. Inhibiting SlNAP2 expression in transgenic tomato plants impedes leaf senescence but enhances fruit yield and sugar content likely due to prolonged leaf photosynthesis in aging tomato plants. Our data indicate that SlNAP2 has a central role in controlling leaf senescence and fruit yield in tomato. Y1 - 2018 U6 - https://doi.org/10.1104/pp.18.00292 SN - 0032-0889 SN - 1532-2548 VL - 177 IS - 3 SP - 1286 EP - 1302 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Kamranfar, Iman A1 - Xue, Gang-Ping A1 - Tohge, Takayuki A1 - Sedaghatmehr, Mastoureh A1 - Fernie, Alisdair A1 - Balazadeh, Salma A1 - Mueller-Roeber, Bernd T1 - Transcription factor RD26 is a key regulator of metabolic reprogramming during dark-induced senescence JF - New phytologist : international journal of plant science N2 - Leaf senescence is a key process in plants that culminates in the degradation of cellular constituents and massive reprogramming of metabolism for the recovery of nutrients from aged leaves for their reuse in newly developing sinks. We used molecular-biological and metabolomics approaches to identify NAC transcription factor (TF) RD26 as an important regulator of metabolic reprogramming in Arabidopsis thaliana. RD26 directly activates CHLOROPLAST VESICULATION (CV), encoding a protein crucial for chloroplast protein degradation, concomitant with an enhanced protein loss in RD26 over-expressors during senescence, but a reduced decline of protein in rd26 knockout mutants. RD26 also directly activates LKR/SDH involved in lysine catabolism, and PES1 important for phytol degradation. Metabolic profiling revealed reduced c-aminobutyric acid (GABA) in RD26 overexpressors, accompanied by the induction of respective catabolic genes. Degradation of lysine, phytol and GABA is instrumental for maintaining mitochondrial respiration in carbon-limiting conditions during senescence. RD26 also supports the degradation of starch and the accumulation of mono-and disaccharides during senescence by directly enhancing the expression of AMY1, SFP1 and SWEET15 involved in carbohydrate metabolism and transport. Collectively, during senescence RD26 acts by controlling the expression of genes across the entire spectrum of the cellular degradation hierarchy. KW - Arabidopsis KW - fatty acid KW - primary metabolism KW - protein and amino acid degradation KW - respiration KW - senescence Y1 - 2018 U6 - https://doi.org/10.1111/nph.15127 SN - 0028-646X SN - 1469-8137 VL - 218 IS - 4 SP - 1543 EP - 1557 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Ferrari, Camilla A1 - Proost, Sebastian A1 - Janowski, Marcin Andrzej A1 - Becker, Jörg A1 - Nikoloski, Zoran A1 - Bhattacharya, Debashish A1 - Price, Dana A1 - Tohge, Takayuki A1 - Bar-Even, Arren A1 - Fernie, Alisdair A1 - Stitt, Mark A1 - Mutwil, Marek T1 - Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida JF - Nature Communications N2 - Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-08703-2 SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Zhang, Youjun A1 - Chen, Moxian A1 - Siemiatkowska, Beata A1 - Toleco, Mitchell Rey A1 - Jing, Yue A1 - Strotmann, Vivien A1 - Zhang, Jianghua A1 - Stahl, Yvonne A1 - Fernie, Alisdair T1 - A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species JF - Plant Communications N2 - Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis. KW - transient expression KW - agro-infiltration KW - subcellular localization KW - protein-protein interaction Y1 - 2019 SN - 2590-3462 VL - 1 IS - 5 PB - Science Direct CY - New York ER - TY - THES A1 - Jing, Yue T1 - Characterization of Serine Carboxypeptidase-like (SCPL) gene family in Brassicaceae Y1 - 2020 ER - TY - THES A1 - Naake, Thomas T1 - Strategies to investigate the natural variation of plant specialized metabolism Y1 - 2020 ER - TY - THES A1 - Mahto, Harendra T1 - In vitro analysis of Early Starvation 1 (ESV1) and Like Early Starvation 1 (LESV) on starch degradation with focus on glucan, water dikinase (GWD) and phosphoglucan, water dikinase (PWD) N2 - 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. N2 - Stärke ist ein unlösliches Polyglucan, das aus zwei Polymeren besteht, nämlich dem verzweigten α-1,4: α-1,6-D-Glucan Amylopektin und dem fast unverzweigten α-1,4-D-Glucan Amylose. Das Wachstum aller Pflanzen hängt direkt von der Akkumulation transitorischer Stärke während des Tages, wenn die Photosynthese stattfindet, und dem anschließenden Stärkeabbau während der Nacht ab. Die Phosphorylierung von Stärke erfolgt durch stärkeverwandte Dikinasen, die α-Glucan-Wasser-Dikinase (GWD) und Phosphoglucan-Wasser-Dikinase (PWD), und ist ein entscheidender Schritt beim Stärkeabbau. Die biochemischen Mechanismen der Phosphorylierung von Stärke sind nicht genau bekannt. Jüngste Studien haben ergeben, dass es zwei stärkebindende Proteine gibt, nämlich Early Starvation1 (ESV1) und Like Early Starvation1 (LESV), die eine wichtige Rolle im Stärkestoffwechsel spielen. Es hat sich gezeigt, dass ESV1- und LESV-Proteine die Stärkephosphorylierungsaktivität der GWD- und PWD-Enzyme beeinflussen, die die Geschwindigkeit des Abbaus von Stärkekörnern steuern. In dieser Arbeit wurden verschiedene In-vitro-Tests durchgeführt, um den Mechanismus der rekombinanten Proteine ESV1 und LESV auf den Stärkeabbau zu identifizieren und zu verstehen.Der Stärkeabbau wurde von den Phosphorylierungsenzymen GWD und PWD getrennt durchgeführt. In verschiedenen enzymatischen Assays wurde der Einfluss von ESV1 und LESV auf die Wirkung von GWD und PWD auf die Oberflächen verschiedener nativer Stärkekörner analysiert. Darüber hinaus haben ESV1 und LESV spezifisch Einflüsse auf die Phosphorylierungsaktivitäten von GWD und PWD auf den Oberflächen der Stärkekörner in einem antagonistischen Muster gezeigt, so dass die GWD-vermittelte Phosphorylierung signifikant reduziert wurde, während die PWD-vermittelte Phosphorylierung signifikant erhöht wurde. In einer anderen Versuchsreihe wurden ISA- und BAM verwendet, um die Struktur der Stärke zu verändern und dann die Auswirkungen der durch beide Dikinasen vermittelten Phosphorylierung in Gegenwart von ESV1 und LESV auf die veränderten Oberflächen der Stärkekörner zu bestimmen. In diesen Ergebnissen wurde ein signifikanter Rückgang der GWD- und PWD-vermittelten Phosphorylierung in allen Behandlungen beobachtet, die entweder nur ESV1- oder LESV-Proteine oder sowohl ESV1 als auch LESV enthielten. Es wurde auch festgestellt, dass LESV vorzugsweise an Amylose und Amylopektin bindet, während ESV1 an hochgeordnete Glucane wie Maltodextrine und Amylopektin bindet, die eine kristalline Struktur aufweisen. Sowohl ESV1- als auch LESV-Proteine haben entweder einzeln oder in Kombination einen Einfluss auf die Aktivität des GWD- und PWD-Phosphateinbaus in die Stärkekörner durch Reduktion gezeigt, jedoch zu unterschiedlichen Prozentsätzen, je nach Stärkequelle, so dass es schwierig ist, ihre spezifische Funktion zu unterscheiden. Die biochemischen Untersuchungen zeigen, dass die Protein-Glucan-Interaktion speziell zwischen ESV1 oder LESV oder in Kombination mit verschiedenen Arten von Stärkekörnern eine sehr starke Oberflächenbindung aufweist, oder es ist möglich, dass beide Proteine nicht nur an die Oberfläche der Stärkekörner binden, sondern auch tief in die Glucanstruktur der Stärkekörner eingedrungen sind. Die Ergebnisse zeigten jedoch auch, dass ESV1 und LESV die Autophosphorylierung der Dikinasen nicht veränderten. Außerdem wurde die Kettenlängenverteilung der freigesetzten Glucanketten nach Behandlung der Stärke mit dem ISA-Enzym im Hinblick auf den Polymerisationsgrad (DP) der verschiedenen Stärkekörner bewertet. Mit Hilfe der Kapillarelektrophorese wurde die Wirkung von LESV und ESV1 auf die Kettenlängenverteilung untersucht. Zusammenfassend bestätigt diese Studie, dass ESV1 und LESV eine wichtige Rolle bei der Organisation und Regulierung des Stärkestoffwechsels spielen. In der zweiten Hälfte wurden Untersuchungen durchgeführt, um zu prüfen, ob der Stoffwechsel von Kohlenhydraten und deren Verteilung zu der höheren Salztoleranz des fakultativen Halophyten Hordeum marinum im Vergleich zum Glykophyten Hordeum vulgare beitragen. Die gleich großen Sämlinge beider Arten wurden 3 Wochen lang bei 0, 150 und 300 mM NaCl hydroponisch gezogen. H. marinum wies eine hohe relative Wachstumsrate auf, die mit einer höheren Fähigkeit der Pflanzen einherging, unter Salzbedingungen eine effiziente Hydratation des Sprossgewebes und die Integrität der Membran aufrechtzuerhalten, als dies bei H. vulgare der Fall war. Unsere Daten deuten also darauf hin, dass die Veränderungen in der Stärkespeicherung, die Verteilung der Konzentrationen löslicher Zucker zwischen Source- und Sinkorganen und auch die Veränderungen in der Menge der am Stärkestoffwechsel beteiligten Enzyme von Bedeutung sind und Einblicke in die Bedeutung des Kohlenhydratstoffwechsels bei Gerstenarten im Hinblick auf die Salztoleranz geben. Obwohl sich diese Ergebnisse noch im Anfangsstadium befinden, könnten sie für andere Forscher bei der Formulierung künftiger Studien von entscheidender Bedeutung sein. Die vorläufigen Ergebnisse der Studien über den Kohlenhydratstoffwechsel und die Verteilung der Kohlenhydrate bei Salzreaktionen im Halophyten H. marinum und im Glykophyten H. vulgare haben gezeigt, dass die Salztoleranz bei Gerstenarten nicht auf osmotische Anpassungen zurückzuführen ist, sondern auf andere Gründe, die in den bisherigen Studien nicht untersucht wurden. Die Aktivität von DPE2 in H. vulgare wurde jedoch nicht wie beobachtet durch die Anwesenheit von NaCl beeinträchtigt. Dagegen waren die Aktivitäten von Pho1 und Pho2 in kultivierter Gerste stark erhöht. Diese Ergebnisse könnten auf eine mögliche Rolle dieser Enzyme bei der Reaktion des Kohlenhydratstoffwechsels auf den Salzgehalt hinweisen. Beim Vergleich von Meeres- und Kulturgerstenarten wurde festgestellt, dass erstere eine größere Vielseitigkeit im Kohlenhydratstoffwechsel und in der Kohlenhydratverteilung aufweisen. KW - Arabidopsis thaliana KW - starch phosphorylation KW - phosphoglucan KW - starch granule surface KW - Early Starvation 1 Y1 - 2022 ER - TY - THES A1 - Seerangan, Kumar T1 - Actin-based regulation of cell and tissue scale morphogenesis in developing leaves T1 - Aktin-basierte Regulierung der Zell- und Gewebeskalenmorphogenese in sich entwickelnden Blättern N2 - 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. N2 - Die Blätter weisen entlang der proximodistalen Achse Zellen mit unterschiedlich komplexer Form auf. Heterogenitäten in den Wachstumsrichtungen innerhalb einzelner Zellen führen zu einer solchen Komplexität der Zellform. Es wurden hochkomplexe und miteinander verbundene Genregulationsnetze und Signalwege identifiziert, die diese Prozesse steuern. Darüber hinaus haben die Organisation der Zytoskelettnetze und die mechanischen Eigenschaften der Zellwand großen Einfluss auf die Regulierung der Zellform. Die Forschung hat gezeigt, dass Mikrotubuli an der Regulierung der Zelluloseablagerung und der Richtung des Zellwachstums beteiligt sind. Eine umfassende Analyse der Regulierung des Aktin-Zytoskeletts bei der Regulierung der Zellform ist jedoch noch nicht ausreichend untersucht worden. Diese Arbeit liefert Beweise dafür, dass Aktin Aspekte des Zellwachstums, der Zellteilung und der gerichteten Expansion reguliert, die die Morphogenese der sich entwickelnden Blätter beeinflussen. Die puzzleartige Morphologie der epidermalen Zellen ist ein ideales System, um den komplexen Prozess der morphogenetischen Prozesse auf zellulärer Ebene zu untersuchen. Hier haben wir Bildgebungsstudien an lebenden Zellen durchgeführt, um die Entwicklung von Epidermiszellen unter Bedingungen zu verfolgen, bei denen das Aktin beeinträchtigt ist. Eine genetische Störung der beiden vorwiegend vegetativ exprimierten Aktin-Gene ACTIN2 und ACTIN7 führt zu einer verzögerten Entstehung der zellulären Wandausstülpungen in Epidermiszellen. Die Störung des Aktins wirkte sich auch auf die Organisation der Mikrotubuli in diesen Zellen aus, von denen bekannt ist, dass sie das Entstehen von Zellwandausstülpungen fördern. Darüber hinaus ergab die Live-Zell-Darstellung der Aktin-Organisation eine Korrelation mit der Zellform, was darauf hindeutet, dass Aktin eine Rolle bei der Morphogenese der Epidermiszellen spielt. Darüber hinaus führt die Unterbrechung von Aktin zu einer Zunahme der Zellgröße entlang der Blattmittelrippe, wobei die Zellen aufgrund der verringerten Zellteilung stark anisotrop sind. Die Verringerung der Zellteilung wirkte sich auch auf die Morphologie des gesamten Blattes aus, wobei die mutierten Blätter stärker gekrümmt waren. Diese Ergebnisse deuten darauf hin, dass Aktin eine zentrale Rolle bei der Regulierung der Morphogenese auf zellulärer und geweblicher Ebene spielt, was wertvolle Einblicke in die Rolle des Aktin-Zytoskeletts bei der Morphogenese von Pflanzen ermöglicht. KW - leaf KW - pavement cell KW - actin/microtubules KW - spatio-temporal regulation KW - Blatt KW - Pflasterzelle KW - Aktin/Mikrotubuli KW - räumlich-zeitliche Regulierung Y1 - 2023 ER - TY - THES A1 - Apriyanto, Ardha T1 - Analysis of starch metabolism in source and sink tissue of plants T1 - Analyse des Stärkestoffwechsels im Source und Sink Gewebe von Pflanzen N2 - Starch is an essential biopolymer produced by plants. Starch can be made inside source tissue (such as leaves) and sink tissue (such as fruits and tubers). Nevertheless, understanding how starch metabolism is regulated in source and sink tissues is fundamental for improving crop production. Despite recent advances in the understanding of starch and its metabolism, there is still a knowledge gap in the source and sink metabolism. Therefore, this study aimed to summarize the state of the art regarding starch structure and metabolism inside plants. In addition, this study aimed to elucidate the regulation of starch metabolism in the source tissue using the leaves of a model organism, Arabidopsis thaliana, and the sink tissue of oil palm (Elaeis guineensis) fruit as a commercial crop. The research regarding the source tissue will focus on the effect of the blockage of starch degradation on the starch parameter in leaves, especially in those of A. thaliana, which lack both disproportionating enzyme 2 (DPE2) and plastidial glucan phosphorylase 1 (PHS1) (dpe2/phs1). The additional elimination of phosphoglucan water dikinase (PWD), starch excess 4 (SEX4), isoamylase 3 (ISA3), and disproportionating enzyme 1 (DPE1) in the dpe2/phs1 mutant background demonstrates the alteration of starch granule number per chloroplast. This study provides insights into the control mechanism of granule number regulation in the chloroplast. The research regarding the sink tissue will emphasize the relationship between starch metabolism and the lipid metabolism pathway in oil palm fruits. This study was conducted to observe the alteration of starch parameters, metabolite abundance, and gene expression during oil palm fruit development with different oil yields. This study shows that starch and sucrose can be used as biomarkers for oil yield in oil palms. In addition, it is revealed that the enzyme isoforms related to starch metabolism influence the oil production in oil palm fruit. Overall, this thesis presents novel information regarding starch metabolism in the source tissue of A.thaliana and the sink tissue of E.guineensis. The results shown in this thesis can be applied to many applications, such as modifying the starch parameter in other plants for specific needs. N2 - Stärke ist ein unverzichtbares Biopolymer, das von Pflanzen sowohl in den Quellgeweben (sources, z. B. Blätter) als auch in den Senkengeweben (sinks, z. B. Früchten und Knollen) gebildet wird. Daher ist ein profundes Wissen über die Regulation des Stärkestoffwechsel in den source und sink Organen von grundlegender Bedeutung für die Verbesserung der Pflanzenproduktion. Trotz der jüngsten Fortschritte im Verständnis des Stärkestoffwechsels bleiben weiterhin viele Fragen über den detaillierten source und sink Metabolismus offen. Ziel dieser Studie war es daher, den aktuellen Forschungsstand über die Struktur und den Stoffwechsel von Stärke in Pflanzen aufzuzeigen. Darüber hinaus sollte in dieser Studie die Regulierung des Stärkestoffwechsels in den Blättern (source) des Modellorganismus Arabidopsis thaliana und in den Ölpalmfrüchten (sink) von Elaeis guineensis, einer Nutzpflanze, aufgeklärt werden. Die Analyse des source Gewebes konzentrierte sich dabei auf die Auswirkungen auf Stärkeparamter wie beispielsweise die Granulazahl durch die Blockierung des Stärkeabbaus in Blättern. Dazu wurde die Arabidopsis Mutante, der das cytosolische Disproportionating Enzym 2 (DPE2) und die plastidiale Glucanphosphorylase 1 (PHS1) fehlen (dpe2/phs1), untersucht. Ebenfalls wurden Dreifachmutanten im Hintergund von dpe2/phs1, denen Starch excess 4 (SEX4), Isoamylase 3, Phosphoglucan-Wasser-Dikinase (PWD) oder das Disproportionating Enzym 1 (DPE1) fehlen, erzeugt. Die Analyse zeigt, dass die Anzahl der Stärkegranula pro Chloroplast nicht festgelegt ist und während des gesamten Wachstums der Pflanze reguliert wird. Diese Daten liefern ein verbessertes Verständnis über die Komplexität der Kontrollmechanismen der Granulazahlregulation in Chloroplasten. Die Untersuchung des sink Gewebes soll die Beziehung zwischen dem Stärkestoffwechsel und dem Lipidstoffwechselweg in Ölpalmenfrüchten verdeutlichen. Diese Studie wurde durchgeführt, um die Veränderung von Stärkeparametern, die Häufigkeit von Metaboliten und die Genexpression während der Entwicklung von Ölpalmenfrüchten mit unterschiedlichen Ölausbeuten zu erforschen. Die Analyse zeigt, dass sowohl Stärke als auch Saccharose als reliable Biomarker für den Ölertrag von Ölpalmen verwendet werden können. Darüber hinaus konnte bewiesen werden, dass die mit dem Stärkestoffwechsel verbundenen Enzymisoformen die Ölproduktion in Ölpalmenfrüchten beeinflussen. Insgesamt liefert diese Arbeit neue Informationen über den Stärkestoffwechsel im source Gewebe von A.thaliana und im sink von E.guineensis. Die in dieser Arbeit gezeigten Ergebnisse können für viele Anwendungen genutzt werden, z. B. für die Veränderung der Stärkeparameter in anderen Pflanzen für spezifische Bedürfnisse. KW - starch KW - oil palm KW - Arabidopsis thaliana KW - source and sink KW - Arabidopsis thaliana KW - Palmöl KW - Source und Sink KW - Stärke Y1 - 2023 ER - TY - JOUR A1 - Córdoba, Sandra Correa A1 - Tong, Hao A1 - Burgos, Asdrubal A1 - Zhu, Feng A1 - Alseekh, Saleh A1 - Fernie, Alisdair A1 - Nikoloski, Zoran T1 - Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism JF - Nature Communications N2 - The use of automated tools to reconstruct lipid metabolic pathways is not warranted in plants. Here, the authors construct Plant Lipid Module for Arabidopsis rosette using constraint-based modeling, demonstrate its integration in other plant metabolic models, and use it to dissect the genetic architecture of lipid metabolism. Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism. KW - Biochemical networks KW - Biochemical reaction networks KW - Genetic models KW - Plant molecular biology Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-40644-9 SN - 2041-1723 VL - 14 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Compart, Julia A1 - Zimmermann, Vincent A1 - Alseekh, Saleh A1 - Fernie, Alisdair A1 - Fettke, Jörg T1 - Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.) JF - Food chemistry N2 - Oil palm (Elaeis guineensis Jacq.) is the most productive oil-producing crop per hectare of land. The oil that accumulates in the mesocarp tissue of the fruit is the highest observed among fruit-producing plants. A comparative analysis between high-, medium-, and low-yielding oil palms, particularly during fruit development, revealed unique characteristics. Metabolomics analysis was able to distinguish accumulation patterns defining of the various developmental stages and oil yield. Interestingly, high- and medium-yielding oil palms exhibited substantially increased sucrose levels compared to low-yielding palms. In addition, parameters such as starch granule morphology, granule size, total starch content, and starch chain length distribution (CLD) differed significantly among the oil yield categories with a clear correlation between oil yield and various starch parameters. These results provide new insights into carbohydrate and starch metabolism for biosynthesis of oil palm fruits, indicating that starch and sucrose can be used as novel, easy-to-analyze, and reliable biomarker for oil yield. KW - carbohydrate KW - mesocarp KW - metabolites KW - oil palm KW - oil yield KW - sucrose; KW - starch Y1 - 2022 U6 - https://doi.org/10.1016/j.foodchem.2022.133361 SN - 0308-8146 SN - 1873-7072 VL - 393 PB - Elsevier CY - New York, NY [u.a.] ER - TY - JOUR A1 - Watanabe, Mutsumi A1 - Tohge, Takayuki A1 - Balazadeh, Salma A1 - Erban, Alexander A1 - Giavalisco, Patrick A1 - Kopka, Joachim A1 - Mueller-Roeber, Bernd A1 - Fernie, Alisdair A1 - Hoefgen, Rainer T1 - Comprehensive Metabolomics Studies of Plant Developmental Senescence JF - Plant Senescence: Methods and Protocols N2 - Leaf senescence is an essential developmental process that involves diverse metabolic changes associated with degradation of macromolecules allowing nutrient recycling and remobilization. In contrast to the significant progress in transcriptomic analysis of leaf senescence, metabolomics analyses have been relatively limited. A broad overview of metabolic changes during leaf senescence including the interactions between various metabolic pathways is required to gain a better understanding of the leaf senescence allowing to link transcriptomics with metabolomics and physiology. In this chapter, we describe how to obtain comprehensive metabolite profiles and how to dissect metabolic shifts during leaf senescence in the model plant Arabidopsis thaliana. Unlike nucleic acid analysis for transcriptomics, a comprehensive metabolite profile can only be achieved by combining a suite of analytic tools. Here, information is provided for measurements of the contents of chlorophyll, soluble proteins, and starch by spectrophotometric methods, ions by ion chromatography, thiols and amino acids by HPLC, primary metabolites by GC/TOF-MS, and secondary metabolites and lipophilic metabolites by LC/ESI-MS. These metabolite profiles provide a rich catalogue of metabolic changes during leaf senescence, which is a helpful database and blueprint to be correlated to future studies such as transcriptome and proteome analyses, forward and reverse genetic studies, or stress-induced senescence studies. KW - Senescence KW - Metabolomics KW - Arabidopsis KW - GC/MS KW - LC/MS KW - HPLC KW - IC Y1 - 2018 SN - 978-1-4939-7672-0 SN - 978-1-4939-7670-6 U6 - https://doi.org/10.1007/978-1-4939-7672-0_28 SN - 1064-3745 SN - 1940-6029 VL - 1744 SP - 339 EP - 358 PB - Humana Press CY - Totowa ER - TY - THES A1 - Apodiakou, Anastasia T1 - Analysis of the regulation of SDI genes, unravelling the role of the SLIM1 transcription factor, and the SNRK3.15 kinase in Arabidopsis under sulfur deprivation Y1 - 2024 ER - TY - THES A1 - Peng, Maolin T1 - The role of prion-like domains in plant temperatur sensing Y1 - 2023 ER - TY - CHAP A1 - Dennis, Alice B. A1 - Inäbnit, Thomas T1 - Physiological and genomic variation among cryptic species of a marsh snail (Melampus bidentatus) T2 - Integrative and comparative biology / Society of Integrative and Comparative Biology Y1 - 2021 U6 - https://doi.org/10.1093/icb/icab001 SN - 1540-7063 SN - 1557-7023 VL - 61 SP - E195 EP - E196 PB - Oxford University Press CY - Oxford ER - TY - THES A1 - Dronsella, Beau B. T1 - Overcoming natural biomass limitations in gram-negative bacteria through synthetic carbon fixation T1 - Überwindung natürlicher Biomasselimitationen in gramnegativen Bakterien mittels synthetischer Kohlenstofffixierung N2 - The carbon demands of an ever-increasing human population and the concomitant rise in net carbon emissions requires CO2 sequestering approaches for production of carbon-containing molecules. Microbial production of carbon-containing products from plant-based sugars could replace current fossil-based production. However, this form of sugar-based microbial production directly competes with human food supply and natural ecosystems. Instead, one-carbon feedstocks derived from CO2 and renewable energy were proposed as an alternative. The one carbon molecule formate is a stable, readily soluble and safe-to-store energetic mediator that can be electrochemically generated from CO2 and (excess off-peak) renewable electricity. Formate-based microbial production could represent a promising approach for a circular carbon economy. However, easy-to-engineer and efficient formate-utilizing microbes are lacking. Multiple synthetic metabolic pathways were designed for better-than-nature carbon fixation. Among them, the reductive glycine pathway was proposed as the most efficient pathway for aerobic formate assimilation. While some of these pathways have been successfully engineered in microbial hosts, these synthetic strains did so far not exceed the performance of natural strains. In this work, I engineered and optimized two different synthetic formate assimilation pathways in gram-negative bacteria to exceed the limits of a natural carbon fixation pathway, the Calvin cycle. The first chapter solidified Cupriavidus necator as a promising formatotrophic host to produce value-added chemicals. The formate tolerance of C. necator was assessed and a production pathway for crotonate established in a modularized fashion. Last, bioprocess optimization was leveraged to produce crotonate from formate at a titer of 148 mg/L. In the second chapter, I chromosomally integrated and optimized the synthetic reductive glycine pathway in C. necator using a transposon-mediated selection approach. The insertion methodology allowed selection for condition-specific tailored pathway expression as improved pathway performance led to better growth. I then showed my engineered strains to exceed the biomass yields of the Calvin cycle utilizing wildtype C. necator on formate. This demonstrated for the first time the superiority of a synthetic formate assimilation pathway and by extension of synthetic carbon fixation efforts as a whole. In chapter 3, I engineered a segment of a synthetic carbon fixation cycle in Escherichia coli. The GED cycle was proposed as a Calvin cycle alternative that does not perform a wasteful oxygenation reaction and is more energy efficient. The pathways simple architecture and reasonable driving force made it a promising candidate for enhanced carbon fixation. I created a deletion strain that coupled growth to carboxylation via the GED pathway segment. The CO2 dependence of the engineered strain and 13C-tracer analysis confirmed operation of the pathway in vivo. In the final chapter, I present my efforts of implementing the GED cycle also in C. necator, which might be a better-suited host, as it is accustomed to formatotrophic and hydrogenotrophic growth. To provide the carboxylation substrate in vivo, I engineered C. necator to utilize xylose as carbon source and created a selection strain for carboxylase activity. I verify activity of the key enzyme, the carboxylase, in the decarboxylative direction. Although CO2-dependent growth of the strain was not obtained, I showed that all enzymes required for operation of the GED cycle are active in vivo in C. necator. I then evaluate my success with engineering a linear and cyclical one-carbon fixation pathway in two different microbial hosts. The linear reductive glycine pathway presents itself as a much simpler metabolic solution for formate dependent growth over the sophisticated establishment of hard-to-balance carbon fixation cycles. Last, I highlight advantages and disadvantages of C. necator as an upcoming microbial benchmark organism for synthetic metabolism efforts and give and outlook on its potential for the future of C1-based manufacturing. N2 - Der Rohstoffbedarf einer ständig wachsenden menschlichen Bevölkerung und der damit einhergehende Anstieg der Kohlenstoffemissionen erfordert Konzepte zur CO2-Bindung für die Produktion von kohlenstoffhaltigen Molekülen. Hier bietet die mikrobielle Produktion von Chemikalien eine nachhaltige Alternative zu den bisher etablierten Syntheseprozessen. Da die Nutzung von pflanzlich hergestelltem Zucker durch die entsprechenden Mikroben allerdings in direkter Konkurrenz zur menschlichen Nahrungsmittelversorgung steht, soll aus CO2 und erneuerbarer Energie synthetisiertes Formiat (Ameisensäure) als alternativer Nährstoff nutzbar gemacht werden. Formiat fungiert als ein stabiler, leicht löslicher und sicher zu lagernder Energiespeicher, der als Ausgangsstoff mikrobieller Produktionen einen vielversprechenden Ansatz für eine nachhaltige Kreislaufwirtschaft eröffnet. Dieses Potenzial wurde bisher nicht realisiert, da es an einfach zu modifizierenden Mikroben, die Formiat effizient nutzen, mangelt. Zwecks mikrobieller Formiatnutzung wurden deshalb synthetische Stoffwechselwege entwickelt, die die Ein-Kohlenstoff Quelle deutlich effizienter als natürliche Alternativen in den Metabolismus einbringen. Die effizienteste Variante für die aerobe Formiat-Assimilation ist hierbei der reduktive Glycin-Stoffwechselweg. Während Letzterer zwar bereits erfolgreich in Mikroben eingebracht wurde, übertraf die Leistung dieser synthetischen Stämme trotz der theoretisch höheren Stoffwechseleffizienz nicht die des natürlichen Stoffwechsels. In dieser Arbeit entwickelte und optimierte ich zwei verschiedene synthetische Ein-Kohlenstoff-Fixierungswege in gramnegativen Bakterien, um die Grenzen der natürlichen CO2 Nutzung zu überschreiten. Das erste Kapitel untersuchte das Potenzial von Cupriavidus necator als vielversprechenden formatotrophen Wirt für die Produktion von Chemikalien mit hohem Mehrwert. Die Ameisensäuretoleranz von C. necator wurde getestet und ein Produktionsweg für Crotonat in einer modularen Weise etabliert. Schließlich wurde Bioprozessoptimierung genutzt, um Crotonat aus Formiat mit einem Titer von 148 mg/L zu produzieren. Im zweiten Kapitel integrierte ich den synthetischen reduktiven Glycinweg anstelle der nativen Formiatassimilierung chromosomal in C. necator und optimierte die Expressionsniveaus der beteiligten Enzyme und somit Wachstum des Stammes mit Hilfe eines transposonbasierten Selektionsansatzes. Die Kombination von randomisierter Insertionsmethodik und erzwungener Nutzung des Stoffwechselwegs für Wachstum auf Formiat ermöglichte hier die Selektion für bedingungsspezifisch optimale Expression des Stoffwechselweges, da eine höhere Operationsrate des Stoffwechselweges zu verbessertem Wachstum führte. Anschließend zeigte ich, dass meine optimierten synthetischen Stämme die Biomasseerträge des Calvin-Zyklus von C. necator auf Formiat übertrafen. Dies zeigte zum ersten Mal die bisher nur theoretisch prognostizierte Überlegenheit eines synthetischen Formiat-Assimilationsweges und damit der synthetischen Kohlenstofffixierung gegenüber natürlicher Kohlenstofffixierung. In Kapitel 3 entwickelte ich ein Segment des GED-Zyklus zur synthetischen CO2-Fixierung in Escherichia coli. Der GED-Zyklus ist eine Alternative zum Calvin-Zyklus, die im Gegensatz zu Letzterem keine ungewollte Aktivität mit Sauerstoff hat und somit energieeffizienter CO2 fixiert. Die einfache Architektur des Kreislaufs mit nur einer kritischen Reaktion macht ihn zu einem vielversprechenden Kandidaten für verbesserte Kohlenstofffixierung. Ich erzeugte einen Deletionsstamm, dessen Wachstum an besagte Reaktion, genauer die Carboxylierung mittels des GED-Segments, gekoppelt war. Die Fähigkeit des Stammes, CO2-abhängig zu wachsen, und die 13C-Tracer-Analyse bestätigten die Funktionalität des Weges in vivo. Im letzten Kapitel versuchte ich den GED-Zyklus auch in C. necator zu implementieren, da C. necator durch sein formatotrophes Wachstum potenziell ein vielversprechenderer Wirt sein könnte. Hierbei war das Wachstum des Calvin-Zyklus abhängigen Wildtyps, wie auch für den reduktiven Glycin-Weg, ein guter Referenzwert für den Vergleich mit den synthetischen Stämmen. Ich veränderte C. necator genetisch, sodass es das GED Substrat Xylose nutzt und zeigte, dass alle Enzyme für den Betrieb des Kohlenstofffixierungsweges in separierten Testeinheiten in vivo in C. necator funktional sind. Schließlich vergleiche ich meine Ergebnisse bezüglich der Entwicklung von linearer und zyklischer Ein-Kohlenstoff-Fixierung in zwei verschiedenen mikrobiellen Wirten. Es zeigt sich, dass der simplere lineare reduktive Glycinweg synthetische Formatotrophie von bisher unerschlossener Effizienz erlaubt, während sich die Realisierung komplexer autokatalytischer Kohlenstofffixierungszyklen als deutlich schwieriger erweist. Ich hebe die Vor- und Nachteile von C. necator als zukünftigem Plattformorganismus für synthetische Stoffwechselprozesse hervor und gebe einen Ausblick auf sein Potenzial für die Zukunft der C1-basierten Produktion. KW - synthetic biology KW - metabolic engineering KW - synthetic metabolism KW - carbon fixation KW - C1 assimilation KW - formate KW - reductive glycine pathway KW - GED cycle KW - cupriavidus necator KW - Ralstonia eutropha KW - H16 KW - Alcaligenes eutrophus KW - Wautersia eutropha KW - Hydrogenomonas eutrophus KW - Escherichia coli KW - bio-economy KW - Calvin cycle KW - Alcaligenes eutrophus KW - C1-Assimilation KW - Calvinzyklus KW - Escherichia coli KW - GED-Zyklus KW - H16 KW - Hydrogenomonas eutrophus KW - Ralstonia eutropha KW - Wautersia eutropha KW - Bioökonomie KW - Kohlenstofffixerung KW - Cupriavidus necator KW - Formiat KW - metabolisches Modifizieren KW - reduktiver Glycinstoffwechselweg KW - synthetische Biologie KW - synthetischer Metabolismus Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-646273 ER - TY - JOUR A1 - Qiu, Liang A1 - Zhang, Haoran A1 - Bick, Thomas A1 - Martin, Johannes A1 - Wendler, Petra A1 - Böker, Alexander A1 - Glebe, Ulrich A1 - Xing, Chengfen T1 - Construction of highly ordered glyco-inside nano-assemblies through RAFT dispersion polymerization of galactose-decorated monomer JF - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition N2 - Glyco-assemblies derived from amphiphilic sugar-decorated block copolymers (ASBCs) have emerged prominently due to their wide application, for example, in biomedicine and as drug carriers. However, to efficiently construct these glyco-assemblies is still a challenge. Herein, we report an efficient technology for the synthesis of glyco-inside nano-assemblies by utilizing RAFT polymerization of a galactose-decorated methacrylate for polymerization-induced self-assembly (PISA). Using this approach, a series of highly ordered glyco-inside nano-assemblies containing intermediate morphologies were fabricated by adjusting the length of the hydrophobic glycoblock and the polymerization solids content. A specific morphology of complex vesicles was captured during the PISA process and the formation mechanism is explained by the morphology of its precursor and intermediate. Thus, this method establishes a powerful route to fabricate glyco-assemblies with tunable morphologies and variable sizes, which is significant to enable the large-scale fabrication and wide application of glyco-assemblies. KW - galactose-decorated monomer KW - glyco-inside nano-assemblies KW - morphology KW - evolution KW - PISA KW - RAFT dispersion polymerization Y1 - 2021 U6 - https://doi.org/10.1002/anie.202015692 SN - 1433-7851 SN - 1521-3773 VL - 60 IS - 20 SP - 11098 EP - 11103 PB - Wiley-VCH CY - Weinheim ER - TY - THES A1 - Riedel, Soraya Lisanne T1 - Development of electrochemical antibody-based and enzymatic assays for mycotoxin analysis in food T1 - Entwicklung elektrochemischer Antikörper- und Enzym-basierter Assays für die Analyse von Mykotoxinen in Lebensmitteln N2 - Electrochemical methods are promising to meet the demand for easy-to-use devices monitoring key parameters in the food industry. Many companies run own lab procedures for mycotoxin analysis, but it is a major goal to simplify the analysis. The enzyme-linked immunosorbent assay using horseradish peroxidase as enzymatic label, together with 3,3',5,5' tetramethylbenzidine (TMB)/H2O2 as substrates allows sensitive mycotoxin detection with optical detection methods. For the miniaturization of the detection step, an electrochemical system for mycotoxin analysis was developed. To this end, the electrochemical detection of TMB was studied by cyclic voltammetry on different screen-printed electrodes (carbon and gold) and at different pH values (pH 1 and pH 4). A stable electrode reaction, which is the basis for the further construction of the electrochemical detection system, could be achieved at pH 1 on gold electrodes. An amperometric detection method for oxidized TMB, using a custom-made flow cell for screen-printed electrodes, was established and applied for a competitive magnetic bead-based immunoassay for the mycotoxin ochratoxin A. A limit of detection of 150 pM (60 ng/L) could be obtained and the results were verified with optical detection. The applicability of the magnetic bead-based immunoassay was tested in spiked beer using a handheld potentiostat connected via Bluetooth to a smartphone for amperometric detection allowing to quantify ochratoxin A down to 1.2 nM (0.5 µg/L). Based on the developed electrochemical detection system for TMB, the applicability of the approach was demonstrated with a magnetic bead-based immunoassay for the ergot alkaloid, ergometrine. Under optimized assay conditions a limit of detection of 3 nM (1 µg/L) was achieved and in spiked rye flour samples ergometrine levels in a range from 25 to 250 µg/kg could be quantified. All results were verified with optical detection. The developed electrochemical detection method for TMB gives great promise for the detection of TMB in many other HRP-based assays. A new sensing approach, based on an enzymatic electrochemical detection system for the mycotoxin fumonisin B1 was established using an Aspergillus niger fumonisin amine oxidase (AnFAO). AnFAO was produced recombinantly in E. coli as maltose-binding protein fusion protein and catalyzes the oxidative deamination of fumonisins, producing hydrogen peroxide. It was found that AnFAO has a high storage and temperature stability. The enzyme was coupled covalently to magnetic particles, and the enzymatically produced H2O2 in the reaction with fumonisin B1 was detected amperometrically in a flow injection system using Prussian blue/carbon electrodes and the custom-made wall-jet flow cell. Fumonisin B1 could be quantified down to 1.5 µM (≈ 1 mg/L). The developed system represents a new approach to detect mycotoxins using enzymes and electrochemical methods. N2 - Zur Entwicklung von einfach zu bedienenden Vor-Ort-Geräten, welche für die Analytik von wichtigen Parametern in der Lebensmittelindustrie eingesetzt werden können, sind elektrochemische Methoden besonders vielversprechend. Viele Unternehmen führen bereits Mykotoxinanalytik in eigenen Laboren am Produktionsstandort durch, dennoch gibt es große Bestrebungen Analysenmethoden weiter zu vereinfachen. Der Enzyme-linked Immunosorbent Assay (ELISA), welcher häufig mit der Meerrettichperoxidase als enzymatischem Label und 3,3',5,5'-Tetramethylbenzidine (TMB)/H2O2 als Enzymsubstraten arbeitet, ermöglicht den sensitiven Mykotoxinnachweis mithilfe optischer Detektionsmethoden. Zur Miniaturisierung des Detektionsschrittes wurde in dieser Arbeit der Aufbau von elektrochemischen Detektionssystemen für die Mykotoxinanalytik untersucht. Dazu wurde zunächst die elektrochemische Reaktion von TMB an verschiedenen Materialien siebgedruckter Elektroden (Kohlenstoff und Gold) sowie bei verschiedenen pH-Werten (pH 1 und pH 4) untersucht. Eine stabile Elektrodenreaktion, welche die Grundlage für den weiteren Aufbau des elektrochemischen Detektionssystems darstellt, konnte bei pH 1 an Goldelektroden erzielt werden. Basierend darauf wurde eine amperometrische Detektionsmethode für oxidiertes TMB entwickelt, wofür eine maßgefertigte Durchflusszelle verwendet wurde. Die amperometrische TMB-Detektion wurde für einen kompetitiven Magnetpartikel-basierten Immunoassay für Ochratoxin A eingesetzt. Mit diesem Assay wurde eine Nachweisgrenze von 150 pM (60 ng L-1) erreicht und die Ergebnisse konnten durch optische Detektion verifiziert werden. Die Anwendbarkeit des Assays konnte in Ochratoxin A dotiertem Bier demonstriert werden, wobei für die Detektion ein tragbarer Potentiostat verwendet wurde, welcher über Bluetooth mit einem Smartphone verbunden war. Hiermit konnten niedrige Ochratoxin A Konzentration von bis zu 1.2 nM (0.5 µg L-1) bestimmt werden. Aufbauend auf dem entwickelten elektrochemischen Detektionssystem für TMB wurde die Anwendbarkeit des Ansatzes auf einen Magnetpartikel-basierten Immunoassay für das Ergotalkaloid Ergometrine, evaluiert. Unter optimierten Bedingungen konnte mit dem Assay eine Nachweisgrenze von 3 nM (1 µg L-1) erreicht werden. In mit Ergometrin versetztem Roggenmehl konnten Konzentrationen von 25 bis 250 µg kg-1 nachgewiesen werden. Die entwickelte elektrochemische Nachweismethode für TMB bietet einen vielversprechenden Ansatz für den Einsatz in vielen anderen Meerrettichperoxidase-basierten Assays. Für das Mykotoxin Fumonisin B1, wurde ein neues sensorisches System entwickelt, welches auf einem enzymatischen elektrochemischen Nachweis basiert. Hierfür wurde eine Aspergillus niger Fumonisin Aminoxidase (AnFAO) rekombinant als Fusionsprotein mit dem Maltose-bindenden Protein exprimiert. AnFAO katalysiert die oxidative Deaminierung von Fumonisinen, wobei H2O2 gebildet wird. Es konnte gezeigt werden, dass AnFAO eine hohe Lagerungs- und Temperaturstabilität hat. Für den Nachweis von Fumonisin B1 wurde das Enzym kovalent an Magnetpartikel gekoppelt. Das enzymatisch produzierte H2O2 konnte anschließend amperometrisch mithilfe von Preußisch Blau/Kohlenstoff-Elektroden in der maßgefertigten Durchflusszelle detektiert werden. Fumonisin B1 konnte bis zu einer Konzentration von 1,5 µM (≈ 1 mg L-1) quantifiziert werden. Das entwickelte System stellt einen neuen Ansatz dar, um Mykotoxine unter Nutzung von Enzymen und elektrochemischen Methoden zu detektieren. KW - mycotoxins KW - Mykotoxine KW - immunoassay KW - Immunoassay KW - food analysis KW - Lebensmittelanalytik KW - enzyme KW - Enzym KW - amperometry KW - Amperometrie Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-607477 ER - TY - JOUR A1 - Karwinkel, Thiemo A1 - Winklhofer, Michael A1 - Janner, Lars Erik A1 - Brust, Vera A1 - Hüppop, Ommo A1 - Bairlein, Franz A1 - Schmaljohann, Heiko T1 - A magnetic pulse does not affect free-flight navigation behaviour of a medium-distance songbird migrant in spring JF - The journal of experimental biology N2 - Current evidence suggests that migratory animals extract map information from the geomagnetic field for true navigation. The sensory basis underlying this feat is elusive, but presumably involves magnetic particles. A common experimental manipulation procedure consists of pre-treating animals with a magnetic pulse, with the aim of re-magnetising particles to alter the internal representation of the external field prior to a navigation task. Although pulsing provoked deflected bearings in caged songbirds, analogous studies with free-flying songbirds yielded inconsistent results. Here, we pulsed European robins (Erithacus rubecula) at an offshore stopover site during spring migration and monitored their free-flight behaviour with a regional-scale network of radio-receiving stations. We found no pulse effect on departure probability, nocturnal departure timing departure direction or consistency of flight direction. This suggests either no use of the geomagnetic map by our birds, or that magnetic pulses do not affect the sensory system underlying geomagnetic map detection. KW - bird migration KW - magnetic map KW - magnetic-particlebased sensor KW - magnetic pulse KW - magnetoreception KW - navigation Y1 - 2022 U6 - https://doi.org/10.1242/jeb.244473 SN - 0022-0949 SN - 1477-9145 VL - 225 IS - 19 PB - Company of Biologists CY - Cambridge ER - TY - JOUR A1 - Wandt, Viktoria Klara Veronika A1 - Winkelbeiner, Nicola Lisa A1 - Bornhorst, Julia A1 - Witt, Barbara A1 - Raschke, Stefanie A1 - Simon, Luise A1 - Ebert, Franziska A1 - Kipp, Anna Patricia A1 - Schwerdtle, Tanja T1 - A matter of concern BT - trace element dyshomeostasis and genomic stability in neurons JF - Redox Biology N2 - Neurons are post-mitotic cells in the brain and their integrity is of central importance to avoid neurodegeneration. Yet, the inability of self-replenishment of post-mitotic cells results in the need to withstand challenges from numerous stressors during life. Neurons are exposed to oxidative stress due to high oxygen consumption during metabolic activity in the brain. Accordingly, DNA damage can occur and accumulate, resulting in genome instability. In this context, imbalances in brain trace element homeostasis are a matter of concern, especially regarding iron, copper, manganese, zinc, and selenium. Although trace elements are essential for brain physiology, excess and deficient conditions are considered to impair neuronal maintenance. Besides increasing oxidative stress, DNA damage response and repair of oxidative DNA damage are affected by trace elements. Hence, a balanced trace element homeostasis is of particular importance to safeguard neuronal genome integrity and prevent neuronal loss. This review summarises the current state of knowledge on the impact of deficient, as well as excessive iron, copper, manganese, zinc, and selenium levels on neuronal genome stability Y1 - 2021 U6 - https://doi.org/10.1016/j.redox.2021.101877 SN - 2213-2317 VL - 41 PB - Elsevier CY - Amsterdam ER - TY - THES A1 - Liu, Qingting T1 - Regulation of Starch Granule Morphogenesis in Arabidopsis thaliana N2 - 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. N2 - Kohlenhydrate spielen eine wichtige Rolle in allen lebenden Organismen, als Grundpfeiler im primären Stoffwechsel, indem sie Energie durch ihre Hydrolyse freisetzen und anschließend wiederverwendet werden können (Apriyanto et al., 2022). Stärke ist die Hauptreserve an Kohlenhydraten in Pflanzen und liefert die essentielle Energie für das Pflanzenwachstum. Darüber hinaus dient Stärke als bedeutende Kohlenhydratquelle in der menschlichen Ernährung. Abgesehen von ihrem Nährwert hat Stärke umfangreiche industrielle Anwendungen in Bereichen wie Futtermittel, Pharmazie, Textilien und der Herstellung biologisch abbaubarer Kunststoffe. Das Verständnis der Mechanismen, die dem Stoffwechsel von Stärke in Pflanzen zugrunde liegen, birgt vielfältige Vorteile. Es trägt nicht nur zur Steigerung des Ernteertrags und zur Verbesserung der Kornqualität bei, sondern kann auch die Effizienz industrieller Anwendungen verbessern. Stärke in Pflanzen wird je nach ihrem Ort und ihrer Funktion in zwei Klassen eingeteilt: transitorische Stärke und Speicherstärke. Transitorische Stärke wird in Chloroplasten autotropher Gewebe/Organe wie Blätter produziert. Sie wird tagsüber synthetisiert und nachts abgebaut. Speicherstärke wird in heterotrophen Geweben/Organen wie Endosperm, Wurzeln und Knollen synthetisiert und für die Pflanzenreproduktion sowie industrielle Anwendungen im menschlichen Leben genutzt. Die meisten Studien zur Aufklärung des Stärkestoffwechsels von Arabidopsis thaliana konzentrieren sich hauptsächlich auf transitorische Stärke. Stärke wird in granularer Form in Chloroplasten und Amyloplasten gespeichert. Die Parameter der Stärkegranula, einschließlich Größe, Morphologie und Anzahl pro Chloroplast, dienen als Indikatoren für den Status des Stärkestoffwechsels. Das Verständnis ihrer regulatorischen Mechanismen ist jedoch noch unvollständig. In meiner Forschung habe ich zunächst eine Methode auf Basis der laser-konfokalen Rastermikroskopie (LCSM) etabliert, um Größe, Morphologie und Anzahl der Stärkegranula innerhalb der Chloroplaste von Arabidopsis thaliana in vivo zu beobachten. Diese Methode ermöglicht eine schnelle und vielseitige Analyse der Parameter der Stärkegranula in zahlreichen Proben. Unter Verwendung dieses Ansatzes verglich ich die Anzahl der Stärkegranula pro Chloroplast zwischen Mesophyllzellen und Schließzellen sowohl bei Wildtyp-Pflanzen (Col-0) als auch bei verschiedenen stärkebezogenen Mutanten. Die Ergebnisse zeigten, dass die Granulanzahl zwischen Mesophyllzellen und Schließzellen, selbst im identischen genetischen Hintergrund, unterschiedlich ist, was darauf hindeutet, dass Schließzellen einen einzigartigen regulatorischen Mechanismus der Stärkegranulanzahl aufweisen. Anschließend richtete ich meine Aufmerksamkeit darauf, die Stärkemorphologie zu untersuchen. Durch mikroskopische Analysen beobachtete ich eine allmähliche Veränderung der Stärkegranulamorphologie bei bestimmten Mutanten während des Blattalters. Insbesondere bei Mutanten wie sex1-8 und dpe2phs1ss4 gab es im Laufe der Zeit eine fortschreitende Veränderung der Stärkegranulamorphologie. Im Gegensatz dazu waren bei Col-0 und den ss4-Mutanten diese morphologischen Veränderungen nicht erkennbar. Diese Entdeckung ermöglicht eine neue Perspektive, um die Entwicklung der Stärkemorphologie zu verstehen. Weitere Untersuchungen zeigten, dass Mutanten, denen entweder das Disproportionierende Enzym 2 (DPE2) oder MALTOSE-EXCESS 1 (MEX1) fehlen, im Laufe des Blattalters allmähliche Veränderungen in der Stärkemorphologie aufwiesen. Bemerkenswerterweise traten die schwerwiegendsten Auswirkungen auf die Stärkemorphologie bei Doppelmutanten auf, die entweder DPE2 oder MEX1 in Verbindung mit einem Mangel an Stärkesynthase 4 (SS4) aufwiesen. Bei diesen Mutationen wurde eine Transformation der Stärkegranulamorphologie von der typischen scheibenförmigen Morphologie zu ovalen und schließlich zu einer kugelförmigen Form festgestellt. Um die Veränderungen in der inneren Struktur der Stärke während dieser Veränderung zu untersuchen, analysierte ich die Kettenlängenverteilung (KLV) des Amylopektins von jungen, mittleren und alten Blättern der Mutanten. Während der Entwicklung der Stärkegranula fand ich eine vermehrte Anwesenheit kurzer Glukanketten innerhalb der Granula, insbesondere bei den Mutanten dpe2ss4 und mex1ss4 sowie der zugrundeliegenden Einzelmutanten. Bemerkenswerterweise zeigte auch die Einzelmutant ss4 eine beeinträchtigte Granulamorphologie, die jedoch nicht durch das Blattalter beeinflusst wurde. Das KLV-Muster des Amylopektins spiegelt eine integrierte Regulation mehrerer an der Stärkesynthese Beteiligter Enzyme wider, einschließlich Stärkesynthasen (SSs) und Stärkeverzweigungs-/entzweigungs-Enzymen (SBEs/DBEs). Daher habe ich die Expression der beteiligten Gene auf Transkriptionsebene und die enzymatische Aktivität ihrer entsprechenden Proteine weiter untersucht. Die Ergebnisse deuten auf veränderte Genexpression mehrerer Regulatoren in diesen Mutanten hin, insbesondere auf dramatische Veränderungen bei dpe2 und dpe2ss4 mit zunehmendem Blattalter. Diese Veränderungen korrelieren mit den beobachteten Veränderungen in der Stärkegranulamorphologie. Zusammenfassend habe ich eine fortschreitende Veränderung der Stärkegranulat-Morphologie identifiziert und charakterisiert, die hauptsächlich auf Defizite in DPE2 und MEX1 zurückzuführen ist. Des Weiteren habe ich das KLV-Muster mit der Granulatmorphogenese sowie der Genexpression und enzymatischen Aktivität von Proteinen, die an der Stärkesynthese beteiligt sind, in Verbindung gebracht. Im Gegensatz zu SS4, dass in die Stärkeinitiierung involviert ist, spielen MEX1 und DPE2 eine Rolle bei Stärkeabbauprozessen. MEX1 befindet sich in der Chloroplastenhülle und DPE2 im Zytoplasma. Unter Berücksichtigung der Lokalisationen und bekannten Funktionen von DPE2, MEX1 und SS4 schließe ich darauf, dass es möglicherweise zwei Wege gibt, die die Stärkemorphologie beeinflussen: einen unter Beeinflussung von SS4 der mit dem Initiierungsprozess verknüpft ist und einen durch den Stärkeabbauprozess beeinflussten verbunden mit DPE2 bzw. MEX1. T2 - Regulation der Stärkegranulat-Morphogenese in Arabidopsis thaliana KW - Arabidopsis thaliana KW - transitory starch KW - starch granule morphology KW - starch metabolism KW - maltose KW - SS4 KW - DPE2 KW - MEX1 Y1 - 2024 ER - TY - JOUR A1 - Raatz, Larissa A1 - Pirhofer-Walzl, Karin A1 - Müller, Marina E.H. A1 - Scherber, Christoph A1 - Joshi, Jasmin Radha T1 - Who is the culprit: Is pest infestation responsible for crop yield losses close to semi-natural habitats? JF - Ecology and Evolution N2 - Semi-natural habitats (SNHs) are becoming increasingly scarce in modern agricultural landscapes. This may reduce natural ecosystem services such as pest control with its putatively positive effect on crop production. In agreement with other studies, we recently reported wheat yield reductions at field borders which were linked to the type of SNH and the distance to the border. In this experimental landscape-wide study, we asked whether these yield losses have a biotic origin while analyzing fungal seed and fungal leaf pathogens, herbivory of cereal leaf beetles, and weed cover as hypothesized mediators between SNHs and yield. We established experimental winter wheat plots of a single variety within conventionally managed wheat fields at fixed distances either to a hedgerow or to an in-field kettle hole. For each plot, we recorded the fungal infection rate on seeds, fungal infection and herbivory rates on leaves, and weed cover. Using several generalized linear mixed-effects models as well as a structural equation model, we tested the effects of SNHs at a field scale (SNH type and distance to SNH) and at a landscape scale (percentage and diversity of SNHs within a 1000-m radius). In the dry year of 2016, we detected one putative biotic culprit: Weed cover was negatively associated with yield values at a 1-m and 5-m distance from the field border with a SNH. None of the fungal and insect pests, however, significantly affected yield, neither solely nor depending on type of or distance to a SNH. However, the pest groups themselves responded differently to SNH at the field scale and at the landscape scale. Our findings highlight that crop losses at field borders may be caused by biotic culprits; however, their negative impact seems weak and is putatively reduced by conventional farming practices. KW - arable weeds KW - cereal leaf beetle KW - fungal pathogens KW - herbivory KW - structural equation model KW - wheat Y1 - 2021 U6 - https://doi.org/10.1002/ece3.8046 SN - 2045-7758 VL - 11 SP - 13232 EP - 13246 PB - Wiley-Blackwell CY - Oxford ET - 19 ER - TY - JOUR A1 - Spikes, Montrai A1 - Rodríguez-Silva, Rodet A1 - Bennett, Kerri-Ann A1 - Bräger, Stefan A1 - Josaphat, James A1 - Torres-Pineda, Patricia A1 - Ernst, Anja A1 - Havenstein, Katja A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario JF - BMC Research Notes N2 - Objective The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Miragoâne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Miragoâne, relative to their congeners throughout the Caribbean. Results For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N  = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Miragoâne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Miragoâne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Miragoâne clade. KW - Cytochrome b KW - Island biogeography KW - Fresh water fish KW - Phylogeny Y1 - 2021 U6 - https://doi.org/10.1186/s13104-021-05843-x SN - 1756-0500 VL - 14 SP - 1 EP - 8 PB - BMC Research Notes / Biomed Central CY - London ER - TY - JOUR A1 - Scharnweber, Inga Kristin A1 - Andersson, Matilda L. A1 - Chaguaceda, Fernando A1 - Eklöv, Peter T1 - Intraspecific differences in metabolic rates shape carbon stable isotope trophic discrimination factors of muscle tissue in the common teleost Eurasian perch (Perca fluviatilis) JF - Ecology and evolution N2 - Stable isotopes represent a unique approach to provide insights into the ecology of organisms. δ13C and δ15N have specifically been used to obtain information on the trophic ecology and food-web interactions. Trophic discrimination factors (TDF, Δ13C and Δ15N) describe the isotopic fractionation occurring from diet to consumer tissue, and these factors are critical for obtaining precise estimates within any application of δ13C and δ15N values. It is widely acknowledged that metabolism influences TDF, being responsible for different TDF between tissues of variable metabolic activity (e.g., liver vs. muscle tissue) or species body size (small vs. large). However, the connection between the variation of metabolism occurring within a single species during its ontogeny and TDF has rarely been considered. Here, we conducted a 9-month feeding experiment to report Δ13C and Δ15N of muscle and liver tissues for several weight classes of Eurasian perch (Perca fluviatilis), a widespread teleost often studied using stable isotopes, but without established TDF for feeding on a natural diet. In addition, we assessed the relationship between the standard metabolic rate (SMR) and TDF by measuring the oxygen consumption of the individuals. Our results showed a significant negative relationship of SMR with Δ13C, and a significant positive relationship of SMR with Δ15N of muscle tissue, but not with TDF of liver tissue. SMR varies inversely with size, which translated into a significantly different TDF of muscle tissue between size classes. In summary, our results emphasize the role of metabolism in shaping-specific TDF (i.e., Δ13C and Δ15N of muscle tissue) and especially highlight the substantial differences between individuals of different ontogenetic stages within a species. Our findings thus have direct implications for the use of stable isotope data and the applications of stable isotopes in food-web studies. KW - fractionation factors KW - metabolism KW - ontogeny KW - standard metabolic rate KW - tissue types KW - δ13C KW - δ15N Y1 - 2021 U6 - https://doi.org/10.1002/ece3.7809 SN - 2045-7758 VL - 11 IS - 14 SP - 9804 EP - 9814 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - JOUR A1 - Cahsan, Binia De A1 - Kiemel, Katrin A1 - Westbury, Michael V. A1 - Lauritsen, Maike A1 - Autenrieth, Marijke A1 - Gollmann, Günter A1 - Schweiger, Silke A1 - Stenberg, Marika A1 - Nyström, Per A1 - Drews, Hauke A1 - Tiedemann, Ralph T1 - Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad JF - Ecology and Evolution N2 - Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Skåne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation. KW - Bombina bombina KW - heat shock protein KW - introgression KW - major histocompatibility complex KW - scaled mass index Y1 - 2021 U6 - https://doi.org/10.1002/ece3.7805 SN - 2045-7758 VL - 11 IS - 14 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - JOUR A1 - Malchow, Anne-Kathleen A1 - Bocedi, Greta A1 - Palmer, Stephen C. F. A1 - Travis, Justin M. J. A1 - Zurell, Damaris T1 - RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes JF - Ecography N2 - Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models. KW - connectivity KW - conservation KW - dispersal KW - evolution KW - population dynamics KW - range dynamics Y1 - 2021 U6 - https://doi.org/10.1111/ecog.05689 SN - 1600-0587 VL - 44 IS - 10 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - JOUR A1 - Cahsan, Binia De A1 - Westbury, Michael V. A1 - Paraskevopoulou, Sofia A1 - Drews, Hauke A1 - Ott, Moritz A1 - Gollmann, Günter A1 - Tiedemann, Ralph T1 - Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian JF - Evolutionary Applications N2 - Due to their isolated and often fragmented nature, range margin populations are especially vulnerable to rapid environmental change. To maintain genetic diversity and adaptive potential, gene flow from disjunct populations might therefore be crucial to their survival. Translocations are often proposed as a mitigation strategy to increase genetic diversity in threatened populations. However, this also includes the risk of losing locally adapted alleles through genetic swamping. Human-mediated translocations of southern lineage specimens into northern German populations of the endangered European fire-bellied toad (Bombina bombina) provide an unexpected experimental set-up to test the genetic consequences of an intraspecific introgression from central population individuals into populations at the species range margin. Here, we utilize complete mitochondrial genomes and transcriptome nuclear data to reveal the full genetic extent of this translocation and the consequences it may have for these populations. We uncover signs of introgression in four out of the five northern populations investigated, including a number of introgressed alleles ubiquitous in all recipient populations, suggesting a possible adaptive advantage. Introgressed alleles dominate at the MTCH2 locus, associated with obesity/fat tissue in humans, and the DSP locus, essential for the proper development of epidermal skin in amphibians. Furthermore, we found loci where local alleles were retained in the introgressed populations, suggesting their relevance for local adaptation. Finally, comparisons of genetic diversity between introgressed and nonintrogressed northern German populations revealed an increase in genetic diversity in all German individuals belonging to introgressed populations, supporting the idea of a beneficial transfer of genetic variation from Austria into North Germany. KW - adaptive introgression KW - admixture KW - Bombina bombina KW - genetic rescue KW - mitogenomes KW - transcriptomics Y1 - 2020 U6 - https://doi.org/10.1111/eva.13229 SN - 1752-4563 VL - 14 IS - 6 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - JOUR A1 - Kath, Nadja J. A1 - Thomas, Mridul K. A1 - Gaedke, Ursula T1 - Mysterious ciliates: seasonally recurrent and yet hard to predict JF - Journal of plankton research N2 - Ciliates represent a crucial link between phytoplankton and bacteria and mesozooplankton in pelagic food webs, but little is known about the processes influencing the dynamics of individual species. Using long-term, high-frequency observations, we compared the diversity and the temporal variability in biomass and species composition of the ciliate community in large, deep, mesotrophic Lake Constance to that of the phytoplankton and rotifer communities in the same lake. Furthermore, we used boosted regression trees to evaluate possible environmental predictors (temperature, three prey groups, four predator/competitor groups) influencing ciliate net growth. The biomass of all ciliate species showed a common, recurrent seasonal pattern, often with peaks in spring and summer. The ciliate community was more diverse than the rotifer community, exhibited highly synchronous dynamics and its species were regularly encountered during the season. The top-down control by copepods likely contributes to the ciliates' synchronized decline prior to the clear-water phase when food concentration is still high. The high temporal autocorrelation of the ciliate biomasses together with the inter-annual recurrent seasonal patterns and the low explanatory power of the environmental predictors suggest that the dynamics of individual ciliate species are strictly controlled, yet it remains difficult to determine the responsible factors. KW - boosted regression trees KW - long-term time series KW - community composition KW - synchrony Y1 - 2022 U6 - https://doi.org/10.1093/plankt/fbac043 SN - 0142-7873 SN - 1464-3774 VL - 44 IS - 6 SP - 903 EP - 922 PB - Oxford Univ. Press CY - Oxford ER - TY - THES A1 - Mirzaee, Zohreh T1 - Ecology and phylogeny of Mantodea of Iran and adjacent areas N2 - Mantodea, commonly known as mantids, have captivated researchers owing to their enigmatic behavior and ecological significance. This order comprises a diverse array of predatory insects, boasting over 2,400 species globally and inhabiting a wide spectrum of ecosystems. In Iran, the mantid fauna displays remarkable diversity, yet numerous facets of this fauna remain poorly understood, with a significant dearth of systematic and ecological research. This substantial knowledge gap underscores the pressing need for a comprehensive study to advance our understanding of Mantodea in Iran and its neighboring regions. The principal objective of this investigation was to delve into the ecology and phylogeny of Mantodea within these areas. To accomplish this, our research efforts concentrated on three distinct genera within Iranian Mantodea. These genera were selected due to their limited existing knowledge base and feasibility for in-depth study. Our comprehensive methodology encompassed a multifaceted approach, integrating morphological analysis, molecular techniques, and ecological observations. Our research encompassed a comprehensive revision of the genus Holaptilon, resulting in the description of four previously unknown species. This extensive effort substantially advanced our understanding of the ecological roles played by Holaptilon and refined its systematic classification. Furthermore, our investigation into Nilomantis floweri expanded its known distribution range to include Iran. By conducting thorough biological assessments, genetic analyses, and ecological niche modeling, we obtained invaluable insights into distribution patterns and genetic diversity within this species. Additionally, our research provided a thorough comprehension of the life cycle, behaviors, and ecological niche modeling of Blepharopsis mendica, shedding new light on the distinctive characteristics of this mantid species. Moreover, we contributed essential knowledge about parasitoids that infect mantid ootheca, laying the foundation for future studies aimed at uncovering the intricate mechanisms governing ecological and evolutionary interactions between parasitoids and Mantodea. N2 - Mantodea, gemeinhin als Gottesanbeterinnen bekannt, haben Forscher aufgrund ihres rätselhaften Verhaltens und ihrer ökologischen Bedeutung in ihren Bann gezogen. Diese Ordnung umfasst eine Vielzahl räuberischer Insekten, von denen es weltweit über 2 400 Arten gibt und die ein breites Spektrum von Ökosystemen bewohnen. Im Iran weist die Gottesanbeterinnen-Fauna eine bemerkenswerte Vielfalt auf, doch zahlreiche Aspekte dieser Fauna sind nach wie vor nur unzureichend erforscht, und es besteht ein erheblicher Mangel an systematischen und ökologischen Untersuchungen. Diese beträchtliche Wissenslücke unterstreicht den dringenden Bedarf an einer umfassenden Studie, um unser Verständnis der Mantodea im Iran und den angrenzenden Regionen zu verbessern. Das Hauptziel dieser Untersuchung bestand darin, die Ökologie und Phylogenie der Mantodea in diesen Gebieten zu erforschen. Um dies zu erreichen, konzentrierten sich unsere Forschungsarbeiten auf drei verschiedene Gattungen innerhalb der iranischen Mantodea. Diese Gattungen wurden aufgrund ihrer begrenzten Wissensbasis und ihrer Eignung für eingehende Untersuchungen ausgewählt. Unsere umfassende Methodik umfasste einen vielschichtigen Ansatz, der morphologische Analysen, molekulare Techniken und ökologische Beobachtungen einbezog. Unsere Forschung umfasste eine umfassende Revision der Gattung Holaptilon, die zur Beschreibung von vier bisher unbekannten Arten führte. Diese umfangreichen Arbeiten haben unser Verständnis der ökologischen Rolle von Holaptilon wesentlich verbessert und die systematische Einordnung der Gattung verfeinert. Darüber hinaus konnten wir durch die Untersuchung von Nilomantis floweri ihr bekanntes Verbreitungsgebiet auf den Iran ausweiten. Durch gründliche biologische Untersuchungen, genetische Analysen und ökologische Nischenmodellierung erhielten wir unschätzbare Einblicke in die Verbreitungsmuster und die genetische Vielfalt dieser Art. Darüber hinaus lieferten unsere Forschungsarbeiten ein umfassendes Verständnis des Lebenszyklus, der Verhaltensweisen und der ökologischen Nischenmodellierung von Blepharopsis mendica und warfen ein neues Licht auf die besonderen Merkmale dieser Mantidenart. Darüber hinaus lieferten wir wichtige Erkenntnisse über Parasitoide, die Ootheken von Gottesanbeterinnen befallen, und legten damit den Grundstein für künftige Studien, die darauf abzielen, die komplizierten Mechanismen aufzudecken, die die ökologischen und evolutionären Wechselwirkungen zwischen Parasitoiden und Mantodea steuern. T2 - Ökologie und Phylogenie der Mantodea des Iran und angrenzender Gebiete KW - Mantodea KW - Ecology KW - Phylogeny KW - Mantodea KW - Ökologie KW - Phylogeni Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-652739 ER - TY - JOUR A1 - Coraman, Emrah A1 - Dietz, Christian A1 - Hempel, Elisabeth A1 - Ghazaryan, Astghik A1 - Levin, Eran A1 - Presetnik, Primoz A1 - Zagmajster, Maja A1 - Mayer, Frieder T1 - Reticulate evolutionary history of a Western Palaearctic Bat Complex explained by multiple mtDNA introgressions in secondary contacts JF - Journal of biogeography N2 - Aim There is an increasing evidence showing that species within various taxonomic groups have reticulate evolutionary histories with several cases of introgression events. Investigating the phylogeography of species complexes can provide insight into these introgressions, and when and where these hybridizations occurred. In this study, we investigate the biogeography of a widely distributed Western Palaearctic bat species complex, namely Myotis nattereri sensu lato. This complex exhibits high genetic diversity and in its western distribution range is composed of deeply diverged genetical lineages. However, little is known about the genetic structure of the eastern populations. We also infer the conservation and taxonomical implications of the identified genetic divergences. Taxon Myotis nattereri sensu lato including M. schaubi. Location Western Palaearctic. Methods We analysed 161 specimens collected from 67 locations and sequenced one mitochondrial and four nuclear DNA markers, and combined these with the available GenBank sequences. We used haplotype networks, PCA, t-SNE and Bayesian clustering algorithms to investigate the population structure and Bayesian trees to infer the phylogenetic relationship of the lineages. Results We identified deeply divergent genetical lineages. In some cases, nuclear and mitochondrial markers were discordant, which we interpret are caused by hybridization between lineages. We identified three such introgression events. These introgressions occurred when spatially separated lineages came into contact after range expansions. Based on the genetic distinction of the identified lineages, we suggest a revision in the taxonomy of this species group with two possible new species: M. hoveli and M. tschuliensis. Main conclusions Our findings suggest that the M. nattereri complex has a reticulate evolutionary history with multiple cases of hybridizations between some of the identified lineages. KW - cryptic species KW - glacial refugia KW - hybridization KW - introgression KW - range expansions KW - the Caucasus Y1 - 2019 U6 - https://doi.org/10.1111/jbi.13509 SN - 0305-0270 SN - 1365-2699 VL - 46 IS - 2 SP - 343 EP - 354 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Rybakova, Daria A1 - Müller, Henry A1 - Olimi, Expedito A1 - Schäfer, Angelika A1 - Cernava, Tomislav A1 - Berg, Gabriele T1 - To defend or to attack? Antagonistic interactions between Serratia plymuthica and fungal plant pathogens, a species-specific volatile dialogue JF - Frontiers in sustainable food systems N2 - Volatile organic compounds (VOCs) are involved in microbial interspecies communication and in the mode of action of various antagonistic interactions. They are important for balancing host-microbe interactions and provide the basis for developing biological control strategies to control plant pathogens. We studied the interactions between the bacterial antagonist Serratia plymuthica HRO-C48 and three fungal plant pathogens Rhizoctonia solani, Leptosphaeria maculans and Verticillium longisporum. Significant differences in fungal growth inhibition by the Serratia-emitted VOCs in pairwise dual culture assays and changes in the transcriptome of the bacterium and in the volatilomes of both interacting partners were observed. Even though the rate of fungal growth inhibition by Serratia was variable, the confrontation of the bacterium with the VOCs of all three fungi changed the levels of expression of the genes involved in stress response, biofilm formation, and the production of antimicrobial VOCs. Pairwise interacting microorganisms switched between defense (downregulation of gene expression) and attack (upregulation of gene expression and metabolism followed by growth inhibition of the interacting partner) modes, subject to the combinations of microorganisms that were interacting. In the attack mode HRO-C48 significantly inhibited the growth of R. solani while simultaneously boosting its own metabolism; by contrast, its metabolism was downregulated when HRO-C48 went into a defense mode that was induced by the L. maculans and V. longisporum VOCs. L. maculans growth was slightly reduced by the one bacterial VOC methyl acetate that induced a strong downregulation of expression of genes involved in almost all metabolic functions in S. plymuthica. Similarly, the interaction between S. plymuthica and V. longisporum resulted in an insignificant growth reduction of the fungus and repressed the rate of bacterial metabolism on the transcriptional level, accompanied by an intense volatile dialogue. Overall, our results indicate that VOCs substantially contribute to the highly break species-specific interactions between pathogens and their natural antagonists and thus deserving of increased consideration for pathogen control. KW - microbiome KW - transcriptome KW - volatilome KW - biocontrol KW - Serratia KW - Verticillium KW - Rhizoctonia KW - Leptospheria Y1 - 2022 U6 - https://doi.org/10.3389/fsufs.2022.1020634 SN - 2571-581X VL - 6 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Huth, Steven A1 - Schwarz, Lisa-Maricia A1 - Gorb, Stanislav N. T1 - Quantifying the influence of pollen aging on the adhesive properties of Hypochaeris radicata pollen JF - Insects N2 - Simple Summary Pollination is the transfer of pollen from a plant's male part (anther) to the corresponding female part (stigma). It is a fundamental biological process that ensures plant reproduction. Most studies investigate pollination from a biological perspective, but the underlying physical processes are poorly understood. Many plants rely on insects to transport pollen and the forces with which pollen adhere to insects and floral surfaces are fundamental for successful pollination. We quantified pollen adhesion by measuring the forces necessary to detach Hypochaeris radicata (catsear, a common insect-pollinated plant) pollen from glass and studied for the first time how the adhesion forces change with pollen aging. Our results show that newly formed adhesion bonds between H. radicata pollen and glass are stronger for fresh pollen than for old ones. On the other hand, when H. radicata pollen age in contact with glass, the adhesion between pollen and glass strengthens over time. These effects are probably caused by the viscous liquid covering most pollen (pollenkitt) changing its viscoelastic properties as it dries. Although pollination is one of the most crucial biological processes that ensures plant reproduction, its mechanisms are poorly understood. Especially in insect-mediated pollination, a pollen undergoes several attachment and detachment cycles when being transferred from anther to insect and from insect to stigma. The influence of the properties of pollen, insect and floral surfaces on the adhesion forces that mediate pollen transfer have been poorly studied. Here, we investigate the adhesive properties of Hypochaeris radicata pollen and their dependence on pollen aging by quantifying the pull-off forces from glass slides using centrifugation and atomic force microscopy. We found that the properties of the pollenkitt-the viscous, lipid liquid on the surface of most pollen grains-influences the forces necessary to detach a pollen from hydrophilic surfaces. Our results show that aged H. radicata pollen form weaker adhesions to hydrophilic glass than fresh ones. On the other hand, when a pollen grain ages in contact with glass, the adhesion between the two surfaces increases over time. This study shows for the first time the pollen aging effect on the pollination mechanism. KW - pollination KW - pollen adhesion KW - pollenkitt KW - atomic force microscopy KW - cryogenic scanning electron microscopy KW - centrifugation Y1 - 2022 U6 - https://doi.org/10.3390/insects13090811 SN - 2075-4450 VL - 13 IS - 9 PB - MDPI CY - Basel ER - TY - JOUR A1 - Bell, M. J. A1 - Jones, E. A1 - Smith, J. A1 - Smith, P. A1 - Yeluripati, J. A1 - Augustin, Jürgen A1 - Juszczak, R. A1 - Olejnik, J. A1 - Sommer, Michael T1 - Simulation of soil nitrogen, nitrous oxide emissions and mitigation scenarios at 3 European cropland sites using the ECOSSE model JF - Nutrient cycling in agroecosystems N2 - The global warming potential of nitrous oxide (N2O) and its long atmospheric lifetime mean its presence in the atmosphere is of major concern, and that methods are required to measure and reduce emissions. Large spatial and temporal variations means, however, that simple extrapolation of measured data is inappropriate, and that other methods of quantification are required. Although process-based models have been developed to simulate these emissions, they often require a large amount of input data that is not available at a regional scale, making regional and global emission estimates difficult to achieve. The spatial extent of organic soils means that quantification of emissions from these soil types is also required, but will not be achievable using a process-based model that has not been developed to simulate soil water contents above field capacity or organic soils. The ECOSSE model was developed to overcome these limitations, and with a requirement for only input data that is readily available at a regional scale, it can be used to quantify regional emissions and directly inform land-use change decisions. ECOSSE includes the major processes of nitrogen (N) turnover, with material being exchanged between pools of SOM at rates modified by temperature, soil moisture, soil pH and crop cover. Evaluation of its performance at site-scale is presented to demonstrate its ability to adequately simulate soil N contents and N2O emissions from cropland soils in Europe. Mitigation scenarios and sensitivity analyses are also presented to demonstrate how ECOSSE can be used to estimate the impact of future climate and land-use change on N2O emissions. KW - Soil N2O emissions KW - Process-based models KW - Land-use KW - Climate change Y1 - 2012 U6 - https://doi.org/10.1007/s10705-011-9479-4 SN - 1385-1314 VL - 92 IS - 2 SP - 161 EP - 181 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Kayler, Zachary A1 - Kaiser, Michael A1 - Gessler, Arthur A1 - Ellerbrock, Ruth H. A1 - Sommer, Michael T1 - Application of delta C-13 and delta N-15 isotopic signatures of organic matter fractions sequentially separated from adjacent arable and forest soils to identify carbon stabilization mechanisms JF - Biogeosciences N2 - Identifying the chemical mechanisms behind soil carbon bound in organo-mineral complexes is necessary to determine the degree to which soil organic carbon is stabilized belowground. Analysis of delta C-13 and delta N-15 isotopic signatures of stabilized OM fractions along with soil mineral characteristics may yield important information about OM-mineral associations and their processing history. We anlayzed the delta C-13 and delta N-15 isotopic signatures from two organic matter (OM) fractions along with soil mineral proxies to identify the likely binding mechanisms involved. We analyzed OM fractions hypothesized to contain carbon stabilized through organo-mineral complexes: (1) OM separated chemically with sodium pyrophosphate (OM(PY)) and (2) OM occluded in micro-structures found in the chemical extraction residue (OM(ER)). Because the OM fractions were separated from five different soils with paired forest and arable land use histories, we could address the impact of land use change on carbon binding and processing mechanisms. We used partial least squares regression to analyze patterns in the isotopic signature of OM with established mineral and chemical proxies indicative for certain binding mechanisms. We found different mechanisms predominate in each land use type. For arable soils, the formation of OM(PY)-Ca-mineral associations was identified as an important OM binding mechanism. Therefore, we hypothesize an increased stabilization of microbial processed OM(PY) through Ca2+ interactions. In general, we found the forest soils to contain on average 10% more stabilized carbon relative to total carbon stocks, than the agricultural counter part. In forest soils, we found a positive relationship between isotopic signatures of OM(PY) and the ratio of soil organic carbon content to soil surface area (SOC/SSA). This indicates that the OM(PY) fractions of forest soils represent layers of slower exchange not directly attached to mineral surfaces. From the isotopic composition of the OM(ER) fraction, we conclude that the OM in this fraction from both land use types have undergone a different pathway to stabilization that does not involve microbial processing, which may include OM which is highly protected within soil micro-structures. Y1 - 2011 U6 - https://doi.org/10.5194/bg-8-2895-2011 SN - 1726-4170 VL - 8 IS - 10 SP - 2895 EP - 2906 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Premke, Katrin A1 - Attermeyer, Katrin A1 - Augustin, Jürgen A1 - Cabezas, Alvaro A1 - Casper, Peter A1 - Deumlich, Detlef A1 - Gelbrecht, Jörg A1 - Gerke, Horst H. A1 - Gessler, Arthur A1 - Grossart, Hans-Peter A1 - Hilt, Sabine A1 - Hupfer, Michael A1 - Kalettka, Thomas A1 - Kayler, Zachary A1 - Lischeid, Gunnar A1 - Sommer, Michael A1 - Zak, Dominik T1 - The importance of landscape diversity for carbon fluxes at the landscape level: small-scale heterogeneity matters JF - Wiley Interdisciplinary Reviews : Water N2 - Landscapes can be viewed as spatially heterogeneous areas encompassing terrestrial and aquatic domains. To date, most landscape carbon (C) fluxes have been estimated by accounting for terrestrial ecosystems, while aquatic ecosystems have been largely neglected. However, a robust assessment of C fluxes on the landscape scale requires the estimation of fluxes within and between both landscape components. Here, we compiled data from the literature on C fluxes across the air–water interface from various landscape components. We simulated C emissions and uptake for five different scenarios which represent a gradient of increasing spatial heterogeneity within a temperate young moraine landscape: (I) a homogeneous landscape with only cropland and large lakes; (II) separation of the terrestrial domain into cropland and forest; (III) further separation into cropland, forest, and grassland; (IV) additional division of the aquatic area into large lakes and peatlands; and (V) further separation of the aquatic area into large lakes, peatlands, running waters, and small water bodies These simulations suggest that C fluxes at the landscape scale might depend on spatial heterogeneity and landscape diversity, among other factors. When we consider spatial heterogeneity and diversity alone, small inland waters appear to play a pivotal and previously underestimated role in landscape greenhouse gas emissions that may be regarded as C hot spots. Approaches focusing on the landscape scale will also enable improved projections of ecosystems’ responses to perturbations, e.g., due to global change and anthropogenic activities, and evaluations of the specific role individual landscape components play in regional C fluxes. WIREs Water 2016, 3:601–617. doi: 10.1002/wat2.1147 Y1 - 2016 U6 - https://doi.org/10.1002/wat2.1147 SN - 2049-1948 SN - 2049-1948 VL - 3 SP - 601 EP - 617 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Palma-Vera, Sergio E. A1 - Reyer, Henry A1 - Langhammer, Martina A1 - Reinsch, Norbert A1 - Derezanin, Lorena A1 - Fickel, Jörns A1 - Qanbari, Saber A1 - Weitzel, Joachim M. A1 - Franzenburg, Soeren A1 - Hemmrich-Stanisak, Georg A1 - Schön, Jennifer T1 - Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits JF - BMC Biology N2 - Background Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology (FBN), generating extreme mouse lines with increased fertility, body mass, protein mass and endurance. For >140 generations, these lines have been maintained alongside an unselected control line, representing a valuable resource for understanding the genetic basis of polygenic traits. However, their history and genomes have not been reported in a comprehensive manner yet. Therefore, the aim of this study is to provide a summary of the breeding history and phenotypic traits of these lines along with their genomic characteristics. We further attempt to decipher the effects of the observed line-specific patterns of genetic variation on each of the selected traits. Results Over the course of >140 generations, selection on the control line has given rise to two extremely fertile lines (>20 pups per litter each), two giant growth lines (one lean, one obese) and one long-distance running line. Whole genome sequencing analysis on 25 animals per line revealed line-specific patterns of genetic variation among lines, as well as high levels of homozygosity within lines. This high degree of distinctiveness results from the combined effects of long-term continuous selection, genetic drift, population bottleneck and isolation. Detection of line-specific patterns of genetic differentiation and structural variation revealed multiple candidate genes behind the improvement of the selected traits. Conclusions The genomes of the Dummerstorf trait-selected mouse lines display distinct patterns of genomic variation harbouring multiple trait-relevant genes. Low levels of within-line genetic diversity indicate that many of the beneficial alleles have arrived to fixation alongside with neutral alleles. This study represents the first step in deciphering the influence of selection and neutral evolutionary forces on the genomes of these extreme mouse lines and depicts the genetic complexity underlying polygenic traits. KW - Mouse KW - Fertility KW - Body mass KW - Endurance KW - Selective breeding KW - Genetic KW - drift KW - Bottleneck KW - Whole genome sequencing KW - Single-nucleotide KW - polymorphism KW - Structural variation Y1 - 2022 U6 - https://doi.org/10.1186/s12915-022-01248-9 SN - 1741-7007 VL - 20 IS - 1 PB - BMC CY - London ER - TY - JOUR A1 - Jacobs, Bas A1 - Schneider, René A1 - Molenaar, Jaap A1 - Filion, Laura A1 - Deinum, Eva E. T1 - Microtubule nucleation complex behavior is critical for cortical array homogeneity and xylem wall patterning JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Plant cell walls are versatile materials that can adopt a wide range of mechanical properties through controlled deposition of cellulose fibrils. Wall integrity requires a sufficiently homogeneous fibril distribution to cope effectively with wall stresses. Additionally, specific conditions, such as the negative pressure in water transporting xylem vessels, may require more complex wall patterns, e.g., bands in protoxylem. The orientation and patterning of cellulose fibrils are guided by dynamic cortical microtubules. New microtubules are predominantly nucleated from parent microtubules causing positive feedback on local microtubule density with the potential to yield highly inhomogeneous patterns. Inhomogeneity indeed appears in all current cortical array simulations that include microtubule-based nucleation, suggesting that plant cells must possess an as-yet unknown balancing mechanism to prevent it. Here, in a combined simulation and experimental approach, we show that a limited local recruitment of nucleation complexes to microtubules can counter the positive feedback, whereas local tubulin depletion cannot. We observe that nucleation complexes preferentially appear at the plasma membrane near microtubules. By incorporating our experimental findings in stochastic simulations, we find that the spatial behavior of nucleation complexes delicately balances the positive feedback, such that differences in local microtubule dynamics-as in developing protoxylem-can quickly turn a homogeneous array into a banded one. Our results provide insight into how the plant cytoskeleton has evolved to meet diverse mechanical requirements and greatly increase the predictive power of computational cell biology studies. KW - plant cortical microtubules KW - nucleation KW - stochastic simulation KW - homogeneity KW - stable coexistence Y1 - 2022 U6 - https://doi.org/10.1073/pnas.2203900119 SN - 0027-8424 SN - 1091-6490 VL - 119 IS - 50 PB - National Acad. of Sciences CY - Washington, DC ER - TY - JOUR A1 - Hou, Xindong A1 - Zhao, Jian A1 - Zhang, Hucai A1 - Preick, Michaela A1 - Hu, Jiaming A1 - Xiao, Bo A1 - Wang, Linying A1 - Deng, Miaoxuan A1 - Liu, Sizhao A1 - Chang, Fengqin A1 - Sheng, Guilian A1 - Lai, Xulong A1 - Hofreiter, Michael A1 - Yuan, Junxia T1 - Paleogenomes reveal a complex evolutionary history of late Pleistocene bison in Northeastern China JF - Genes N2 - Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct. KW - ancient DNA KW - most recent common ancestor KW - fossil KW - genetic diversity KW - admixture Y1 - 2022 U6 - https://doi.org/10.3390/genes13101684 SN - 2073-4425 VL - 13 IS - 10 PB - MDPI CY - Basel ER - TY - JOUR A1 - Liebchen, Uwe A1 - Weinelt, Ferdinand A1 - Scharf, Christina A1 - Schröder, Ines A1 - Paal, Michael A1 - Zoller, Michael A1 - Kloft, Charlotte A1 - Jung, Jette A1 - Michelet, Robin T1 - Combination of pharmacokinetic and pathogen susceptibility information to optimize meropenem treatment of Gram-negative infections in critically iII patients JF - Antimicrobial Agents and Chemotherapy N2 - Meropenem is one of the most frequently used antibiotics to treat life-threatening infections in critically ill patients. This study aimed to develop a meropenem dosing algorithm for the treatment of Gram-negative infections based on intensive care unit (ICU)-specific resistance data. Antimicrobial susceptibility testing of Gram-negative bacteria obtained from critically ill patients was carried out from 2016 to 2020 at a tertiary care hospital. Based on the observed MIC distribution, stochastic simulations (n = 1,000) of an evaluated pharmacokinetic meropenem model, and a defined pharmacokinetic/pharmacodynamic target (100%T->4xMIC while minimum concentrations were <44.5 mg/L), dosing recommendations for patients with varying renal function were derived. Pathogen-specific MIC distributions were used to calculate the cumulative fraction of response (CFR), and the overall MIC distribution was used to calculate the local pathogen-independent mean fraction of response (LPIFR) for the investigated dosing regimens. A CFR/LPIFR of >90% was considered adequate. The observed MIC distribution significantly differed from the EUCAST database. Based on the 6,520 MIC values included, a three-level dosing algorithm was developed. If the pathogen causing the infection is unknown (level 1), known (level 2), known to be neither Pseudomonas aeruginosa nor Acinetobacrer baumannii, or classified as susceptible (level 3), a continuous infusion of 1.5 g daily reached sufficient target attainment independent of renal function. In all other cases, dosing needs to be adjusted based on renal function. ICU-specific susceptibility data should be assessed regularly and integrated into dosing decisions. The presented workflow may serve as a blueprint for other antimicrobial settings. KW - meropenem KW - critically ill KW - antimicrobial susceptibility testing KW - Gram negative KW - dosing algorithm Y1 - 2022 U6 - https://doi.org/10.1128/aac.01831-21 SN - 0066-4804 SN - 1098-6596 VL - 66 IS - 2 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Masigol, Hossein A1 - Rezakhani, Forough A1 - Pourmoghaddam, Mohammad Javad A1 - Khodaparast, Seyed Akbar A1 - Grossart, Hans-Peter T1 - The introduction of two new species of aquatic fungi from Anzali Lagoon, Northern Iran JF - Diversity N2 - During a survey of aquatic fungi from Anzali Lagoon in Iran, several fungal specimens were isolated from freshwater habitats. Morphological evidence and comparing sequencing based on rDNA (ITS and LSU) and protein-coding genes (TEF1 and TUB2) showed that some isolates belong to undescribed fungal species. These isolates belong to Arthrobotrys and Sarocladium, two ascomycetes genera. Arthrobotrys hyrcanus, sp. nov., differs from closely related species such as A. dianchiensis by its larger conidia and septation of primary conidia. Sarocladium pseudokiliense, sp. nov., was similar to S. kiliense, but distinguished by its conidial shape and the absence of adelophialides and chlamydospores. Morphological descriptions, illustrations and multilocus phylogenetic analysis for both new species are provided. KW - Arthrobotrys KW - Ascomycota KW - freshwater fungi KW - molecular phylogeny KW - morphological KW - Sarocladium KW - taxonomy Y1 - 2022 U6 - https://doi.org/10.3390/d14100889 SN - 1424-2818 VL - 14 IS - 10 PB - MDPI CY - Basel ER - TY - JOUR A1 - Meier, Laura A1 - Brauns, Mario A1 - Grimm, Volker A1 - Weitere, Markus A1 - Frank, Karin T1 - MASTIFF: a mechanistic model for cross-scale analyses of the functioning of multiple stressed riverine ecosystems JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Riverine ecosystems provide various ecosystem services. One of these services is the biological control of eutrophication by grazing macroinvertebrates. However, riverine ecosystems are subject to numerous stressors that affect community structure, functions, and stability properties. To manage rivers in response to these stressors, a better understanding of the ecological functions underlying services is needed. This requires consideration of local and regional processes, which requires a metacommunity approach that links local food webs through drift and dispersal. This takes into account long-distance interactions that can compensate for local effects of stressors. Our modular model MASTIFF (Multiple Aquatic STressors In Flowing Food webs) is stage-structured, spatially explicit, and includes coupled food webs consisting of benthic resource-consumer interactions between biofilm and three competing macroinvertebrate functional types. River segments are unidirectionally connected through organismal drift and bidirectionally connected through dispersal. Climate and land use stressors along the river can be accounted for. Biocontrol of biofilm eutrophication is used as an exemplary functional indicator. We present the model and the underlying considerations, and show in an exemplary application that explicit consideration of drift and dispersal is essential for understanding the spatiotemporal biocontrol of eutrophication. The combination of drift and dispersal reduced eutrophication events. While dispersal events were linked to specific periods in the species life cycles and therefore had limited potential to control, drift was ubiquitous and thus responded more readily to changing habitat conditions. This indicates that drift is an important factor for coping with stress situations. Finally, we outline and discuss the potential and possibilities of MASTIFF as a tool for mechanistic, cross-scale analyses of multiple stressors to advance knowledge of riverine ecosystem functioning. KW - modeling KW - riverine ecosystems KW - drift and dispersal KW - multiple stressors KW - functioning KW - biocontrol of eutrophication Y1 - 2022 U6 - https://doi.org/10.1016/j.ecolmodel.2022.110007 SN - 0304-3800 SN - 1872-7026 VL - 470 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - De Frenne, Pieter A1 - Graae, Bente J. A1 - Kolb, Annette A1 - Shevtsova, Anna A1 - Baeten, Lander A1 - Brunet, Jörg A1 - Chabrerie, Olivier A1 - Cousins, Sara A. O. A1 - Decocq, Guillaume A1 - Dhondt, Rob A1 - Diekmann, Martin A1 - Gruwez, Robert A1 - Heinken, Thilo A1 - Hermy, Martin A1 - Oster, Mathias A1 - Saguez, Robert A1 - Stanton, Sharon A1 - Tack, Wesley A1 - Vanhellemont, Margot A1 - Verheyen, Kris T1 - An intraspecific application of the leaf-height-seed ecology strategy scheme to forest herbs along a latitudinal gradient JF - Ecography : pattern and diversity in ecology ; research papers forum N2 - We measured LHS traits in 41 Anemone nemorosa and 44 Milium effusum populations along a 1900-2300 km latitudinal gradient from N France to N Sweden. We then applied multilevel models to identify the effects of regional (temperature, latitude) and local (soil fertility and acidity, overstorey canopy cover) environmental factors on LHS traits. Both species displayed a significant 4% increase in plant height with every degree northward shift (almost a two-fold plant height difference between the southernmost and northernmost populations). Neither seed mass nor SLA showed a significant latitudinal cline. Temperature had a large effect on the three LHS traits of Anemone. Latitude, canopy cover and soil nutrients were related to the SLA and plant height of Milium. None of the investigated variables appeared to be related to the seed mass of Milium. The variation in LHS traits indicates that the ecological strategy determined by the position of each population in this three-factor triangle is not constant along the latitudinal gradient. The significant increase in plant height suggests greater competitive abilities for both species in the northernmost populations. We also found that the studied environmental factors affected the LHS traits of the two species on various scales: spring-flowering Anemone was affected more by temperature, whereas early-summer flowering Milium was affected more by local and other latitude-related factors. Finally, previously reported cross-species correlations between LHS traits and latitude were generally unsupported by our within-species approach. Y1 - 2011 U6 - https://doi.org/10.1111/j.1600-0587.2010.06399.x SN - 0906-7590 VL - 34 IS - 1 SP - 132 EP - 140 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Ullrich, Jessica A1 - Göhmann, Philip Jonas A1 - Zemella, Anne A1 - Kubick, Stefan T1 - Oligomerization of the heteromeric γ-aminobutyric acid receptor GABAB in a eukaryotic cell-free system JF - Scientific reports N2 - Understanding the assembly mechanism and function of membrane proteins is a fundamental problem in biochemical research. Among the membrane proteins, G protein-coupled receptors (GPCRs) represent the largest class in the human body and have long been considered to function as monomers. Nowadays, the oligomeric assembly of GPCRs is widely accepted, although the functional importance and therapeutic intervention remain largely unexplored. This is partly due to difficulties in the heterologous production of membrane proteins. Cell-free protein synthesis (CFPS) with its endogenous endoplasmic reticulum-derived structures has proven as a technique to address this issue. In this study, we investigate for the first time the conceptual CFPS of a heteromeric GPCR, the gamma-aminobutyric acid receptor type B (GABA(B)), from its protomers BR1 and BR2 using a eukaryotic cell-free lysate. Using a fluorescence-based proximity ligation assay, we provide evidence for colocalization and thus suggesting heterodimerization. We prove the heterodimeric assembly by a bioluminescence resonance energy transfer saturation assay providing the manufacturability of a heterodimeric GPCR by CFPS. Additionally, we show the binding of a fluorescent orthosteric antagonist, demonstrating the feasibility of combining the CFPS of GPCRs with pharmacological applications. These results provide a simple and powerful experimental platform for the synthesis of heteromeric GPCRs and open new perspectives for the modelling of protein-protein interactions. Accordingly, the presented technology enables the targeting of protein assemblies as a new interface for pharmacological intervention in disease-relevant dimers. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-24885-0 SN - 2045-2322 VL - 12 IS - 1 PB - Springer Nature CY - [London] ER - TY - THES A1 - Hempel, Elisabeth T1 - Resolving the evolutionary history of two hippotragin antelopes using archival and ancient DNA N2 - African antelopes are iconic but surprisingly understudied in terms of their genetics, especially when it comes to their evolutionary history and genetic diversity. The age of genomics provides an opportunity to investigate evolution using whole nuclear genomes. Decreasing sequencing costs enable the recovery of multiple loci per genome, giving more power to single specimen analyses and providing higher resolution insights into species and populations that can help guide conservation efforts. This age of genomics has only recently begun for African antelopes. Many African bovids have a declining population trend and hence, are often endangered. Consequently, contemporary samples from the wild are often hard to collect. In these cases, ex situ samples from contemporary captive populations or in the form of archival or ancient DNA (aDNA) from historical museum or archaeological/paleontological specimens present a great research opportunity with the latter two even offering a window to information about the past. However, the recovery of aDNA is still considered challenging from regions with prevailing climatic conditions that are deemed adverse for DNA preservation like the African continent. This raises the question if DNA recovery from fossils as old as the early Holocene from these regions is possible. This thesis focuses on investigating the evolutionary history and genetic diversity of two species: the addax (Addax nasomaculatus) and the blue antelope (Hippotragus leucophaeus). The addax is critically endangered and might even already be extinct in the wild, while the blue antelope became extinct ~1800 AD, becoming the first extinct large African mammal species in historical times. Together, the addax and the blue antelope can inform us about current and past extinction events and the knowledge gained can help guide conservation efforts of threatened species. The three studies used ex situ samples and present the first nuclear whole genome data for both species. The addax study used historical museum specimens and a contemporary sample from a captive population. The two studies on the blue antelope used mainly historical museum specimens but also fossils, and resulted in the recovery of the oldest paleogenome from Africa at that time. The aim of the first study was to assess the genetic diversity and the evolutionary history of the addax. It found that the historical wild addax population showed only limited phylogeographic structuring, indicating that the addax was a highly mobile and panmictic population and suggesting that the current European captive population might be missing the majority of the historical mitochondrial diversity. It also found the nuclear and mitochondrial diversity in the addax to be rather low compared to other wild ungulate species. Suggestions on how to best save the remaining genetic diversity are presented. The European zoo population was shown to exhibit no or only minor levels of inbreeding, indicating good prospects for the restoration of the species in the wild. The trajectory of the addax’s effective population size indicated a major bottleneck in the late Pleistocene and a low effective population size well before recent human impact led to the species being critically endangered today. The second study set out to investigate the identities of historical blue antelope specimens using aDNA techniques. Results showed that six out of ten investigated specimens were misidentified, demonstrating the blue antelope to be one of the scarcest mammal species in historical natural history collections, with almost no bone reference material. The preliminary analysis of the mitochondrial genomes suggested a low diversity and hence low population size at the time of the European colonization of southern Africa. Study three presents the results of the analyses of two blue antelope nuclear genomes, one ~200 years old and another dating to the early Holocene, 9,800–9,300 cal years BP. A fossil-calibrated phylogeny dated the divergence time of the three historically extant Hippotragus species to ~2.86 Ma and demonstrated the blue and the sable antelope (H. niger) to be sister species. In addition, ancient gene flow from the roan (H. equinus) into the blue antelope was detected. A comparison with the roan and the sable antelope indicated that the blue antelope had a much lower nuclear diversity, suggesting a low population size since at least the early Holocene. This concurs with findings from the fossil record that show a considerable decline in abundance after the Pleistocene–Holocene transition. Moreover, it suggests that the blue antelope persisted throughout the Holocene regardless of a low population size, indicating that human impact in the colonial era was a major factor in the blue antelope’s extinction. This thesis uses aDNA analyses to provide deeper insights into the evolutionary history and genetic diversity of the addax and the blue antelope. Human impact likely was the main driver of extinction in the blue antelope, and is likely the main factor threatening the addax today. This thesis demonstrates the value of ex situ samples for science and conservation, and suggests to include genetic data for conservation assessments of species. It further demonstrates the beneficial use of aDNA for the taxonomic identification of historically important specimens in natural history collections. Finally, the successful retrieval of a paleogenome from the early Holocene of Africa using shotgun sequencing shows that DNA retrieval from samples of that age is possible from regions generally deemed unfavorable for DNA preservation, opening up new research opportunities. All three studies enhance our knowledge of African antelopes, contributing to the general understanding of African large mammal evolution and to the conservation of these and similarly threatened species. N2 - Afrikanische Antilopen sind sehr bekannte Tiere. Allerdings sind sie genetisch wenig untersucht, vor allem hinsichtlich ihrer Evolutionsgeschichte und genetischen Diversität. Das Zeitalter der Genomik ermöglicht es, Evolution mit Hilfe von kompletten nukleären Genomen zu untersuchen. Durch sinkende Sequenzierkosten können zahlreiche Genloci pro Genom gewonnen werden, wodurch Analysen mit nur einem Exemplar mehr Aussagekraft zukommt und tiefere Erkenntnisse über Arten und Populationen zulassen, die Artenschutzbemühungen unterstützen können. Für afrikanische Antilopen hat dieses Zeitalter gerade erst begonnen. Viele afrikanische Boviden haben einen sinkenden Populationstrend und sind daher häufig gefährdet. Dies erschwert es oft, Proben freilebender Tiere zu bekommen. In diesen Fällen bieten ex situ Proben von in Gefangenschaft lebenden Tieren oder in Form von alter DNA (aDNA) aus naturhistorischen Sammlungen eine gute Forschungsmöglichkeit. Letztere ermöglicht zudem den Zugang zu Informationen aus der Vergangenheit. Es gilt noch immer als Herausforderung, aDNA aus Regionen zu erlangen, deren Bedingungen schlecht für den Erhalt von DNA sind. Dies wirft die Frage auf, ob es möglich ist, aDNA aus Fossilien vom Beginn des Holozäns aus Afrika zu erhalten. Das Ziel dieser Doktorarbeit war die Erforschung der Evolutionsgeschichte und der genetischen Diversität der Mendesantilope (Addax nasomaculatus) und des Blaubocks (Hippotragus leucophaeus). Die Mendesantilope ist vom Aussterben bedroht und könnte in freier Wildbahn bereits ausgestorben sein. Der Blaubock starb ca. 1800 aus und war das erste afrikanische Großsäugetier, das in historischer Zeit ausstarb. Beide Arten können unsere Kenntnisse über derzeitige und vergangene Aussterbeereignisse erweitern, um den Schutz bedrohter Arten zu unterstützen. Die drei Studien dieser Doktorarbeit nutzten ex situ Proben und präsentieren die ersten kompletten nukleären Genome dieser beiden Arten. Die Studie über die Mendesantilope nutzte historische Präparate aus naturhistorischen Sammlungen sowie eine rezente Probe eines Tieres aus Gefangenschaft. Beide Blaubock-Studien nutzten vor allem Präparate aus naturhistorischen Sammlungen, aber auch Fossilien, woraus das zu diesem Zeitpunkt älteste Paläogenom aus Afrika resultierte. Die erste Studie untersuchte die genetische Diversität und Evolutionsgeschichte der Mendesantilope. Es zeigte sich, dass ihre historische Wildpopulation nur eine geringe phylogeographische Strukturierung aufwies, was auf eine sehr mobile und panmiktische Population hindeutet. Dies legt nahe, dass die rezente europäische Zoopopulation vermutlich Großteile der historischen mitochondrialen Diversität verloren hat. Zusätzlich zeigte sich, dass die nukleäre und mitochondriale Diversität relativ gering waren im Vergleich zu anderen wilden Huftierarten. Es werden Möglichkeiten zum Erhalt der verbliebenen Diversität aufgezeigt. Die europäische Zoopopulation zeigte keine beziehungsweise nur geringe Anzeichen von Inzucht, was für gute Wiederauswilderungsaussichten spricht. Die effektive Populationsgröße der Mendesantilope weist einen starken genetischen Flaschenhals im späten Pleistozän auf. Zudem war sie bereits deutlich niedrig, bevor der derzeitige menschliche Einfluss zu ihrer heutigen Bedrohung führte. Die zweite Stude untersuchte mit Hilfe von aDNA die Identitäten historischer Blaubock-Präparate. Nur vier der zehn untersuchten Präparate stellten sich als Blauböcke heraus. Somit ist der Blaubock eine der seltensten Säugetierarten in naturhistorischen Sammlungen, für die es zudem kaum Knochenreferenzmaterial gibt. Die vorläufige Analyse des mitochondrialen Genoms deutet auf eine geringe Diversität und daher eine geringe Populationsgröße zur Zeit der europäischen Kolonialisierung Südafrikas hin. Die dritte Studie analysierte zwei nukleäre Blaubockgenome, ein ~200 Jahre altes Präparat und eines aus dem frühen Holozän, 9.800–9.300 Jahre. Ein mit Hilfe von Fossilien kalibrierter Stammbaum datiert die Aufspaltung der drei historisch rezenten Hippotragus-Arten auf ~2,86 Mio. Jahre und zeigt die Rappenantilope (H. niger) und den Blaubock als Schwesterarten. Darüber hinaus wurde früherer Genfluss der Pferdeantilope (H. equinus) zum Blaubock festgestellt. Der Vergleich der drei Hippotragus-Arten legt nahe, dass der Blaubock eine deutlich geringere nukleäre Diversität besaß und somit seit mindestens dem frühen Holozän nur über eine geringe Populationsgröße verfügte. Dies stimmt mit Ergebnissen aus dem Fossilbericht überein, die eine deutliche Häufigkeitsabnahme nach dem Übergang des Pleistozäns zum Holozän aufzeigen. Außerdem suggeriert es, dass der Blaubock unabhängig von einer geringen Populationsgröße das Holozän überdauerte und sein Aussterben stark durch den Menschen während der Kolonialzeit beeinflusst wurde. Diese Doktorarbeit bietet mit Hilfe von aDNA gewonnene Erkenntnisse über die Evolutionsgeschichte und die genetische Diversität der Mendesantilope und des Blaubocks. Der menschliche Einfluss war vermutlich der Hauptaussterbegrund des Blaubocks. Dies gilt wahrscheinlich ebenso für die heutige Bedrohung der Mendesantilope. Diese Doktorarbeit zeigt den Wert von ex situ Proben für die Wissenschaft und den Artenschutz und legt die Einbindung von genetischen Daten für die Bewertung des Gefährdungsstatus einer Art nahe. Des Weiteren demonstriert sie die Nutzung von aDNA für taxonomische Bestimmungen von historisch wichtigen Präparaten in naturhistorischen Sammlungen. Die erfolgreiche Gewinnung eines Paläogenoms aus dem frühen Holozän Afrikas mittels shotgun-Sequenzierung zeigt, dass die DNA-Gewinnung aus Proben diesen Alters aus Regionen möglich ist, deren Bedingungen allgemein als ungünstig für den Erhalt von DNA gelten. Dies eröffnet neue Forschungsmöglichkeiten. Alle drei Studien erweitern unser Wissen über afrikanische Antilopen und tragen damit zum allgemeinen Verständnis der Evolution von afrikanischen Großsäugetieren sowie zu deren Erhalt und dem ähnlich gefährdeter Arten bei. KW - Addax nasomaculatus KW - antelope KW - aDNA KW - conservation KW - museomics KW - extinction KW - South Africa KW - Blue antelope KW - Hippotragus leucophaeus KW - bluebuck KW - Addax nasomaculatus KW - Blaubock KW - Hippotragus leucophaeus KW - Südafrika KW - aDNA KW - Antilope KW - Artenschutz KW - Aussterben KW - museomics Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-647718 ER - TY - GEN A1 - Kindermann, Liana A1 - Dobler, Magnus A1 - Niedeggen, Daniela A1 - Chimbioputo Fabiano, Ezequiel A1 - Linstädter, Anja T1 - Dataset on woody aboveground biomass, disturbance losses, and wood density from an African savanna ecosystem T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - This dataset comprises tree inventories and damage assessments performed in Namibia's semi-arid Zambezi Region. Data were sampled in savannas and savanna woodlands along steep gradients of elephant population densities to capture the effects of those (and other) disturbances on individual-level and stand-level aboveground woody biomass (AGB). The dataset contains raw data on dendrometric measures and processed data on specific wood density (SWD), woody aboveground biomass, and biomass losses through disturbance impacts. Allometric proxies (height, canopy diameters, and in adult trees also stem circumferences) were recorded for n = 6,179 tree and shrub individuals. Wood samples were taken for each encountered species to measure specific wood density. These measurements have been used to estimate woody aboveground biomass via established allometric models, advanced through our improved methodologies and workflows that accounted for tree and shrub architecture shaped by disturbance impacts. To this end, we performed a detailed damage assessment on each woody individual in the field. In addition to estimations of standing biomass, our new method also delivered data on biomass losses to different disturbance agents (elephants, fire, and others) on the level of plant individuals and stands. The data presented here have been used within a study published with Ecological Indicators (Kindermann et al., 2022) to evaluate the benefits of our improved methodology in comparison to a standard reference method of aboveground biomass estimations. Additionally, it has been employed in a study on carbon storage and sequestration in vegetation and soils (Sandhage-Hofmann et al., 2021). The raw data of dendrometric measurements can be subjected to other available allometric models for biomass estimation. The processed data can be used to analyze disturbance impacts on woody aboveground biomass, or for regional carbon storage estimates. The data on species-specific wood density can be used for application to other dendrometric datasets to (re-) estimate biomass through allometric models requiring wood density. It can further be used for plant functional trait analyses. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1265 KW - Damage assessment KW - Disturbance impacts KW - Disturbance indicator KW - Elephant disturbance KW - Tree allometry KW - Specific wood density KW - Woody aboveground biomass KW - Wood specific gravity Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-561607 SN - 1866-8372 SP - 1 EP - 16 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Sandhage-Hofmann, Alexandra A1 - Angombe, Simon A1 - Kindermann, Liana A1 - Linstädter, Anja A1 - Mörchen, Ramona T1 - Conservation with elephants and agricultural intensification BT - effects on lignin and n-alkanes in soils of sub-Saharan Africa JF - Geoderma : an international journal of soil science N2 - Nature conservation is currently shaping many terrestrial ecosystems in Africa. This is particularly evident in Sub-Saharan Africa (SSA), where conservation is intended to recover wildlife populations, with special focus on elephants. Rising numbers of elephants induce woody biomass losses but increase soil organic carbon (SOC) stocks from decaying wood and dung. We hypothesized that these increases under wildlife conservation in SSA go along with rising contents of plant residues in SOC, traceable by the molecular markers lignin and n-alkanes. In contrast, agricultural intensification would reduce them due to lower C input and faster SOC turnover through tillage. To test this, we analyzed lignin by the CuO oxidation method and n-alkanes by fast pressurized solvent extraction in topsoils (0-10 cm) of Arenosols and corresponding plant samples (trees, grasses and crops). Sampling sites followed conservation gradients with low, medium and high elephant densities and intensification gradients with rangeland and cropland in the woodland savanna of the Namibian Zambezi Region. Patterns of lignin-derived phenols were retained in the soil, whereas n-alkanes showed shifts in chain lengths. n-Alkanes also showed no clear increase or decrease under conservation or intensification, respectively. Differently, lignin-derived phenols showed lower values under intensification than under conservation. Confirming our hypothesis, rising SOC contents with rising elephant densities (from 4.4 at low to 5.7 g kg(-1) SOC at high elephant densities) went along with an increasing accumulation of lignin-derived phenols (24.4-34.8 g kg(-1) VSCOC). This increase is associated with the input of woody debris to the soil, as indicated by V-units and carbon isotopes, modulated by clay and woody biomass. We conclude, that increasing input of woody residues into soil by browsing behaviour of elephants is an important mechanism for controlling SOC supply in the context of wildlife conservation and is traceable with lignin-derived phenols, but not with n-alkanes. KW - lignin-derived phenols KW - n-alkanes KW - soil organic carbon KW - wildlife conservation KW - agricultural intensification Y1 - 2022 U6 - https://doi.org/10.1016/j.geoderma.2022.116009 SN - 0016-7061 SN - 1872-6259 VL - 425 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Egli, Lukas A1 - Mehrabi, Zia A1 - Seppelt, Ralf T1 - More farms, less specialized landscapes, and higher crop diversity stabilize food supplies JF - Environmental research letters N2 - Theoretical and empirical studies show increased diversity in crops, supply chains, and markets helps stabilize food systems. At the same time global commodity markets and industrial agriculture have driven homogenization of local and regional production systems, and consolidated power in fewer larger specialized farms and distributers. This is a global challenge, with no obvious global solutions. An important question therefore, is how individual countries can build their own resilience through maintaining or increasing diversity within their borders. Here we show, using farm level data from Germany, that spreading production risk by growing the same crops across different farms carries stabilizing benefits by allowing for increased spatiotemporal asynchrony within crops. We also find that increasing asynchrony between the year-to-year production of different crops has stabilizing effects on food supply. Importantly, the benefits of increasing crop diversity are lower in specialized landscapes growing the same crop on large patches. Our results illustrate clear benefits of diversified crops, producers, and agricultural landscapes to buffer supply side shocks, and for incorporation in subsidies and other regulatory measures aimed at stabilizing food systems. KW - agroecology KW - climate variability KW - resilience KW - spatial heterogeneity KW - supply shocks Y1 - 2021 U6 - https://doi.org/10.1088/1748-9326/abf529 SN - 1748-9326 VL - 16 IS - 5 PB - IOP Publ. Ltd. CY - Bristol ER - TY - THES A1 - Kindermann, Liana T1 - Trees, shrubs, and land-use change T1 - Bäume, Büsche und Landnutzungswandel BT - The future of carbon storage in an African Savanna BT - Die Zukunft der Kohlenstoffspeicherung in einer Afrikanischen Savanne N2 - The global drylands cover nearly half of the terrestrial surface and are home to more than two billion people. In many drylands, ongoing land-use change transforms near-natural savanna vegetation to agricultural land to increase food production. In Southern Africa, these heterogenous savanna ecosystems are also recognized as habitats of many protected animal species, such as elephant, lion and large herds of diverse herbivores, which are of great value for the tourism industry. Here, subsistence farmers and livestock herder communities often live in close proximity to nature conservation areas. Although these land-use transformations are different regarding the future they aspire to, both processes, nature conservation with large herbivores and agricultural intensification, have in common, that they change the vegetation structure of savanna ecosystems, usually leading to destruction of trees, shrubs and the woody biomass they consist of. Such changes in woody vegetation cover and biomass are often regarded as forms of land degradation and forest loss. Global forest conservation approaches and international programs aim to stop degradation processes, also to conserve the carbon bound within wood from volatilization into earth’s atmosphere. In search for mitigation options against global climate change savannas are increasingly discussed as potential carbon sinks. Savannas, however, are not forests, in that they are naturally shaped by and adapted to disturbances, such as wildfires and herbivory. Unlike in forests, disturbances are necessary for stable, functioning savanna ecosystems and prevent these ecosystems from forming closed forest stands. Their consequently lower levels of carbon storage in woody vegetation have long been the reason for savannas to be overlooked as a potential carbon sink but recently the question was raised if carbon sequestration programs (such as REDD+) could also be applied to savanna ecosystems. However, heterogenous vegetation structure and chronic disturbances hamper the quantification of carbon stocks in savannas, and current procedures of carbon storage estimation entail high uncertainties due to methodological obstacles. It is therefore challenging to assess how future land-use changes such as agricultural intensification or increasing wildlife densities will impact the carbon storage balance of African drylands. In this thesis, I address the research gap of accurately quantifying carbon storage in vegetation and soils of disturbance-prone savanna ecosystems. I further analyse relevant drivers for both ecosystem compartments and their implications for future carbon storage under land-use change. Moreover, I show that in savannas different carbon storage pools vary in their persistence to disturbance, causing carbon bound in shrub vegetation to be most likely to experience severe losses under land-use change while soil organic carbon stored in subsoils is least likely to be impacted by land-use change in the future. I start with summarizing conventional approaches to carbon storage assessment and where and for which reasons they fail to accurately estimated savanna ecosystem carbon storage. Furthermore, I outline which future-making processes drive land-use change in Southern Africa along two pathways of land-use transformation and how these are likely to influence carbon storage. In the following chapters, I propose a new method of carbon storage estimation which is adapted to the specific conditions of disturbance-prone ecosystems and demonstrate the advantages of this approach in relation to existing forestry methods. Specifically, I highlight sources for previous over- and underestimation of savanna carbon stocks which the proposed methodology resolves. In the following chapters, I apply the new method to analyse impacts of land-use change on carbon storage in woody vegetation in conjunction with the soil compartment. With this interdisciplinary approach, I can demonstrate that indeed both, agricultural intensification and nature conservation with large herbivores, reduce woody carbon storage above- and belowground, but partly sequesters this carbon into the soil organic carbon stock. I then quantify whole-ecosystem carbon storage in different ecosystem compartments (above- and belowground woody carbon in shrubs and trees, respectively, as well as topsoil and subsoil organic carbon) of two savanna vegetation types (scrub savanna and savanna woodland). Moreover, in a space-for-time substitution I analyse how land-use changes impact carbon storage in each compartment and in the whole ecosystem. Carbon storage compartments are found to differ in their persistence to land-use change with carbon bound in shrub biomass being least persistent to future changes and subsoil organic carbon being most stable under changing land-use. I then explore which individual land-use change effects act as drivers of carbon storage through Generalized Additive Models (GAMs) and uncover non-linear effects, especially of elephant browsing, with implications for future carbon storage. In the last chapter, I discuss my findings in the larger context of this thesis and discuss relevant implications for land-use change and future-making decisions in rural Africa. N2 - Weltweit bedecken Trockengebiete fast die Hälfte der Erdoberfläche und sind die Heimat von mehr als zwei Milliarden Menschen. In vielen Regionen wird durch den fortschreitenden Landnutzungswandel die naturnahe Savannenvegetation in landwirtschaftliche Flächen umgewandelt, um die Nahrungsmittelproduktion zu steigern. Im südlichen Afrika sind diese diversen Savannenökosysteme auch als Lebensraum für viele geschützte Tierarten wie Elefanten, Löwen und große Herden vielfältiger Pflanzenfresser bekannt, die großen Wert für die Tourismusbranche haben. Im Umfeld vieler großer Schutzgebiete leben Kleinbauern und Viehhirten oft in unmittelbarer Nachbarschaft zu diesen – oft gefährlichen – Tieren. Obwohl sich beide Landnutzungen im Hinblick darauf unterscheiden welche Zukunftsvision verfolgt wird, haben sie doch beide gemeinsam, dass sowohl Schutzgebiete mit großen Pflanzenfressern wie Elefanten als auch die Landwirtschaft, die Vegetationsstruktur von Savannenökosystemen verändern. In der Regel reduzieren beide Prozesse die holzige Biomasse im Ökosystem, indem Bäume und Sträucher entfernt, zerstört oder durch Fraßverhalten und Holzeinschlag geschädigt werden. Solche Veränderungen der holzigen Vegetationsschicht samt Einflüssen auf die Biomasse werden oft als Formen von Umweltzerstörung oder Waldverlust betrachtet. Globale Waldschutzkonzepte und internationale Programme zielen darauf ab, solche Degradationsprozesse zu stoppen und den im Holz gebundenen Kohlenstoff vor der Verflüchtigung in die Erdatmosphäre zu bewahren. Auf der Suche nach Möglichkeiten zur Eindämmung des globalen Klimawandels werden Savannen zunehmend als potenzielle Kohlenstoffsenken diskutiert. Savannen sind von Wäldern jedoch fundamental verschieden, da sie von Natur aus durch starke Störungen, wie z. B. Elefantenfraß und Buschfeuer, geprägt und an diese evolutionär angepasst sind. Anders als in Wäldern sind hier Störungen für Funktion und Stabilität von offenen Savannenökosysteme notwendig und verhindern, dass sie sich zu geschlossenen Waldbeständen oder undurchdringlichen Gestrüppen entwickeln. Folglich ist die Kohlenstoffspeicherung in der holzigen Vegetation in Savannen geringer als in Wäldern und dies war lange Zeit der Grund dafür, dass Savannen keine Beachtung als potenzielle Kohlenstoffsenke fanden. In letzter Zeit wurde jedoch zunehmend die Frage aufgeworfen, ob Programme zur Kohlenstoffbindung (wie REDD+) auch auf Savannenökosysteme angewendet werden könnten. Die heterogene Vegetationsstruktur und chronischen Störungen erschweren jedoch erheblich die Quantifizierung der Kohlenstoffvorräte in Savannen, so dass die derzeitigen Verfahren zur Schätzung der Kohlenstoffspeicherung aufgrund methodischer Hindernisse mit großen Unsicherheiten verbunden sind. Daher ist es auch schwierig abzuschätzen, wie sich künftige Landnutzungsänderungen wie die Intensivierung der Landwirtschaft oder die Erhöhung von Wildtierdichten auf die Kohlenstoffspeicher der afrikanischen Trockengebiete auswirken werden. In dieser Arbeit fasse ich zunächst die konventionellen Ansätze zur Quantifizierung von Kohlenstoffspeichern zusammen und zeige auf, wo und aus welchen Gründen sie in Savannenökosystemen versagen. Darüber hinaus skizziere ich entlang zweier Pfade der Landnutzungsänderung, welche Zukunftsvorstellungen den Landnutzungswandel im südlichen Afrika vorantreiben und wie diese voraussichtlich die Kohlenstoffspeicherung beeinflussen werden. In den folgenden Kapiteln entwickele ich eine neue Methode zur Schätzung der Kohlenstoffspeicherung, die an die spezifischen Bedingungen störungsanfälliger Ökosysteme angepasst ist, und zeige die Vorteile dieses Ansatzes gegenüber den bisherigen forstwirtschaftlichen Methoden auf. In den beiden daran anschließenden Kapiteln wende ich die neue Methode an, um die Auswirkungen von Landnutzungsänderungen auf die Kohlenstoffspeicherung zu analysieren und berücksichtige dabei auch das Verhältnis von holziger Biomasse zu im Boden gespeichertem Kohlenstoff. Mit diesem interdisziplinären Ansatz kann ich zeigen, dass sowohl die Intensivierung der Landwirtschaft als auch der Naturschutz mit großen Pflanzenfressern die ober- und unterirdische Kohlenstoffspeicherung in Büschen und Bäumen verringern, dieser Kohlenstoff jedoch nicht verloren geht, sondern teilweise in den organischen Kohlenstoffbestand des Bodens eingelagert wird. Anschließend quantifiziere ich die Kohlenstoffspeicherung im gesamten Ökosystem sowie in verschiedenen Ökosystemkompartimenten (ober- und unterirdischer Holzkohlenstoff in Sträuchern bzw. Bäumen sowie organischer Kohlenstoff im Ober- und Unterboden) von zwei verschiedenen Vegetationstypen der Studienregion. Darüber hinaus analysiere ich in einer Raum-Zeit-Substitution, wie sich zukünftige Landnutzungsänderungen auf die Kohlenstoffspeicherung in jedem Kompartiment und im gesamten Ökosystem auswirken. Die hier untersuchten Kohlenstoffspeicher unterscheiden sich in ihrer Beständigkeit gegenüber Landnutzungsänderungen, wobei jener Kohlenstoff, der in der Strauchbiomasse gebunden ist sich als am wenigsten beständig gegenüber künftigen Änderungen herausgestellt hat; demgegenüber ist der organische Kohlenstoff im Unterboden bei veränderter Landnutzung am stabilsten. Anschließend untersuche ich mit Hilfe von statistischen Modellen (Generalized Additive Models, GAMs), welche individuellen Landnutzungsfaktoren die Kohlenstoffspeicherung beeinflussen, und decke nichtlineare Effekte auf. Insbesondere Elefantenfraß kann zunächst positive Auswirkungen auf die Kohlenstoffspeicherung haben, die sich bei weiterer Intensivierung jedoch ins Gegenteil verkehrt. Dies muss bei zukünftigen Planungen berücksichtigt werden. Im letzten Kapitel diskutiere ich meine Ergebnisse im größeren Kontext dieser Arbeit und erörtere relevante Implikationen für Landnutzungsänderungen und zukünftige Entscheidungen. KW - biology KW - plant ecology KW - carbon storage KW - savanna KW - woodland KW - vegetation ecology KW - disturbance ecology KW - soil organic carbon KW - Biologie KW - Kohlenstoffspeicherung KW - Störungsökologie KW - Pflanzenökologie KW - Savanne KW - Organischer Bodenkohlenstoff KW - Vegetationsökologie KW - Baumsavanne Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-648943 ER - TY - JOUR A1 - Kindermann, Liana A1 - Dobler, Magnus A1 - Niedeggen, Daniela A1 - Linstädter, Anja T1 - A new protocol for estimation of woody aboveground biomass in disturbance-prone ecosystems JF - Ecological indicators : integrating monitoring, assessment and management N2 - Almost one third of global drylands are open forests and savannas, which are typically shaped by frequent natural disturbances such as wildfire and herbivory. Studies on ecosystem functions and services of woody vegetation require robust estimates of aboveground biomass (AGB). However, most methods have been developed for comparatively undisturbed forest ecosystems. As they are not tailored to accurately quantify AGB of small and irregular growth forms, their application on these growth forms may lead to unreliable or even biased AGB estimates in disturbance-prone dryland ecosystems. Moreover, these methods cannot quantify AGB losses caused by disturbance agents. Here we propose a methodology to estimate individual-and stand-level woody AGB in disturbance-prone ecosystems. It consists of flexible field sampling routines and estimation workflows for six growth classes, delineated by size and damage criteria. It also comprises a detailed damage assessment, harnessing the ecological archive of woody growth for past disturbances. Based on large inventories collected along steep gradients of elephant disturbances in African dryland ecosystems, we compared the AGB estimates generated with our proposed method against estimates from a less adapted forest inventory method. We evaluated the necessary stepwise procedures of method adaptation and analyzed each step's effect on stand-level AGB estimation. We further explored additional advantages of our proposed method with regard to disturbance impact quantification. Results indicate that a majority of growth forms and individuals in savanna vegetation could only be assessed if methods of AGB estimation were adapted to the conditions of a disturbance-prone ecosystem. Furthermore, our damage assessment demonstrated that one third to half of all woody AGB was lost to disturbances. Consequently, less adapted methods may be insufficient and are likely to render inaccurate AGB estimations. Our proposed method has the potential to accurately quantify woody AGB in disturbance-prone ecosystems, as well as AGB losses. Our method is more time consuming than conventional allometric approaches, yet it can cover sufficient areas within reasonable timespans, and can also be easily adapted to alternative sampling schemes. KW - Damage assessment KW - Disturbance impacts KW - Tree growth classes KW - Method KW - comparison KW - Flexible sampling strategy KW - Tree allometry KW - Woody KW - aboveground biomass Y1 - 2021 U6 - https://doi.org/10.1016/j.ecolind.2021.108466 SN - 1470-160X SN - 1872-7034 VL - 135 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Kindermann, Liana A1 - Dobler, Magnus A1 - Niedeggen, Daniela A1 - Chimbioputo Fabiano, Ezequiel A1 - Linstädter, Anja T1 - Dataset on woody aboveground biomass, disturbance losses, and wood density from an African savanna ecosystem JF - Data in Brief N2 - This dataset comprises tree inventories and damage assessments performed in Namibia's semi-arid Zambezi Region. Data were sampled in savannas and savanna woodlands along steep gradients of elephant population densities to capture the effects of those (and other) disturbances on individual-level and stand-level aboveground woody biomass (AGB). The dataset contains raw data on dendrometric measures and processed data on specific wood density (SWD), woody aboveground biomass, and biomass losses through disturbance impacts. Allometric proxies (height, canopy diameters, and in adult trees also stem circumferences) were recorded for n = 6,179 tree and shrub individuals. Wood samples were taken for each encountered species to measure specific wood density. These measurements have been used to estimate woody aboveground biomass via established allometric models, advanced through our improved methodologies and workflows that accounted for tree and shrub architecture shaped by disturbance impacts. To this end, we performed a detailed damage assessment on each woody individual in the field. In addition to estimations of standing biomass, our new method also delivered data on biomass losses to different disturbance agents (elephants, fire, and others) on the level of plant individuals and stands. The data presented here have been used within a study published with Ecological Indicators (Kindermann et al., 2022) to evaluate the benefits of our improved methodology in comparison to a standard reference method of aboveground biomass estimations. Additionally, it has been employed in a study on carbon storage and sequestration in vegetation and soils (Sandhage-Hofmann et al., 2021). The raw data of dendrometric measurements can be subjected to other available allometric models for biomass estimation. The processed data can be used to analyze disturbance impacts on woody aboveground biomass, or for regional carbon storage estimates. The data on species-specific wood density can be used for application to other dendrometric datasets to (re-) estimate biomass through allometric models requiring wood density. It can further be used for plant functional trait analyses. KW - Damage assessment KW - Disturbance impacts KW - Disturbance indicator KW - Elephant disturbance KW - Tree allometry KW - Specific wood density KW - Woody aboveground biomass KW - Wood specific gravity Y1 - 2022 U6 - https://doi.org/10.1016/j.dib.2022.108155 SN - 2352-3409 VL - 42 SP - 1 EP - 16 PB - Elsevier CY - Amsterdam, Niederlande ER - TY - JOUR A1 - Sandhage-Hofmann, Alexandra A1 - Linstädter, Anja A1 - Kindermann, Liana A1 - Angombe, Simon A1 - Amelung, Wulf T1 - Conservation with elevated elephant densities sequesters carbon in soils despite losses of woody biomass JF - Global change biology N2 - Nature conservation and restoration in terrestrial ecosystems is often focused on increasing the numbers of megafauna, expecting them to have positive impacts on ecological self-regulation processes and biodiversity. In sub-Saharan Africa, conservation efforts also aspire to protect and enhance biodiversity with particular focus on elephants. However, elephant browsing carries the risk of woody biomass losses. In this context, little is known about how increasing elephant numbers affects carbon stocks in soils, including the subsoils. We hypothesized that (1) increasing numbers of elephants reduce tree biomass, and thus the amount of C stored therein, resulting (2) in a loss of soil organic carbon (SOC). If true, a negative carbon footprint could limit the sustainability of elephant conservation from a global carbon perspective. To test these hypotheses, we selected plots of low, medium, and high elephant densities in two national parks and adjacent conservancies in the Namibian component of the Kavango Zambezi Transfrontier Area (KAZA), and quantified carbon storage in both woody vegetation and soils (1 m). Analyses were supplemented by the assessment of soil carbon isotopic composition. We found that increasing elephant densities resulted in a loss of tree carbon storage by 6.4 t ha(-1). However, and in contrast to our second hypothesis, SOC stocks increased by 4.7 t ha(-1) with increasing elephant densities. These higher SOC stocks were mainly found in the topsoil (0-30 cm) and were largely due to the formation of SOC from woody biomass. A second carbon input source into the soils was megaherbivore dung, which contributed with 0.02-0.323 t C ha(-1) year(-1) to ecosystem carbon storage in the low and high elephant density plots, respectively. Consequently, increasing elephant density does not necessarily lead to a negative C footprint, as soil carbon sequestration and transient C storage in dung almost compensate for losses in tree biomass. KW - carbon sequestration KW - conservation KW - elephants KW - soil organic carbon KW - woody biomass Y1 - 2021 U6 - https://doi.org/10.1111/gcb.15779 SN - 1354-1013 SN - 1365-2486 VL - 27 IS - 19 SP - 4601 EP - 4614 PB - Blackwell Science CY - Oxford [u.a.] ER - TY - JOUR A1 - Wassermann, Birgit A1 - Abdelfattah, Ahmed A1 - Cernava, Tomislav A1 - Wicaksono, Wisnu A1 - Berg, Gabriele T1 - Microbiome-based biotechnology for reducing food loss post harvest JF - Current opinion in biotechnology N2 - Microbiomes have an immense potential to enhance plant resilience to various biotic and abiotic stresses. However, intrinsic microbial communities respond to changes in their host's physiology and environment during plant's life cycle. The potential of the inherent plant microbiome has been neglected for a long time, especially for the postharvest period. Currently, close to 50% of all produced fruits and vegetables are lost either during production or storage. Biological control of spoilage and storage diseases is still lacking sufficiency. Today, novel multiomics technologies allow us to study the microbiome and its responses on a community level, which will help to advance current classic approaches and develop more effective and robust microbiome-based solutions for fruit and vegetable storability, quality, and safety. Y1 - 2022 U6 - https://doi.org/10.1016/j.copbio.2022.102808 SN - 0958-1669 SN - 1879-0429 VL - 78 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Arnold, Patrick A1 - Hagemann, Justus A1 - Gilissen, Emmanuel A1 - Hofreiter, Michael T1 - Otter shrew mitogenomes (Afrotheria, Potamogalidae) reconstructed from historical museum skins JF - Mitochondrial DNA. Part B N2 - African otter shrews (Potamogalidae) are Afrotherian mammals adapted to a semi-aquatic lifestyle. Given their rareness, genetic data on otter shrews are limited. By applying laboratory methods tuned for the recovery of archival DNA and an iterative mapping approach, we reconstructed whole mitochondrial genomes of the Giant (Potamogale velox) and Ruwenzori pygmy otter shrew (Micropotamogale ruwenzorii) from historical museum skins. Phylogenetic analyses are consistent with previous reports in recovering a sister relationship between African otter shrews and Malagasy tenrecs. The long branches separating both lineages, however, support their recognition as separate families. KW - tenrecs KW - Afrotheria KW - Africa KW - historical DNA Y1 - 2022 U6 - https://doi.org/10.1080/23802359.2022.2122747 SN - 2380-2359 VL - 7 IS - 9 SP - 1699 EP - 1701 PB - Taylor & Francis Group CY - London ER - TY - JOUR A1 - Wicaksono, Wisnu Adi A1 - Erschen, Sabine A1 - Krause, Robert A1 - Müller, Henry A1 - Cernava, Tomislav A1 - Berg, Gabriele T1 - Enhanced survival of multi-species biofilms under stress is promoted by low-abundant but antimicrobial-resistant keystone species JF - Journal of hazardous materials : environmental control, risk assessment, impact and management N2 - Multi-species biofilms are more resistant against stress compared to single-species biofilms. However, the mechanisms underlying this common observation remain elusive. Therefore, we studied biofilm formation of well-known opportunistic pathogens (Acinetobacter baumanii, Enterococcus faecium, Escherichia coli, Staphylococcus haemolyticus and Stenotrophomonas maltophilia) in various approaches. Synergistic effects in their multi species biofilms were observed. Using metatranscriptomics, changes in the gene expression of the involved members became evident, and provided explanations for the improved survivability under nutrient limitation and exposure to disinfectants. Genes encoding proteins for vitamin B6 synthesis and iron uptake were linked to synergism in the multi-species biofilm under nutrient-limited conditions. Our study indicates that sub-lethal concentrations of an alcohol-based disinfectant enhance biofilm yields in multi-species assemblages. A reduction of the dominant taxa in the multi-species biofilm under disinfectant pressure allowed minor taxa to bloom. The findings underline the importance of minor but antimicrobial-resistant species that serve as "protectors" for the whole assemblage due to upregulation of genes involved in defence mechanisms and biofilm formation. This ultimately results in an increase in the total yield of the multi-species biofilm. We conclude that inter-species interactions may be crucial for the survival of opportunistic pathogens; especially under conditions that are typically found under hospital settings. KW - Biofilm KW - Opportunistic pathogen KW - Synergism KW - Multi-species KW - Metatranscriptomic Y1 - 2022 U6 - https://doi.org/10.1016/j.jhazmat.2021.126836 SN - 0304-3894 SN - 1873-3336 VL - 422 PB - Science Direct CY - New York, NY [u.a.] ER - TY - JOUR A1 - Yang, Sizhong A1 - Liebner, Susanne A1 - Svenning, Mette Marianne A1 - Tveit, Alexander Tøsdal T1 - Decoupling of microbial community dynamics and functions in Arctic peat soil exposed to short term warming JF - Molecular ecology N2 - Temperature is an important factor governing microbe-mediated carbon feedback from permafrost soils. The link between taxonomic and functional microbial responses to temperature change remains elusive due to the lack of studies assessing both aspects of microbial ecology. Our previous study reported microbial metabolic and trophic shifts in response to short-term temperature increases in Arctic peat soil, and linked these shifts to higher CH4 and CO2 production rates (Proceedings of the National Academy of Sciences of the United States of America, 112, E2507-E2516). Here, we studied the taxonomic composition and functional potential of samples from the same experiment. We see that along a high-resolution temperature gradient (1-30 degrees C), microbial communities change discretely, but not continuously or stochastically, in response to rising temperatures. The taxonomic variability may thus in part reflect the varied temperature responses of individual taxa and the competition between these taxa for resources. These taxonomic responses contrast the stable functional potential (metagenomic-based) across all temperatures or the previously observed metabolic or trophic shifts at key temperatures. Furthermore, with rising temperatures we observed a progressive decrease in species diversity (Shannon Index) and increased dispersion of greenhouse gas (GHG) production rates. We conclude that the taxonomic variation is decoupled from both the functional potential of the community and the previously observed temperature-dependent changes in microbial function. However, the reduced diversity at higher temperatures might help explain the higher variability in GHG production at higher temperatures. KW - microbial community KW - permafrost KW - species diversity KW - stochastic KW - temperature gradient Y1 - 2021 U6 - https://doi.org/10.1111/mec.16118 SN - 0962-1083 SN - 1365-294X VL - 30 IS - 20 SP - 5094 EP - 5104 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - JOUR A1 - Olimi, Expedito A1 - Bickel, Samuel A1 - Wicaksono, Wisnu Adi A1 - Kusstatscher, Peter A1 - Matzer, Robert A1 - Cernava, Tomislav A1 - Berg, Gabriele T1 - Deciphering the microbial composition of biodynamic preparations and their effects on the apple rhizosphere microbiome JF - Frontiers in soil science N2 - Soil microbial communities are crucial for plant growth and are already depleted by anthropogenic activities. The application of microbial transplants provides a strategy to restore beneficial soil traits, but less is known about the microbiota of traditional inoculants used in biodynamic agriculture. In this study, we used amplicon sequencing and quantitative PCR to decipher microbial communities of composts, biodynamic manures, and plant preparations from Austria and France. In addition, we investigated the effect of extracts derived from biodynamic manure and compost on the rhizosphere microbiome of apple trees. Microbiota abundance, composition, and diversity of biodynamic manures, plant preparations, and composts were distinct. Microbial abundances ranged between 1010-1011 (bacterial 16S rRNA genes) and 109-1011 (fungal ITS genes). The bacterial diversity was significantly higher in biodynamic manures compared to compost without discernible differences in abundance. Fungal diversity was not significantly different while abundance was increased in biodynamic manures. The microbial communities of biodynamic manures and plant preparations were specific for each production site, but all contain potentially plant-beneficial bacterial genera. When applied in apple orchards, biodynamic preparations (extracts) had the non-significant effect of reducing bacterial and fungal abundance in apple rhizosphere (4 months post-application), while increasing fungal and lowering bacterial Shannon diversity. One to four months after inoculation, individual taxa indicated differential abundance. We observed the reduction of the pathogenic fungus Alternaria, and the enrichment of potentially beneficial bacterial genera such as Pseudomonas. Our study paves way for the science-based adaptation of empirically developed biodynamic formulations under different farming practices to restore the vitality of agricultural soils. KW - biodynamic farming KW - compost microbiome KW - biodynamic manures KW - biodynamic preparations KW - rhizosphere microbiome KW - 16S rRNA/ITS amplicon sequencing KW - organic soil amendments Y1 - 2022 U6 - https://doi.org/10.3389/fsoil.2022.1020869 SN - 2673-8619 VL - 2 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Hashemi, Seirana A1 - Razaghi-Moghadam, Zahra A1 - Laitinen, Roosa A. E. A1 - Nikoloski, Zoran T1 - Relative flux trade-offs and optimization of metabolic network functionalities JF - Computational and structural biotechnology journal N2 - Trade-offs between traits are present across different levels of biological systems and ultimately reflect constraints imposed by physicochemical laws and the structure of underlying biochemical networks. Yet, mechanistic explanation of how trade-offs between molecular traits arise and how they relate to optimization of fitness-related traits remains elusive. Here, we introduce the concept of relative flux trade-offs and propose a constraint-based approach, termed FluTOr, to identify metabolic reactions whose fluxes are in relative trade-off with respect to an optimized fitness-related cellular task, like growth. We then employed FluTOr to identify relative flux trade-offs in the genome-scale metabolic networks of Escherichia coli, Saccharomyces cerevisiae, and Arabidopsis thaliana. For the metabolic models of E. coli and S. cerevisiae we showed that: (i) the identified relative flux trade-offs depend on the carbon source used and that (ii) reactions that participated in relative trade-offs in both species were implicated in cofactor biosynthesis. In contrast to the two microorganisms, the relative flux trade-offs for the metabolic model of A. thaliana did not depend on the available nitrogen sources, reflecting the differences in the underlying metabolic network as well as the considered environments. Lastly, the established connection between relative flux trade-offs allowed us to identify overexpression targets that can be used to optimize fitness-related traits. Altogether, our computational approach and findings demonstrate how relative flux trade-offs can shape optimization of metabolic tasks, important in biotechnological applications. KW - Trade-offs KW - Metabolic networks KW - Fluxes KW - Overexpression targets KW - Growth Y1 - 2022 U6 - https://doi.org/10.1016/j.csbj.2022.07.038 SN - 2001-0370 VL - 20 SP - 3963 EP - 3971 PB - Research Network of Computational and Structural Biotechnology (RNCSB) CY - Gotenburg ER - TY - JOUR A1 - Laitinen, Roosa A. E. A1 - Nikoloski, Zoran T1 - Genetic basis of plasticity in plants JF - Journal of experimental botany N2 - The ability of an organism to change its phenotype in response to different environments, termed plasticity, is a particularly important characteristic to enable sessile plants to adapt to rapid changes in their surroundings. Plasticity is a quantitative trait that can provide a fitness advantage and mitigate negative effects due to environmental perturbations. Yet, its genetic basis is not fully understood. Alongside technological limitations, the main challenge in studying plasticity has been the selection of suitable approaches for quantification of phenotypic plasticity. Here, we propose a categorization of the existing quantitative measures of phenotypic plasticity into nominal and relative approaches. Moreover, we highlight the recent advances in the understanding of the genetic architecture underlying phenotypic plasticity in plants. We identify four pillars for future research to uncover the genetic basis of phenotypic plasticity, with emphasis on development of computational approaches and theories. These developments will allow us to perform specific experiments to validate the causal genes for plasticity and to discover their role in plant fitness and evolution. KW - Genetic architecture KW - GWA KW - GxE interaction KW - hub genes KW - plant adaptation KW - plasticity KW - variance Y1 - 2018 U6 - https://doi.org/10.1093/jxb/ery404 SN - 0022-0957 SN - 1460-2431 VL - 70 IS - 3 SP - 739 EP - 745 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Thongthaisong, Patch A1 - Kasada, Minoru A1 - Grossart, Hans-Peter A1 - Wollrab, Sabine T1 - Critical role of parasite-mediated energy pathway on community response to nutrient enrichment JF - Ecology and evolution N2 - Parasites form an integral part of food webs, however, they are often ignored in classic food web theory or limited to the investigation of trophic transmission pathways. Specifically, direct consumption of parasites by nonhost predators is rarely considered, while it can contribute substantially to energy flow in food webs. In aquatic systems, chytrids constitute a major group of fungal parasites whose free-living infective stages (zoospores) form a highly nutritional food source to zooplankton. Thereby, the consumption of zoospores can create an energy pathway from otherwise inedible phytoplankton to zooplankton ( "mycoloop "). This parasite-mediated energy pathway might be of special importance during phytoplankton blooms dominated by inedible or toxic primary producers like cyanobacteria, which are on the rise with eutrophication and global warming. We theoretically investigated community dynamics and energy transfer in a food web consisting of an edible nonhost and an inedible host phytoplankton species, a parasitic fungus, and a zooplankton species grazing on edible phytoplankton and fungi. Food web dynamics were investigated along a nutrient gradient contrasting nonadaptive zooplankton species representative for filter feeders like cladocerans and zooplankton with the ability to actively adapt their feeding preferences like many copepod species. Overall, the importance of the mycoloop for zooplankton increases with nutrient availability. This increase is smooth for nonadaptive consumers. For adaptive consumers, we observe an abrupt shift from an almost exclusive preference for edible phytoplankton at low nutrient levels to a strong preference for parasitic fungi at high nutrient levels. The model predicts that parasitic fungi could contribute up to 50% of the zooplankton diet in nutrient-rich environments, which agrees with empirical observations on zooplankton gut content from eutrophic systems during blooms of inedible diatoms or cyanobacteria. Our findings highlight the role of parasite-mediated energy pathways for predictions of energy flow and community composition under current and future environmental change. KW - adaptive preference KW - energy flow KW - food web KW - mycoloop KW - parasite-mediated KW - energy pathway KW - parasites KW - parasitic fungi Y1 - 2022 U6 - https://doi.org/10.1002/ece3.9622 SN - 2045-7758 VL - 12 IS - 12 PB - John Wiley & Sons, Inc. CY - [Hoboken] ER - TY - JOUR A1 - Rodriguez Cubillos, Andres Eduardo A1 - Tong, Hao A1 - Alseekh, Saleh A1 - de Abreu e Lima, Francisco Anastacio A1 - Yu, Jing A1 - Fernie, Alisdair A1 - Nikoloski, Zoran A1 - Laitinen, Roosa A. E. T1 - Inheritance patterns in metabolism and growth in diallel crosses of Arabidopsis thaliana from a single growth habitat JF - Heredity N2 - Metabolism is a key determinant of plant growth and modulates plant adaptive responses. Increased metabolic variation due to heterozygosity may be beneficial for highly homozygous plants if their progeny is to respond to sudden changes in the habitat. Here, we investigate the extent to which heterozygosity contributes to the variation in metabolism and size of hybrids of Arabidopsis thaliana whose parents are from a single growth habitat. We created full diallel crosses among seven parents, originating from Southern Germany, and analysed the inheritance patterns in primary and secondary metabolism as well as in rosette size in situ. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed more pronounced non-additive inheritance patterns which could be attributed to epistasis. In addition, we showed that glucosinolates, among other secondary metabolites, were positively correlated with a proxy for plant size. Therefore, our study demonstrates that heterozygosity in local A. thaliana population generates metabolic variation and may impact several tasks directly linked to metabolism. Y1 - 2018 U6 - https://doi.org/10.1038/s41437-017-0030-5 SN - 0018-067X SN - 1365-2540 VL - 120 IS - 5 SP - 463 EP - 473 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Ferner, Jessica A1 - Linstädter, Anja A1 - Rogass, Christian A1 - Südekum, Karl-Heinz A1 - Schmidtlein, Sebastian T1 - Towards forage resource monitoring in subtropical savanna grasslands BT - going multispectral or hyperspectral? JF - European journal of remote sensing N2 - Forage supply of savanna grasslands plays a crucial role for local food security and consequently, a reliable monitoring system could help to better manage vital forage resources. To help installing such a monitoring system, we investigated whether in-situ hyperspectral data could be resampled to match the spectral resolution of multi- and hyperspectral satellites; if the type of sensor affected model transfer; and if spatio-temporal patterns of forage characteristics could be related to environmental drivers. We established models for forage quantity (green biomass) and five forage quality proxies (metabolisable energy, acid/neutral detergent fibre, ash, phosphorus). Hyperspectral resolution of the Hyperion satellite mostly resulted in higher accuracies (i.e. higher R-2, lower RMSE). When applied to satellite data, though, the greater quality of the multispectral Sentinel-2 satellite data leads to more realistic forage maps. By analysing a three-year time series, we found plant phenology and cumulated precipitation to be the most important environmental drivers of forage supply. We conclude that none of the investigated satellites provide optimal conditions for monitoring purposes. Future hyperspectral satellite missions like EnMAP, combining the high information level of Hyperion with the good data quality and resolution of Sentinel-2, will provide the prerequisites for installing a regular monitoring service. KW - Africa KW - rangelands KW - remote-sensing based monitoring KW - forage KW - biomass KW - production KW - nutritive value Y1 - 2021 U6 - https://doi.org/10.1080/22797254.2021.1934556 SN - 2279-7254 VL - 54 IS - 1 SP - 364 EP - 384 PB - geoLAB, Laboratory of Geomatics CY - Florence ER - TY - THES A1 - Alhajturki, Dema T1 - Characterization of altered inflorescence architecture in Arabidopsis thaliana BG-5 x Kro-0 hybrid T1 - Charakterisierung veränderter Blütenstandarchitektur in Arabidopsis thaliana BG-5 x Kro-0-Hybrid N2 - A reciprocal cross between two A. thaliana accessions, Kro-0 (Krotzenburg, Germany) and BG-5 (Seattle, USA), displays purple rosette leaves and dwarf bushy phenotype in F1 hybrids when grown at 17 °C and a parental-like phenotype when grown at 21 °C. This F1 temperature-dependent-dwarf-bushy phenotype is characterized by reduced growth of the primary stem together with an increased number of branches. The reduced stem growth was the strongest at the first internode. In addition, we found that a temperature switch from 21 °C to 17 °C induced the phenotype only before the formation of the first internode of the stem. Similarly, the F1 dwarf-bushy phenotype could not be reversed when plants were shifted from 17 °C to 21 °C after the first internode was formed. Metabolic analysis showed that the F1 phenotype was associated with a significant upregulation of anthocyanin(s), kaempferol(s), salicylic acid, jasmonic acid and abscisic acid. As it has been previously shown that the dwarf-bushy phenotype is linked to two loci, one on chromosome 2 from Kro-0 and one on chromosome 3 from BG-5, an artificial micro-RNA approach was used to investigate the necessary genes on these intervals. From the results obtained, it was found that two genes, AT2G14120 that encodes for a DYNAMIN RELATED PROTEIN3B and AT2G14100 that encodes a member of the Cytochrome P450 family protein CYP705A13, were necessary for the appearance of the F1 phenotype on chromosome 2. It was also discovered that AT3G61035 that encodes for another cytochrome P450 family protein CYP705A13 and AT3G60840 that encodes for a MICROTUBULE-ASSOCIATED PROTEIN65-4 on chromosome 3 were both necessary for the induction of the F1 phenotype. To prove the causality of these genes, genomic constructs of the Kro-0 candidate genes on chromosome 2 were transferred to BG-5 and genomic constructs of the chromosome 3 candidate genes from BG-5 were transferred to Kro-0. The T1 lines showed that these genes are not sufficient alone to induce the phenotype. In addition to the F1 phenotype, more severe phenotypes were observed in the F2 generations that were grouped into five different phenotypic classes. Whilst seed yield was comparable between F1 hybrids and parental lines, three phenotypic classes in the F2 generation exhibited hybrid breakdown in the form of reproductive failure. This F2 hybrid breakdown was less sensitive to temperature and showed a dose-dependent effect of the loci involved in F1 phenotype. The severest class of hybrid breakdown phenotypes was observed only in the population of backcross with the parent Kro-0, which indicates a stronger contribution of the BG-5 allele when compared to the Kro-0 allele on the hybrid breakdown phenotypes. Overall, the findings of my thesis provide a further understanding of the genetic and metabolic factors underlying altered shoot architecture in hybrid dysfunction. N2 - Die reziproke Kreuzung der zwei A. thaliana-Akzessionen Kro-0 aus Krotzenburg (Deutschland) sowie BG-5 aus Seattle (USA) manifestiert sich in einem Zwergbusch-Phänotyp in den F1 Hybriden bei 17 °C. Dagegen zeigen die Nachkommen bei 21 °C einen Phänotyp, der den Eltern ähnelt. Somit handelt es sich bei dieser Kreuzung um einen temperaturabhängigen Phänotyp. Dieser ist gekennzeichnet durch einen gestörten Wuchs des Primärstammes sowie einer vermehrten Anzahl an gebildeten Seitenzweigen. Das gestörte Wachstum des Hauptsprosses ist am gravierendsten rund um das 1. Internodium der Pflanzen. Es konnte gezeigt werden, dass durch einen Temperaturwechsel von 21 °C auf 17 °C der Phänotyp nur induziert werden kann vor der Bildung des 1. Internodiums. Im Gegenzug dazu ist ebenfalls die Rettung des parentalen Phänotyps nur möglich vor der Bildung des 1. Internodiums am Hauptspross. Des Weiteren zeigten metabolische und hormonelle Analysen der F1 Hybriden eine signifikante Erhöhung von Anthozyanen, Kaempferol, Salizylsäure, Jasmonsäure sowie Abscisinsäure. In Vorarbeiten wurde der Phänotyp bereits mit zwei verschiedenen Loci verknüpft, einer befindet sich auf Chromosom 2 der Elternlinie Kro-0, der andere auf Chromosom 3 von BG-5. Mittels eines micro-RNA Versuches konnte ich zeigen, dass die zwei Gene AT2G14120 DYNAMIN RELATED PROTEIN3B und CYP705A13, welches zur Familie des Zytochrom P450 gehört, auf dem Chromosom 2 von Kro-0 involviert sind. Auf Chromosom 3 von BG-5 gehören die Gene CYP76C8P (AT3G61035) sowie MICROTUBULE-ASSOCIATED65-4 (AT3G60840) zu den verantwortlichen Genen. Es wurden genomische Konstrukte der Kro-0-Kandidatengene auf BG-5 übertragen sowie ebenfalls genomische Konstrukte der Chr3-Kandidatengene auf Kro-0 übertragen. Die T1-Linien bewiesen keines dieser Gene als allein ausreichend. Zusätzlich zu dem F1-Phänotyp wurden in den F2-Generationen, die in fünf verschiedene phänotypische Klassen eingeteilt waren, schwerwiegendere Phänotypen beobachtet. Während die Samenausbeute zwischen F1-Hybriden und Elternlinien vergleichbar war, zeigten drei phänotypische Klassen in der F2-Generationen einen Hybridabbau in Form von Fortpflanzungsversagen. Dieser F2-Hybridabbau war weniger temperaturempfindlich und zeigte einen dosisabhängigen Effekt, basierend auf der genetischen Architektur der am F1-Phänotyp beteiligten Loci. Die schwerste Klasse von hybriden Abbauphänotypen wurde nur in der Population von Rückkreuzungen mit dem Elternteil Kro-0 beobachtet, was einen stärkeren Beitrag des BG-5-Allels im Vergleich zu dem Kro-0-Allel auf den hybriden Abbauphänotypen anzeigt. Insgesamt liefern die Ergebnisse meiner Dissertation ein weiteres Verständnis der genetischen und metabolischen Faktoren, die der veränderten Sprossarchitektur bei hybrider Dysfunktion zugrunde liegen. KW - hybrid incompatibility KW - hybride Inkompatibilität KW - hybrid breakdown KW - Hybridzerfall KW - altered shoot branching KW - veränderte Triebverzweigung Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-420934 ER - TY - THES A1 - Hashemi Ranjbar, Seirana T1 - Plasticity and trade-offs in plant metabolic networks N2 - A biological trade-off situation denotes the dependence between traits whereby an increase in the value of one of the traits leads to a decrease in the value of at least one of the others. Understanding trade-offs in cellular systems is relevant to understanding the limits and constraints to tuning desired phenotypes. Therefore, it is mainly the case for rates (i.e. fluxes) of biochemical reactions that shape not only molecular traits, like metabolite concentrations but also determine physiological traits, like growth. Intracellular fluxes are the final phenotype from transcriptional and (post)translational regulation. Quantifying intracellular fluxes provides insights into cellular physiology under particular growth conditions and can be used to characterize the metabolic activity of different pathways. However, estimating fluxes from labelling experiments is labour-intensive; therefore, developing approaches to accurately and precisely predict intracellular fluxes is essential. This thesis addresses two main problems: (i) identifying flux trade-offs and (ii) predicting accurate and precise reaction flux at a genome-scale level. To this end, the concept of an absolute flux trade-off is defined, and a constraint-based approach, termed FluTO, was developed to identify absolute flux trade-offs. FluTO is cast as a mixed integer programming approach applied to genome-scale metabolic models of E. coli, S. cerevisiae, and A. thaliana, imposing realistic constraints on growth and nutrient uptake.. The findings showed that trade-offs are not only species-specific but also specific to carbon sources. In addition, we found that different models of a single species have a different number of reactions in trade-offs. We also showed that absolute flux trade-offs depend on the biomass reaction used to model the growth of A. thaliana under different carbon and nitrogen conditions. Findings reflect the strong relation between nitrogen, carbon, and sulphur metabolisms in the leaves of C3 plants. The concept of relative trade-offs was introduced to further study trade-offs in metabolic networks. A constraint-based approach, FluTOr, was proposed to identify reactions whose fluxes are in relative trade-off concerning an optimized fitness-related cellular task, like growth. FluTOr was employed to find the relative flux trade-offsin the genome-scale metabolic networks of E. coli, S. cerevisiae, and A. thaliana. The results showed that in contrast to the A. thaliana model, the relative trade-offs in the two microorganisms depend on the carbon source, reflecting the differences in the underlying metabolic network. Furthermore, applying FluTOr also showed that reactions that participated in relative trade-offs were implicated in cofactor biosynthesis in the two microorganisms. Prediction of reaction fluxes in the constraint-based metabolic framework is usually performed by parsimonious flux balance analysis (pFBA), employing the principle of efficient usage of protein resources. However, we argued that principles related to the coordination of flux values, neglected in previous studies, provide other means to predict intracellular fluxes. To this end, we designed a constraint-based approach, termed complex-balanced FBA (cbFBA), to predict steady-state flux distributions that maximize the number of balanced complexes in a flux distribution, whereby multi-reaction dependencies are maximized. The comparative analysis showed a better agreement of the flux distributions resulting from cbFBA compared to pFBA with experimentally measured fluxes from 17 E. coli strains and 26 S. cerevisiae knock-out mutants. The results also showed that the predictions from cbFBA are more precise than those from pFBA since cbFBA results in a smaller space of alternative solutions than pFBA. N2 - Eine biologische Abwägungssituation bezeichnet die Abhängigkeit zwischen Merkmalen, wobei ein Anstieg des Wertes eines der Merkmale zu einer Abnahme des Wertes mindestens eines der anderen Merkmale führt. Das Verständnis von Abwägungen in zellulären Systemen ist relevant, um die Grenzen und Einschränkungen bei der Differenzierung gewünschter Phänotypen zu verstehen. Dieses ist häufig der Fall bei Fließgeschwindigkeiten (d.h. Ströme) biochemischer Reaktionen, die nicht nur molekulare Merkmale wie Metabolitkonzentrationen beschreiben, sondern auch physiologische Merkmale wie Wachstum bestimmen. Intrazelluläre Ströme sind der endgültige Phänotyp der transkriptionellen und (post)translationalen Regulation. Die Quantifizierung intrazellulärer Ströme liefert Einblicke in die Zellphysiologie unter bestimmten Wachstumsbedingungen und kann verwendet werden, um die Stoffwechselaktivität verschiedener Wege zu charakterisieren. Die Schätzung von Strömen aus Markierungsexperimenten ist jedoch arbeitsintensiv. Daher ist die Entwicklung von Ansätzen zur genauen und präzisen Vorhersage intrazellulärer Ströme unerlässlich. Diese Dissertation befasst sich mit zwei Hauptproblemen: (i) Identifizierung von Abwägungspunkten (Trade-offs) zwischen Strömen und (ii) Vorhersage des genauen und präzisen Reaktionsflusses auf Genomebene. Zu diesem Zweck wird das Konzept eines absoluten Trade-offs von Strömen definiert und ein Constraint-basierter Ansatz namens FluTO entwickelt, um absolute Trade-offs von Strömen zu identifizieren. FluTO ist als gemischter ganzzahliger Programmieransatz konzipiert, der auf genomweite Stoffwechselmodelle von E. coli, S. cerevisiae und A. thaliana angewendet wird und realistische Einschränkungen für Wachstum und Nährstoffaufnahme auferlegt. Die Ergebnisse zeigten, dass Trade-offs nicht nur artspezifisch, sondern auch spezifisch für Kohlenstoffquellen sind. Darüber hinaus haben wir festgestellt, dass verschiedene Modelle einer einzelnen Art eine unterschiedliche Anzahl von Reaktionen in Trade-offs aufweisen. Wir haben auch gezeigt, dass absolute Trade-offs von Strömen von der Biomassereaktion abhängen, die verwendet wird, um das Wachstum von A. thaliana unter verschiedenen Kohlenstoff- und Stickstoffbedingungen zu modellieren. Die Ergebnisse spiegeln die starke Beziehung zwischen dem Stickstoff-, Kohlenstoff- und Schwefelstoffwechsel in den Blättern von C3-Pflanzen wieder. Das Konzept der relativen Trade-Offs wurde eingeführt, um Trade-Offs in metabolischen Netzwerken weiter zu untersuchen. Ein Constraint-basierter Ansatz, FluTOr, wurde entwickelt, um Reaktionen zu identifizieren, deren Ströme in einem relativen Trade-off bezüglich einer optimierten fitnessbezogenen zellulären Aufgabe wie Wachstum stehen. FluTOr wurde eingesetzt, um die relativen Trade-offs von Strömen in den metabolischen Netzwerken von E. coli, S. cerevisiae und A. thaliana auf Genomebene zu finden. Die Ergebnisse zeigten, dass im Gegensatz zum A. Thaliana Modell die relativen Trade-offs in den beiden Mikroorganismen von der Kohlenstoffquelle abhängen, was die Unterschiede im zugrunde liegenden metabolischen Netzwerk wiederspiegelt. Darüber hinaus zeigte die Anwendung von FluTOr auch, dass Reaktionen, die an relativen Trade-offs teilnahmen, an der Cofaktor-Biosynthese in den beiden Mikroorganismen beteiligt waren. Die Vorhersage von Reaktionsflüssen mittels Constraint-basierten metabolischen Methoden wird normalerweise durch eine überschaubare Flussbilanzanalyse (pFBA) durchgeführt, die das Prinzip der effizienten Nutzung von Proteinressourcen anwendet. Wir argumentierten jedoch, dass Prinzipien im Zusammenhang mit der Koordination von Flusswerten, die in früheren Studien vernachlässigt wurden, andere Mittel zur Vorhersage intrazellulärer Ströme bieten. Zu diesem Zweck haben wir einen Constraint-basierten Ansatz entwickelt, der als Complex-Balanced FBA (cbFBA) bezeichnet wird, um Steady-State-Verteilungen von Strömen vorherzusagen, die die Anzahl der ausgewogenen Komplexe in einer Verteilung von Strömen maximieren, wodurch Abhängigkeiten von mehreren Reaktionen maximiert werden. Die vergleichende Analyse zeigte eine bessere Übereinstimmung der Verteilungen von Strömen, die sich aus cbFBA im Vergleich zu pFBA ergaben, mit experimentell gemessenen Strömen von 17 E. coli Stämmen und 26 S. cerevisiae Knock-out-Mutanten. Die Ergebnisse zeigten auch, dass die Vorhersagen von cbFBA genauer sind als die von pFBA, da cbFBA zu weniger alternativen Lösungen führt als pFBA. T2 - Plastizität und Kompromisse in pflanzlichen Stoffwechselnetzwerken KW - trade-off KW - cbFBA KW - metabolic network KW - balanced complex KW - reaction rate KW - Kompromiss KW - cbFBA KW - metabolisches Netzwerk KW - ausgewogener Komplex KW - Reaktionsgeschwindigkeit Y1 - 2023 ER - TY - JOUR A1 - Tong, Hao A1 - Küken, Anika A1 - Razaghi-Moghadam, Zahra A1 - Nikoloski, Zoran T1 - Characterization of effects of genetic variants via genome-scale metabolic modelling JF - Cellular and molecular life sciences : CMLS N2 - Genome-scale metabolic networks for model plants and crops in combination with approaches from the constraint-based modelling framework have been used to predict metabolic traits and design metabolic engineering strategies for their manipulation. With the advances in technologies to generate large-scale genotyping data from natural diversity panels and other populations, genome-wide association and genomic selection have emerged as statistical approaches to determine genetic variants associated with and predictive of traits. Here, we review recent advances in constraint-based approaches that integrate genetic variants in genome-scale metabolic models to characterize their effects on reaction fluxes. Since some of these approaches have been applied in organisms other than plants, we provide a critical assessment of their applicability particularly in crops. In addition, we further dissect the inferred effects of genetic variants with respect to reaction rate constants, abundances of enzymes, and concentrations of metabolites, as main determinants of reaction fluxes and relate them with their combined effects on complex traits, like growth. Through this systematic review, we also provide a roadmap for future research to increase the predictive power of statistical approaches by coupling them with mechanistic models of metabolism. KW - Single-nucleotide polymorphisms KW - Metabolic models KW - Genome-wide KW - association studies KW - Genomic selection Y1 - 2021 U6 - https://doi.org/10.1007/s00018-021-03844-4 SN - 1420-682X SN - 1420-9071 VL - 78 IS - 12 SP - 5123 EP - 5138 PB - Springer International Publishing AG CY - Cham ER - TY - JOUR A1 - Pandey, Prashant K. A1 - Yu, Jing A1 - Omranian, Nooshin A1 - Alseekh, Saleh A1 - Vaid, Neha A1 - Fernie, Alisdair A1 - Nikoloski, Zoran A1 - Laitinen, Roosa A. E. T1 - Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations JF - Plant Direct N2 - Nitrogen (N) is central for plant growth, and metabolic plasticity can provide a strategy to respond to changing N availability. We showed that two local A. thaliana populations exhibited differential plasticity in the compounds of photorespiratory and starch degradation pathways in response to three N conditions. Association of metabolite levels with growth-related and fitness traits indicated that controlled plasticity in these pathways could contribute to local adaptation and play a role in plant evolution. KW - Arabidopsis thaliana KW - natural variation KW - nitrogen availability KW - photorespiration KW - plasticity Y1 - 2019 U6 - https://doi.org/10.1002/pld3.186 SN - 2475-4455 VL - 3 IS - 11 PB - John Wiley & sonst LTD CY - Chichester ER - TY - THES A1 - Rodriguez Cubillos, Andres Eduardo T1 - Understanding the impact of heterozygosity on metabolism, growth and hybrid necrosis within a local Arabidopsis thaliana collection site T1 - Den Einfluss von Heterozygotie auf Stoffwechsel, Wachstum und Hybridnekrose innerhalb einer lokalen Arabidopsis thaliana-Sammelstelle verstehen N2 - Plants are unable to move away from unwanted environments and therefore have to locally adapt to changing conditions. Arabidopsis thaliana (Arabidopsis), a model organism in plant biology, has been able to rapidly colonize a wide spectrum of environments with different biotic and abiotic challenges. In recent years, natural variation in Arabidopsis has shown to be an excellent resource to study genes underlying adaptive traits and hybridization’s impact on natural diversity. Studies on Arabidopsis hybrids have provided information on the genetic basis of hybrid incompatibilities and heterosis, as well as inheritance patterns in hybrids. However, previous studies have focused mainly on global accessions and yet much remains to be known about variation happening within a local growth habitat. In my PhD, I investigated the impact of heterozygosity at a local collection site of Arabidopsis and its role in local adaptation. I focused on two different projects, both including hybrids among Arabidopsis individuals collected around Tübingen in Southern Germany. The first project sought to understand the impact of hybridization on metabolism and growth within a local Arabidopsis collection site. For this, the inheritance patterns in primary and secondary metabolism, together with rosette size of full diallel crosses among seven parents originating from Southern Germany were analyzed. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed pronounced non-additive inheritance patterns. In addition, defense metabolites, mainly glucosinolates, displayed the highest degree of variation from the midparent values and were positively correlated with a proxy for plant size. In the second project, the role of ACCELERATED CELL DEATH 6 (ACD6) in the defense response pathway of Arabidopsis necrotic hybrids was further characterized. Allelic interactions of ACD6 have been previously linked to hybrid necrosis, both among global and local Arabidopsis accessions. Hence, I characterized the early metabolic and ionic changes induced by ACD6, together with marker gene expression assays of physiological responses linked to its activation. An upregulation of simple sugars and metabolites linked to non-enzymatic antioxidants and the TCA cycle were detected, together with putrescine and acids linked to abiotic stress responses. Senescence was found to be induced earlier in necrotic hybrids and cytoplasmic calcium signaling was unaffected in response to temperature. In parallel, GFP-tagged constructs of ACD6 were developed. This work therefore gave novel insights on the role of heterozygosity in natural variation and adaptation and expanded our current knowledge on the physiological and molecular responses associated with ACD6 activation. N2 - Pflanzen sind sessile Organismen, die nicht in der Lage sind sich unerwünschten Lebensräumen zu entziehen, sodass sie sich an verschiedene Umweltbedingungen anpassen müssen. Arabidopsis thaliana (Arabidopsis) als Modellorganismus der Pflanzenbiologie war in der Lage eine Vielzahl von Lebensräumen zu kolonisieren und dabei verschiedenen biotischen und abiotischen Problemen zu trotzen. Natürliche Variation in Arabidopsis hat sich in den letzten Jahren als Mittel bewährt, um Gene zu analysieren, welche für adaptive Eigenschaften und natürliche Vielfalt verantwortlich sind. Studien über Arabidopsis-Hybride haben Erkenntnisse über die genetische Basis von Hybridinkompatibilitäten, Heterosis und Vererbungsmustern von Hybriden geliefert. Jedoch haben diese sich bisher lediglich mit globalen ökotyp befasst, sodass noch viele Informationen über Variation in einem lokalen Wachstumsgebiet fehlen. In meiner Doktorarbeit habe ich den Einfluss von Heterozygotie in einer lokalen Arabidopsis-Population und deren Rolle bei der Adaption untersucht. Dabei habe ich mich auf zwei Themen fokussiert. Beide Themen beinhalteten Arabidopsis-Hybride zwischen Individuen, welche in der Region um Tübingen in Deutschland gesammelt wurden. Das erste Projekt zielte darauf ab, den Einfluss der Hybridisierung auf den Metabolismus und das Wachstum der Pflanzen in einer lokalen Arabidopsis-Population zu verstehen. Dafür wurden das Vererbungsmuster von Primär- und Sekundärmetaboliten, sowie die Rosettengröße von diallelen Kreuzungen zwischen sieben Elternpflanzen analysiert. Im Vergleich zum Primärstoffwechsel variierten Sekundärmetabolite stärker und zeigten nicht-additive Vererbungsmuster. Zusätzlich zeigten Abwehrstoffe – hauptsächlich Glukosinolate – die höchste Abweichung vom Mittelwert beider Eltern und waren in positiver Korrelation mit der Größe der Pflanzen. In dem zweiten Projekt wurde die Rolle von ACCELERATED CELL DEATH 6 (ACD6) im Abwehrsignalweg von nekrotischen Arabidopsis-Hybriden detaillierter charakterisiert. Da die genetische Interaktion zwischen ACD6-Allelen von globalen und lokalen Arabidopsis-ökotypen bereits mit Hybridnekrose verknüpft wurde, habe ich frühe Metaboliten-, Ionen- und Expressionsänderungen von Markergenen charakterisiert, welche durch die Aktivierung von ACD6 induziert wurden. Eine Erhöhung von einfachen Zuckern und Metaboliten nicht-enzymatischer Antioxidantien und dem TCA-Zyklus wurde detektiert, sowie von Putrescin und anderen Säuren abiotischer Stressantworten. Es wurde nachgewiesen, dass Seneszenz früher in nekrotischen Hybriden induziert und zytoplasmatisches Calcium-Signaling nicht durch Temperatur beeinflusst wurde. Zusätzlich wurden GFP-markierte Konstrukte von ACD6 generiert. Zusammenfassend kann gesagt werden, dass diese Arbeit weitere Erkenntnisse über die Rolle von Heterozygotie in natürlicher Variation und Adaptation liefert und sie unser Wissen über die physiologischen und molekularen Veränderungen, verursacht durch die ACD6-Aktivierung, erweitert. KW - arabidopsis KW - diallel KW - nonadditive KW - inheritance KW - metabolism KW - variation KW - ACD6 KW - adaptation KW - defense KW - necrosis KW - Arabidopsis KW - Dialel KW - nicht additiv KW - Erbe KW - Stoffwechsel KW - Variation KW - ACD6 KW - Anpassung KW - Verteidigung KW - Nekrose Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-416758 ER - TY - JOUR A1 - Kissling, W. D. A1 - Dormann, Carsten F. A1 - Groeneveld, Juergen A1 - Hickler, Thomas A1 - Kühn, Ingolf A1 - McInerny, Greg J. A1 - Montoya, Jose M. A1 - Römermann, Christine A1 - Schiffers, Katja A1 - Schurr, Frank Martin A1 - Singer, Alexander A1 - Svenning, Jens-Christian A1 - Zimmermann, Niklaus E. A1 - O'Hara, Robert B. T1 - Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents JF - Journal of biogeography N2 - Aim Biotic interactions within guilds or across trophic levels have widely been ignored in species distribution models (SDMs). This synthesis outlines the development of species interaction distribution models (SIDMs), which aim to incorporate multispecies interactions at large spatial extents using interaction matrices. Location Local to global. Methods We review recent approaches for extending classical SDMs to incorporate biotic interactions, and identify some methodological and conceptual limitations. To illustrate possible directions for conceptual advancement we explore three principal ways of modelling multispecies interactions using interaction matrices: simple qualitative linkages between species, quantitative interaction coefficients reflecting interaction strengths, and interactions mediated by interaction currencies. We explain methodological advancements for static interaction data and multispecies time series, and outline methods to reduce complexity when modelling multispecies interactions. Results Classical SDMs ignore biotic interactions and recent SDM extensions only include the unidirectional influence of one or a few species. However, novel methods using error matrices in multivariate regression models allow interactions between multiple species to be modelled explicitly with spatial co-occurrence data. If time series are available, multivariate versions of population dynamic models can be applied that account for the effects and relative importance of species interactions and environmental drivers. These methods need to be extended by incorporating the non-stationarity in interaction coefficients across space and time, and are challenged by the limited empirical knowledge on spatio-temporal variation in the existence and strength of species interactions. Model complexity may be reduced by: (1) using prior ecological knowledge to set a subset of interaction coefficients to zero, (2) modelling guilds and functional groups rather than individual species, and (3) modelling interaction currencies and species effect and response traits. Main conclusions There is great potential for developing novel approaches that incorporate multispecies interactions into the projection of species distributions and community structure at large spatial extents. Progress can be made by: (1) developing statistical models with interaction matrices for multispecies co-occurrence datasets across large-scale environmental gradients, (2) testing the potential and limitations of methods for complexity reduction, and (3) sampling and monitoring comprehensive spatio-temporal data on biotic interactions in multispecies communities. KW - Community ecology KW - ecological networks KW - global change KW - guild assembly KW - multidimensional complexity KW - niche theory KW - prediction KW - species distribution model KW - species interactions KW - trait-based community modules Y1 - 2012 U6 - https://doi.org/10.1111/j.1365-2699.2011.02663.x SN - 0305-0270 VL - 39 IS - 12 SP - 2163 EP - 2178 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Pavlova, Viola A1 - Nabe-Nielsen, Jacob A1 - Dietz, Rune A1 - Svenning, Jens-Christian A1 - Vorkamp, Katrin A1 - Riget, Frank Farso A1 - Sonne, Christian A1 - Letcher, Robert J. A1 - Grimm, Volker T1 - Field metabolic rate and PCB adipose tissue deposition efficiency in East Greenland polar bears derived from contaminant monitoring data JF - PLoS one N2 - Climate change will increasingly affect the natural habitat and diet of polar bears (Ursus maritimus). Understanding the energetic needs of polar bears is therefore important. We developed a theoretical method for estimating polar bear food consumption based on using the highly recalcitrant polychlorinated biphenyl (PCB) congener, 2,2',4,4',55-hexaCB (CB153) in bear adipose tissue as an indicator of food intake. By comparing the CB153 tissue concentrations in wild polar bears with estimates from a purposely designed individual-based model, we identified the possible combinations of field metabolic rates (FMR) and CB153 deposition efficiencies in East Greenland polar bears. Our simulations indicate that if 30% of the CB153 consumed by polar bear individuals were deposited into their adipose tissue, the corresponding FMR would be only two times the basal metabolic rate. In contrast, if the modelled CB153 deposition efficiency were 10%, adult polar bears would require six times more energy than that needed to cover basal metabolism. This is considerably higher than what has been assumed for polar bears in previous studies though it is similar to FMRs found in other marine mammals. An implication of this result is that even relatively small reductions in future feeding opportunities could impact the survival of East Greenland polar bears. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pone.0104037 SN - 1932-6203 VL - 9 IS - 8 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Svenning, Jens-Christian A1 - Gravel, Dominique A1 - Holt, Robert D. A1 - Schurr, Frank Martin A1 - Thuiller, Wilfried A1 - Muenkemueller, Tamara A1 - Schiffers, Katja H. A1 - Dullinger, Stefan A1 - Edwards, Thomas C. A1 - Hickler, Thomas A1 - Higgins, Steven I. A1 - Nabel, Julia E. M. S. A1 - Pagel, Jörn A1 - Normand, Signe T1 - The influence of interspecific interactions on species range expansion rates JF - Ecography : pattern and diversity in ecology ; research papers forum Y1 - 2014 U6 - https://doi.org/10.1111/j.1600-0587.2013.00574.x SN - 0906-7590 SN - 1600-0587 VL - 37 IS - 12 SP - 1198 EP - 1209 PB - Wiley-Blackwell CY - Hoboken ER - TY - THES A1 - Plötner, Björn T1 - F2 hybrid chlorosis in a cross between the Arabidopsis thaliana accessions Shahdara and Lovvik-5 Y1 - 2015 ER - TY - THES A1 - Swiadek, Magdalena Agnieszka T1 - Hybrid necrosis in local populations of Arabidopsis thaliana Y1 - 2015 ER - TY - THES A1 - Ulbricht-Jones, Elena Sofia T1 - The virescent and narrow leaf phenotype of a plastome-genome-incompatible Oenothera hybrid is associated with the plastid gene accD and fatty acid synthesis Y1 - 2017 ER - TY - JOUR A1 - Cheshmeh, Sahar A1 - Elahi, Negin A1 - Ghayyem, Maysa A1 - Mosaieby, Elaheh A1 - Moradi, Shima A1 - Pasdar, Yahya A1 - Tahmasebi, Susan A1 - Moradinazar, Mehdi T1 - Effect of green cardamom on the expression of genes implicated in obesity and diabetes among obese women with polycystic ovary syndrome BT - a double blind randomized controlled trial JF - Genes & nutrition N2 - Background: Polycystic ovary syndrome (PCOS) is an endocrine disease in which related to obesity, metabolic disorders and is considered as one of the main causes of infertility in women. This trial was investigated the effects of green cardamom on the expression of genes implicated in obesity and diabetes among obese women with PCOS. Methods: One hundred ninety-four PCOS women were randomly divided two groups: intervention (n = 99; 3 g/day green cardamom) and control groups (n = 95). All of them were given low calorie diet. Anthropometric, glycemic and androgen hormones were assessed before and after 16-week intervention. The reverse transcription-polymerase chain reaction (RT-PCR) method was used to measure fat mass and obesity-associated (FTO), peroxisome proliferative activating receptor- (PPAR-), carnitine palmitoyltransferase 1A (CPT1A), acetyl-CoA carboxylase beta (ACAB), leptin receptor (LEPR), ghrelin, and lamin A/C (LAMIN) genes expression in each group. Results: Anthropometric indices were significantly decreased after intervention in both two studied groups. Glycemic indices and androgen hormones were significantly improved in the intervention group compared to the control group. The expression levels of FTO, CPT1A, LEPR, and LAMIN were significantly downregulated compared to control group (P < 0.001), as well as, PPAR-y was significantly upregulated in the intervention group after intervention with green cardamom compared to control group (P < 0.001). Conclusion: This current study showed that the administration of green cardamom is a beneficial approach for improving anthropometric, glycemic, and androgen hormones, as well as obesity and diabetes genes expression in PCOS women under the low-calorie diet. KW - polycystic ovary syndrome KW - green cardamom KW - obesity genes KW - diabetes genes Y1 - 2022 U6 - https://doi.org/10.1186/s12263-022-00719-6 SN - 1555-8932 SN - 1865-3499 VL - 17 IS - 1 PB - Springer CY - Berlin ER - TY - JOUR A1 - Mitzscherling, Julia A1 - MacLean, Joana A1 - Lipus, Daniel A1 - Bartholomäus, Alexander A1 - Mangelsdorf, Kai A1 - Lipski, Andre A1 - Roddatis, Vladimir A1 - Liebner, Susanne A1 - Wagner, Dirk T1 - Paenalcaligenes niemegkensis sp. nov., a novel species of the family Alcaligenaceae isolated from plastic waste JF - International journal of systematic and evolutionary microbiology N2 - Strain NGK35T is a motile, Gram-stain-negative, rod-shaped (1.0-2.1 mu m long and 0.6-0.8 mu m wide), aerobic bacterium that was isolated from plastic-polluted landfill soil. The strain grew at temperatures between 6 and 37 degrees C (optimum, 28 degrees C), in 0-10 % NaCl (optimum, 1 %) and at pH 6.0-9.5 (optimum, pH 7.5-8.5). It was positive for cytochrome c oxidase, catalase as well as H2S production, and hydrolysed casein and urea. It used a variety of different carbon sources including citrate, lactate and pyruvate. The predominant membrane fatty acids were C-16:1 cis9 and C-16:0, followed by C-17:0 cyclo and C-18:1 cis11. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine, followed by diphosphatidyglycerol. The only quinone was ubiquinone Q-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK35(T) belongs to the genus Paenalcaligenes (family Alcaligenaceae), appearing most closely related to Paenalcaligenes hominis CCUG 53761A(T) (96.90 %) and Paenalcaligenes suwonensis ABC02-12(T) (96.94 %). The genomic DNA G+C content of strain NGK35(T) was 52.1 mol%. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Paenalcaligenes. Based on phenotypic and molecular characterization, strain NGK35(T) can clearly be differentiated from its phylogenetic neighbours establishing a novel species, for which the name Paenalcaligenes niemegkensis sp. nov. is proposed. The type strain is NGK35T (=DSM 113270(T)=NCCB 100854(T)). Y1 - 2022 U6 - https://doi.org/10.1099/ijsem.0.005333 SN - 1466-5026 SN - 1466-5034 VL - 72 IS - 4 PB - Microbiology Society CY - London ER - TY - JOUR A1 - Grzesiuk, Malgorzata A1 - Pietrzak, Barbara A1 - Wacker, Alexander A1 - Pijanowska, Joanna T1 - Photosynthetic activity in both algae and cyanobacteria changes in response to cues of predation JF - Frontiers in plant science N2 - A plethora of adaptive responses to predation has been described in microscopic aquatic producers. Although the energetic costs of these responses are expected, with their consequences going far beyond an individual, their underlying molecular and metabolic mechanisms are not fully known. One, so far hardly considered, is if and how the photosynthetic efficiency of phytoplankton might change in response to the predation cues. Our main aim was to identify such responses in phytoplankton and to detect if they are taxon-specific. We exposed seven algae and seven cyanobacteria species to the chemical cues of an efficient consumer, Daphnia magna, which was fed either a green alga, Acutodesmus obliquus, or a cyanobacterium, Synechococcus elongatus (kairomone and alarm cues), or was not fed (kairomone alone). In most algal and cyanobacterial species studied, the quantum yield of photosystem II increased in response to predator fed cyanobacterium, whereas in most of these species the yield did not change in response to predator fed alga. Also, cyanobacteria tended not to respond to a non-feeding predator. The modal qualitative responses of the electron transport rate were similar to those of the quantum yield. To our best knowledge, the results presented here are the broadest scan of photosystem II responses in the predation context so far. KW - phytoplankton KW - grazing KW - predation KW - Daphnia KW - phenotypic plasticity KW - biotic stress KW - photosystem KW - PAM Y1 - 2022 U6 - https://doi.org/10.3389/fpls.2022.907174 SN - 1664-462X VL - 13 PB - Frontiers Media CY - Lausanne ER -