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 - 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 - 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 - THES A1 - Arend, Marius T1 - Comparing genome-scale models of protein-constrained metabolism in heterotrophic and photosynthetic microorganisms N2 - Genome-scale metabolic models are mathematical representations of all known reactions occurring in a cell. Combined with constraints based on physiological measurements, these models have been used to accurately predict metabolic fluxes and effects of perturbations (e.g. knock-outs) and to inform metabolic engineering strategies. Recently, protein-constrained models have been shown to increase predictive potential (especially in overflow metabolism), while alleviating the need for measurement of nutrient uptake rates. The resulting modelling frameworks quantify the upkeep cost of a certain metabolic flux as the minimum amount of enzyme required for catalysis. These improvements are based on the use of in vitro turnover numbers or in vivo apparent catalytic rates of enzymes for model parameterization. In this thesis several tools for the estimation and refinement of these parameters based on in vivo proteomics data of Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii have been developed and applied. The difference between in vitro and in vivo catalytic rate measures for the three microorganisms was systematically analyzed. The results for the facultatively heterotrophic microalga C. reinhardtii considerably expanded the apparent catalytic rate estimates for photosynthetic organisms. Our general finding pointed at a global reduction of enzyme efficiency in heterotrophy compared to other growth scenarios. Independent of the modelled organism, in vivo estimates were shown to improve accuracy of predictions of protein abundances compared to in vitro values for turnover numbers. To further improve the protein abundance predictions, machine learning models were trained that integrate features derived from protein-constrained modelling and codon usage. Combining the two types of features outperformed single feature models and yielded good prediction results without relying on experimental transcriptomic data. The presented work reports valuable advances in the prediction of enzyme allocation in unseen scenarios using protein constrained metabolic models. It marks the first successful application of this modelling framework in the biotechnological important taxon of green microalgae, substantially increasing our knowledge of the enzyme catalytic landscape of phototrophic microorganisms. N2 - Genomweite Stoffwechselmodelle sind mathematische Darstellungen aller bekannten Reaktionen, die in einer Zelle ablaufen. In Kombination mit Einschränkungen, die auf physiologischen Messungen beruhen, wurden diese Modelle zur genauen Vorhersage von Stoffwechselflüssen und Auswirkungen von Manipulationene (z. B. Knock-outs) sowie zum Entwerfen von Metabolic Engineering Strategien verwendet. In jüngster Zeit hat sich gezeigt, dass proteinlimitierte Modelle, welche die Menge an Proteinen in einer Zelle als Modelbeschränkungen integrieren, ein erweitertes Modellierungspotenzial besitzen (insbesondere beim Überflussstoffwechsel) und gleichzeitig die Messungen der Nährstoffaufnahmerate eines Organismus optional machen. Die resultierenden Modelle quantifizieren die Unterhaltskosten eines bestimmten Stoffwechselflusses als die für die Katalyse erforderliche Mindestmenge an Enzymen. Die beobachtete Verbesserungen in den Voraussagefähigkeiten solcher Modelle werden durch die Parameterisierung mit unterschiedlichen in vitro und in vivo Approximationen der maximalen katalytischen Effizienz (Wechselzahl) aller Enyzme eines Organismus ermöglicht. In dieser Arbeit wurden verschiedene Verfahren zur Schätzung und Verfeinerung dieser Parameter auf der Grundlage von in vivo Proteomikdaten der Organismen Escherichia coli, Saccharomyces cerevisiae und Chlamydomonas reinhardtii entwickelt und angewendet. Der Unterschied zwischen den in vitro und in vivo berechneten katalytischen Raten für die drei Mikroorganismen wurde systematisch analysiert. Die Ergebnisse für die fakultativ heterotrophe Mikroalge C. reinhardtii erweitern die Menge an verfügbaren enzymkatalytischen Parametern für photosynthetische Organismen erheblich. Weiterhin deuten unsere Ergbnisse für C. reinhardtii auf eine globale Verringerung der Enzymeffizienz bei Heterotrophie im Vergleich zu anderen Wachstumsszenarien hin. Unabhängig vom modellierten Organismus konnte gezeigt werden, dass geschätzte in vivo Wechselzahlen die Genauigkeit der Vorhersagen von Proteinmengen im Vergleich zu in vitro Werten verbessern. Um die Vorhersagen von Proteinmengen weiter zu verbessern, wurden Modelle aus dem Bereich des maschinellen Lernens trainiert, die Prediktoren basierend auf der proteinlimitierten Modellierung und der Proteinsequenz integrieren. Die Kombination der beiden Arten von Prediktoren übertraf die Leistung von Modellen mit nur einer Art von Prediktoren und lieferte gute Vorhersageergebnisse, ohne auf experimentelle Transkriptionsdaten angewiesen zu sein. Die vorgestellte Arbeit stellt einen wertvollen Fortschritt bei der Vorhersage der Enzymallokation in unbekannten Szenarien unter Verwendung von proteinlimitierten Stoffwechselmodellen dar. Sie markiert die erste erfolgreiche Anwendung dieses Modellierungsverfahren in dem biotechnologisch wichtigen Taxon der grünen Mikroalgen und erweitert unser Wissen über die enzymkatalytische Landschaft phototropher Mikroorganismen entscheidend. T2 - Vergleich und Analyse genomweiter Modelle des protein-limitierten Metabolismus in heterotrophen und photosynthetischen Microorganismen KW - Metabolic Modeling KW - Systems Biology KW - Computational Biology KW - Proteomics KW - computergestützte Biologie KW - metabolische Modellierung KW - Proteomics KW - Systembiologie Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-651470 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 - Wendering, Philipp A1 - Nikoloski, Zoran T1 - Genome-scale modeling specifies the metabolic capabilities of Rhizophagus irregularis JF - mSystems N2 - Rhizophagus irregularis is one of the most extensively studied arbuscular mycorrhizal fungi (AMF) that forms symbioses with and improves the performance of many crops. Lack of transformation protocol for R. irregularis renders it challenging to investigate molecular mechanisms that shape the physiology and interactions of this AMF with plants. Here, we used all published genomics, transcriptomics, and metabolomics resources to gain insights into the metabolic functionalities of R. irregularis by reconstructing its high-quality genome-scale metabolic network that considers enzyme constraints. Extensive validation tests with the enzyme-constrained metabolic model demonstrated that it can be used to (i) accurately predict increased growth of R. irregularis on myristate with minimal medium; (ii) integrate enzyme abundances and carbon source concentrations that yield growth predictions with high and significant Spearman correlation (rS = 0.74) to measured hyphal dry weight; and (iii) simulate growth rate increases with tighter association of this AMF with the host plant across three fungal structures. Based on the validated model and system-level analyses that integrate data from transcriptomics studies, we predicted that differences in flux distributions between intraradical mycelium and arbuscles are linked to changes in amino acid and cofactor biosynthesis. Therefore, our results demonstrated that the enzyme-constrained metabolic model can be employed to pinpoint mechanisms driving developmental and physiological responses of R. irregularis to different environmental cues. In conclusion, this model can serve as a template for other AMF and paves the way to identify metabolic engineering strategies to modulate fungal metabolic traits that directly affect plant performance. IMPORTANCE Mounting evidence points to the benefits of the symbiotic interactions between the arbuscular mycorrhiza fungus Rhizophagus irregularis and crops; however, the molecular mechanisms underlying the physiological responses of this fungus to different host plants and environments remain largely unknown. We present a manually curated, enzyme-constrained, genome-scale metabolic model of R. irregularis that can accurately predict experimentally observed phenotypes. We show that this high-quality model provides an entry point into better understanding the metabolic and physiological responses of this fungus to changing environments due to the availability of different nutrients. The model can be used to design metabolic engineering strategies to tailor R. irregularis metabolism toward improving the performance of host plants. KW - Rhizophagus irregularis KW - metabolic modeling Y1 - 2022 U6 - https://doi.org/10.1128/msystems.01216-21 SN - 2379-5077 VL - 7 IS - 1 PB - American Society for Microbiology CY - Washington, DC ER - TY - CHAP A1 - Fayyaz, Susann A1 - Hartmann, Bolette A1 - Hanack, Katja A1 - Michelchen, Sophia A1 - Kreiling, Reinhard T1 - Development of a hematopoietic stem cell (murine system) based system as an alternative for the in vivo T-cell-dependent antibody response (TDAR) assay within the EOGRTS: case-study with Parabens T2 - Toxicology letters Y1 - 2022 U6 - https://doi.org/10.1016/j.toxlet.2022.07.483 SN - 0378-4274 SN - 1879-3169 VL - 368 SP - S175 EP - S176 PB - Elsevier Science CY - Amsterdam [u.a.] 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 - THES A1 - Karakas, Esra T1 - High-resolution studies of epistasis in tomato metabolism T1 - Hochauflösende Studien zur Epistasierung des Tomatenstoffwechsels N2 - The inclusion of exotic germplasm serves as a crucial means to enhance allelic and consequently phenotypic diversity in inbred crop species. Such species have experienced a reduction in diversity due to artificial selection focused on a limited set of traits. The natural biodiversity within ecosystems presents an opportunity to explore various traits influencing plant survival, reproductive fitness and yield potential. In agricultural research, the study of wild species closely related to cultivated plants serves as a means to comprehend the genetic foundations of past domestication events and the polymorphisms essential for future breeding efforts to develop superior varieties. In order to examine the metabolic composition, pinpoint quantitative trait loci (QTL) and facilitate their resolution an extensive large-scale analysis of metabolic QTL (mQTL) was conducted on tomato backcross inbred lines (BILs) derived from a cross between the wild species S. pennellii (5240) incorporated into the background of S. lycopersicum cv. LEA determinate inbred which can be grown in open fields and cv. TOP indeterminate which can be grown in greenhouse conditions. A large number of mQTL associated with primary secondary and lipid metabolism in fruit were identified across the two BIL populations. Epistasis, the interactions between genes at different loci, has been an interest in molecular and quantitative genetics for many decades. The study of epistasis requires the analysis of very large populations with multiple independent genotypes that carry specific genomic regions. In order to understand the genetic basis of tomato fruit metabolism, I extended the work to investigate epistatic interactions of the genomic regions. In addition, two candidate genes were identified through quantitative trait loci underlying fruit-specific sucrose and jasmonic acid derivatives. Finally, in this study, I assessed the genetic framework of fruit metabolic traits with a high level of detail, utilizing the newly created Solanum pennellii (5240) backcrossed introgression lines (n=3000). This investigation resulted in the discovery of promising candidate loci associated with significant fruit quality traits, including those to the abundance of glutamic acid and aspartic acid crucial elements contributing to the development of acidity and flavors. N2 - Die Einbeziehung von exotischem Keimplasma ist ein wichtiges Mittel zur Verbesserung der allelischen und folglich auch der phänotypischen Vielfalt bei Inzuchtpflanzenarten. Bei diesen Arten hat die künstliche Selektion, die sich auf eine begrenzte Anzahl von Merkmalen konzentriert, zu einem Rückgang der Vielfalt geführt. Die natürliche Artenvielfalt in Ökosystemen bietet die Möglichkeit, verschiedene Merkmale zu erforschen, die das Überleben, die Reproduktionsfähigkeit und das Ertragspotenzial von Pflanzen beeinflussen. In der Agrarforschung dient die Untersuchung von Wildarten, die eng mit Kulturpflanzen verwandt sind, als Mittel zum Verständnis der genetischen Grundlagen vergangener Domestizierungsereignisse und der Polymorphismen, die für künftige Züchtungsbemühungen zur Entwicklung besserer Sorten wichtig sind. Um die metabolische Zusammensetzung zu untersuchen, quantitative Merkmalsloci (QTL) zu identifizieren und ihre Auflösung zu erleichtern, wurde eine umfangreiche Analyse metabolischer QTL (mQTL) an Tomaten-Rückkreuzungs-Inzuchtlinien (BILs) durchgeführt, die aus einer Kreuzung zwischen der Wildart S. pennellii (5240), die in den Hintergrund von S. lycopersicum cv. LEA determinate inbred, die im Freiland angebaut werden kann, und cv. TOP indeterminate, die unter Gewächshausbedingungen angebaut werden kann. In den beiden BIL-Populationen wurde eine große Anzahl von mQTL identifiziert, die mit dem primären Sekundär- und Lipidstoffwechsel in der Frucht in Verbindung stehen. Epistase, die Wechselwirkungen zwischen Genen an verschiedenen Loci, ist seit vielen Jahrzehnten ein Thema in der molekularen und quantitativen Genetik. Die Untersuchung der Epistase erfordert die Analyse sehr großer Populationen mit mehreren unabhängigen Genotypen, die bestimmte genomische Regionen tragen. Um die genetischen Grundlagen des Tomatenfruchtstoffwechsels zu verstehen, habe ich die Arbeit erweitert, um epistatische Interaktionen der genomischen Regionen zu untersuchen. Darüber hinaus wurden zwei Kandidatengene identifiziert, die über quantitative Merkmalsloci den fruchttypischen Saccharose- und Jasmonsäurederivaten zugrunde liegen. Schließlich habe ich in dieser Studie das genetische Gerüst der Fruchtstoffwechselmerkmale mit einem hohen Detaillierungsgrad bewertet, wobei ich die neu geschaffenen Solanum pennellii (5240) Rückkreuzungslinien (n=3000) verwendet habe. Diese Untersuchung führte zur Entdeckung vielversprechender Kandidatenloci, die mit bedeutenden Fruchtqualitätsmerkmalen assoziiert sind, einschließlich derjenigen, die mit der Fülle von Glutaminsäure und Asparaginsäure in Verbindung stehen - entscheidende Elemente, die zur Entwicklung von Säure und Aromen beitragen. KW - Epistasis KW - QTL mapping KW - metabolomics KW - backcross inbred line (BIL) KW - Epistase KW - QTL KW - Metabolomik KW - Rückkreuzungsinzuchtlinie (BIL) Y1 - 2024 ER - TY - JOUR A1 - Matz, Timon W. A1 - Wang, Yang A1 - Kulshreshtha, Ritika A1 - Sampathkumar, Arun A1 - Nikoloski, Zoran T1 - Topological properties accurately predict cell division events and organization of shoot apical meristem in Arabidopsis thaliana JF - Development : Company of Biologists N2 - Cell division and the resulting changes to the cell organization affect the shape and functionality of all tissues. Thus, understanding the determinants of the tissue-wide changes imposed by cell division is a key question in developmental biology. Here, we use a network representation of live cell imaging data from shoot apical meristems (SAMs) in Arabidopsis thaliana to predict cell division events and their consequences at the tissue level. We show that a support vector machine classifier based on the SAM network properties is predictive of cell division events, with test accuracy of 76%, which matches that based on cell size alone. Furthermore, we demonstrate that the combination of topological and biological properties, including cell size, perimeter, distance and shared cell wall between cells, can further boost the prediction accuracy of resulting changes in topology triggered by cell division. Using our classifiers, we demonstrate the importance of microtubule-mediated cell-to-cell growth coordination in influencing tissue-level topology. Together, the results from our network-based analysis demonstrate a feedback mechanism between tissue topology and cell division in A. thaliana SAMs. KW - Arabidopsis thaliana KW - cell division KW - classification models KW - networks KW - shoot apical meristem KW - topology Y1 - 2022 U6 - https://doi.org/10.1242/dev.201024 SN - 0950-1991 SN - 1477-9129 VL - 149 IS - 16 PB - Company of Biologists CY - Cambridge ER - TY - JOUR A1 - Mollavali, Mohanna A1 - Börnke, Frederik T1 - Characterization of trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase genes of tomato (Solanum lycopersicum L.) and analysis of their differential expression in response to temperature JF - International journal of molecular sciences N2 - In plants, the trehalose biosynthetic pathway plays key roles in the regulation of carbon allocation and stress adaptation. Engineering of the pathway holds great promise to increase the stress resilience of crop plants. The synthesis of trehalose proceeds by a two-step pathway in which a trehalose-phosphate synthase (TPS) uses UDP-glucose and glucose-6-phosphate to produce trehalose-6 phosphate (T6P) that is subsequently dephosphorylated by trehalose-6 phosphate phosphatase (TPP). While plants usually do not accumulate high amounts of trehalose, their genome encodes large families of putative trehalose biosynthesis genes, with many members lacking obvious enzymatic activity. Thus, the function of putative trehalose biosynthetic proteins in plants is only vaguely understood. To gain a deeper insight into the role of trehalose biosynthetic proteins in crops, we assessed the enzymatic activity of the TPS/TPP family from tomato (Solanum lycopersicum L.) and investigated their expression pattern in different tissues as well as in response to temperature shifts. From the 10 TPS isoforms tested, only the 2 proteins belonging to class I showed enzymatic activity, while all 5 TPP isoforms investigated were catalytically active. Most of the TPS/TPP family members showed the highest expression in mature leaves, and promoter-reporter gene studies suggest that the two class I TPS genes have largely overlapping expression patterns within the vasculature, with only subtle differences in expression in fruits and flowers. The majority of tomato TPS/TPP genes were induced by heat stress, and individual family members also responded to cold. This suggests that trehalose biosynthetic pathway genes could play an important role during temperature stress adaptation. In summary, our study represents a further step toward the exploitation of the TPS and TPP gene families for the improvement of tomato stress resistance. KW - trehalose metabolism KW - heat stress KW - Solanum lycopersicum KW - yeast complementation Y1 - 2022 U6 - https://doi.org/10.3390/ijms231911436 SN - 1661-6596 SN - 1422-0067 VL - 23 IS - 19 PB - MDPI CY - Basel ER - TY - JOUR A1 - Gätjen, Dominic A1 - Wieczorek, Marek A1 - Listek, Martin A1 - Tomszak, Florian A1 - Nölle, Volker A1 - Hanack, Katja A1 - Droste, Miriam Susanna T1 - A switchable secrete-and-capture system enables efficient selection of Pichia pastoris clones producing high yields of Fab fragments JF - Journal of immunological methods N2 - Pichia pastoris (syn. Komagataella phaffii) represents a commonly used expression system in the biotech industry. High clonal variation of transformants, however, typically results in a broad range of specific productivities for secreted proteins. To isolate rare clones with exceedingly high product titers, an extensive number of clones need to be screened. In contrast to high-throughput screenings of P. pastoris clones in microtiter plates, secrete-and -capture methodologies have the potential to efficiently isolate high-producer clones among millions of cells through fluorescence-activated cell sorting (FACS).Here, we describe a novel approach for the non-covalent binding of fragment antigen-binding (Fab) proteins to the cell surface for the isolation of high-producing clones. Eight different single-chain variable fragment (scFv)-based capture matrices specific for the constant part of the Fabs were fused to the Saccharomyces cerevisiae alpha -agglutinin (SAG1) anchor protein for surface display in P. pastoris. By encoding the capture matrix on an episomal plasmid harboring inherently unstable autonomously replicating sequences (ARS), this secrete-and -capture system offers a switchable scFv display. Efficient plasmid clearance upon removal of selective pres-sure enabled the direct use of isolated clones for subsequent Fab production. Flow-sorted clones (n = 276) displaying high amounts of Fabs showed a significant increase in median Fab titers detected in the cell-free supernatant (CFS) compared to unsorted clones (n = 276) when cells were cultivated in microtiter plates (fac-tor in the range of-21-49). Fab titers of clones exhibiting the highest product titer observed for each of the two approaches were increased by up to 8-fold for the sorted clone. Improved Fab yields of sorted cells vs. unsorted cells were confirmed in an upscaled shake flask cultivation of selected candidates (factor in the range of-2-3). Hence, the developed display-based selection method proved to be a valuable tool for efficient clone screening in the early stages of our bioprocess development. KW - Fab fragment production KW - Pichia pastoris KW - FACS KW - yeast surface display high throughput screening Y1 - 2022 U6 - https://doi.org/10.1016/j.jim.2022.113383 SN - 0022-1759 SN - 1872-7905 VL - 511 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Banerjee, Pallavi A1 - Silva, Daniel Varon A1 - Lipowsky, Reinhard A1 - Santer, Mark T1 - The importance of side branches of glycosylphosphatidylinositol anchors BT - a molecular dynamics perspective JF - Glycobiology N2 - Many proteins are anchored to the cell surface of eukaryotes using a unique family of glycolipids called glycosylphosphatidylinositol (GPI) anchors. These glycolipids also exist without a covalently bound protein, in particular on the cell surfaces of protozoan parasites where they are densely populated. GPIs and GPI-anchored proteins participate in multiple cellular processes such as signal transduction, cell adhesion, protein trafficking and pathogenesis of Malaria, Toxoplasmosis, Trypanosomiasis and prion diseases, among others. All GPIs share a common conserved glycan core modified in a cell-dependent manner with additional side glycans or phosphoethanolamine residues. Here, we use atomistic molecular dynamic simulations and perform a systematic study to evaluate the structural properties of GPIs with different side chains inserted in lipid bilayers. Our results show a flop-down orientation of GPIs with respect to the membrane surface and the presentation of the side chain residues to the solvent. This finding agrees well with experiments showing the role of the side residues as active epitopes for recognition of GPIs by macrophages and induction of GPI-glycan-specific immune responses. Protein-GPI interactions were investigated by attaching parasitic GPIs to Green Fluorescent Protein. GPIs are observed to recline on the membrane surface and pull down the attached protein close to the membrane facilitating mutual contacts between protein, GPI and the lipid bilayer. This model is efficient in evaluating the interaction of GPIs and GPI-anchored proteins with membranes and can be extended to study other parasitic GPIs and proteins and develop GPI-based immunoprophylaxis to treat infectious diseases. KW - conformation KW - GFP KW - glycan recognition KW - GPI KW - molecular dynamics Y1 - 2022 U6 - https://doi.org/10.1093/glycob/cwac037 SN - 1460-2423 VL - 32 IS - 11 SP - 933 EP - 948 PB - Oxford Univ. Press CY - Cary ER - TY - JOUR A1 - Szangolies, Leonna A1 - Rohwäder, Marie-Sophie A1 - Jeltsch, Florian T1 - Single large AND several small habitat patches BT - a community perspective on their importance for biodiversity JF - Basic and applied ecology : Journal of the Gesellschaft für Ökologie N2 - The debate whether single large or several small (SLOSS) patches benefit biodiversity has existed for decades, but recent literature provides increasing evidence for the importance of small habitats. Possible beneficial mechanisms include reduced presence of preda-tors and competitors in small habitat areas or specific functions such as stepping stones for dispersal. Given the increasing amount of studies highlighting individual behavioral differences that may influence these functions, we hypothesize that the advantage of small versus large habitat patches not only depends on patch functionality but also on the presence of animal personalities (i.e., risk-tolerant vs. risk-averse). Using an individual-based, spatially-explicit community model, we analyzed the diversity of mammal communities in landscapes consisting of a few large habitat islands interspersed with different amounts and sizes of small habitat patches. Within these heterogeneous environments, individuals compete for resources and form home-ranges, with only risk-tolerant individuals using habitat edges. Results show that when risk-tolerant individuals exist, small patches increase species diversity. A strong peak occurs at approximately 20% habitat cover in small patches when those small habitats are only used for foraging but not for breeding and home-range core position. Additional usage as stepping stones for juvenile dispersal further increases species persistence. Over-all, our results reveal that a combination of a few large and several small habitat patches promotes biodiversity by enhancing land-scape heterogeneity. Here, heterogeneity is created by pronounced differences in habitat functionality, increasing edge density, and variability in habitat use by different behavioral types. The finding that a combination of single large AND several small (SLASS) patches is needed for effective biodiversity preservation has implications for advancing landscape conservation. Particularly in struc-turally poor agricultural areas, modern technology enables precise management with the opportunity to create small foraging habitats by excluding less profitable agricultural land from cultivation. KW - SLOSS KW - fragmentation KW - heterogeneity KW - community KW - coexistence KW - coviability KW - competition KW - home-ranges KW - inter-individual difference KW - personality Y1 - 2022 U6 - https://doi.org/10.1016/j.baae.2022.09.004 SN - 1439-1791 SN - 1618-0089 VL - 65 SP - 16 EP - 27 PB - Elsevier CY - München 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 - 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 - JOUR A1 - Langary, Damoun A1 - Küken, Anika A1 - Nikoloski, Zoran T1 - The effective deficiency of biochemical networks JF - Scientific reports N2 - The deficiency of a (bio)chemical reaction network can be conceptually interpreted as a measure of its ability to support exotic dynamical behavior and/or multistationarity. The classical definition of deficiency relates to the capacity of a network to permit variations of the complex formation rate vector at steady state, irrespective of the network kinetics. However, the deficiency is by definition completely insensitive to the fine details of the directionality of reactions as well as bounds on reaction fluxes. While the classical definition of deficiency can be readily applied in the analysis of unconstrained, weakly reversible networks, it only provides an upper bound in the cases where relevant constraints on reaction fluxes are imposed. Here we propose the concept of effective deficiency, which provides a more accurate assessment of the network’s capacity to permit steady state variations at the complex level for constrained networks of any reversibility patterns. The effective deficiency relies on the concept of nonstoichiometric balanced complexes, which we have already shown to be present in real-world biochemical networks operating under flux constraints. Our results demonstrate that the effective deficiency of real-world biochemical networks is smaller than the classical deficiency, indicating the effects of reaction directionality and flux bounds on the variation of the complex formation rate vector at steady state. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-41767-1 SN - 2045-2322 VL - 13 PB - Springer Nature CY - London ER - TY - JOUR A1 - Küken, Anika A1 - Treves, Haim A1 - Nikoloski, Zoran T1 - A simulation-free constrained regression approach for flux estimation in isotopically nonstationary metabolic flux analysis with applications in microalgae JF - Frontiers in plant science : FPLS N2 - Introduction Flux phenotypes from different organisms and growth conditions allow better understanding of differential metabolic networks functions. Fluxes of metabolic reactions represent the integrated outcome of transcription, translation, and post-translational modifications, and directly affect growth and fitness. However, fluxes of intracellular metabolic reactions cannot be directly measured, but are estimated via metabolic flux analysis (MFA) that integrates data on isotope labeling patterns of metabolites with metabolic models. While the application of metabolomics technologies in photosynthetic organisms have resulted in unprecedented data from 13CO2-labeling experiments, the bottleneck in flux estimation remains the application of isotopically nonstationary MFA (INST-MFA). INST-MFA entails fitting a (large) system of coupled ordinary differential equations, with metabolite pools and reaction fluxes as parameters. Here, we focus on the Calvin-Benson cycle (CBC) as a key pathway for carbon fixation in photosynthesizing organisms and ask if approaches other than classical INST-MFA can provide reliable estimation of fluxes for reactions comprising this pathway. Methods First, we show that flux estimation with the labeling patterns of all CBC intermediates can be formulated as a single constrained regression problem, avoiding the need for repeated simulation of time-resolved labeling patterns. Results We then compare the flux estimates of the simulation-free constrained regression approach with those obtained from the classical INST-MFA based on labeling patterns of metabolites from the microalgae Chlamydomonas reinhardtii, Chlorella sorokiniana and Chlorella ohadii under different growth conditions. Discussion Our findings indicate that, in data-rich scenarios, simulation-free regression-based approaches provide a suitable alternative for flux estimation from classical INST-MFA since we observe a high qualitative agreement (rs=0.89) to predictions obtained from INCA, a state-of-the-art tool for INST-MFA. KW - metabolic flux analysis KW - INST-MFA KW - regression KW - 13C labeling KW - algae Y1 - 2023 U6 - https://doi.org/10.3389/fpls.2023.1140829 SN - 1664-462X VL - 14 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Nendel, Claas A1 - Reckling, Moritz A1 - Debaeke, Philippe A1 - Schulz, Susanne A1 - Berg-Mohnicke, Michael A1 - Constantin, Julie A1 - Fronzek, Stefan A1 - Hoffmann, Munir A1 - Jakšić, Snežana A1 - Kersebaum, Kurt-Christian A1 - Klimek-Kopyra, Agnieszka A1 - Raynal, Hélène A1 - Schoving, Céline A1 - Stella, Tommaso A1 - Battisti, Rafael T1 - Future area expansion outweighs increasing drought risk for soybean in Europe JF - Global change biology N2 - The European Union is highly dependent on soybean imports from overseas to meet its protein demands. Individual Member States have been quick to declare self-sufficiency targets for plant-based proteins, but detailed strategies are still lacking. Rising global temperatures have painted an image of a bright future for soybean production in Europe, but emerging climatic risks such as drought have so far not been included in any of those outlooks. Here, we present simulations of future soybean production and the most prominent risk factors across Europe using an ensemble of climate and soybean growth models. Projections suggest a substantial increase in potential soybean production area and productivity in Central Europe, while southern European production would become increasingly dependent on supplementary irrigation. Average productivity would rise by 8.3% (RCP 4.5) to 8.7% (RCP 8.5) as a result of improved growing conditions (plant physiology benefiting from rising temperature and CO2 levels) and farmers adapting to them by using cultivars with longer phenological cycles. Suitable production area would rise by 31.4% (RCP 4.5) to 37.7% (RCP 8.5) by the mid-century, contributing considerably more than productivity increase to the production potential for closing the protein gap in Europe. While wet conditions at harvest and incidental cold spells are the current key challenges for extending soybean production, the models and climate data analysis anticipate that drought and heat will become the dominant limitations in the future. Breeding for heat-tolerant and water-efficient genotypes is needed to further improve soybean adaptation to changing climatic conditions. KW - genotypes KW - legumes KW - maturity groups KW - protein crops KW - protein transition KW - resilience Y1 - 2022 U6 - https://doi.org/10.1111/gcb.16562 SN - 1354-1013 SN - 1365-2486 VL - 29 IS - 5 SP - 1340 EP - 1358 PB - Wiley-Blackwell CY - Ocford [u.a] ER - TY - JOUR A1 - Shikangalah, Rosemary A1 - Mapani, Benjamin A1 - Mapaure, Isaac A1 - Herzschuh, Ulrike T1 - Responsiveness of Dichrostachys cinerea to seasonal variations in temperature and rainfall in central Namibia JF - Flora N2 - Woody plants provide natural archives of climatic variation which can be investigated by applying dendroclimatological methods. Such studies are limited in Southern Africa but have great potential of improving our understanding of past climates and plant functional adaptations in the region. This study therefore investigated the responsiveness of Dichrostachys cinerea to seasonal variations in temperature and rainfall at two sites in central Namibia, Waterberg and Kuzikus. Dichrostachys cinerea is one of the encroacher species thriving well in Namibia. A moving correlation and response function analysis were used to test its responsiveness to seasonal climatic variations over time. Dichrostachys cinerea growth rings showed relationships to late summer warming, lasting up to half of the rainy season. The results also revealed that past temperatures had been fluctuating and their influence on growth rings had been intensifying over the years, but to varying extents between the two sites. Temperature was a more important determinant of ring growth at the drier site (Kuzikus), while rainfall was more important at the wetter site (Waterberg). Growth ring responsiveness to rainfall was not immediate but showed a rather lagged pattern. We conclude that D. cinerea differentially responds to variations in rainfall and temperature across short climatic gradients. This study showed that the species, due to its somewhat wide ecological amplitude, has great potential for dendroclimatological studies in tropical regions. KW - Dendroclimatology KW - Dichrostachys cinerea KW - Growth rings KW - Namibia KW - Seasonal variation Y1 - 2021 U6 - https://doi.org/10.1016/j.flora.2021.151974 SN - 0367-2530 SN - 1618-0585 VL - 286 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Pohanková, Eva A1 - Hlavinka, Petr A1 - Kersebaum, Kurt-Christian A1 - Rodríguez, Alfredo A1 - Balek, Jan A1 - Bednařík, Martin A1 - Dubrovský, Martin A1 - Gobin, Anne A1 - Hoogenboom, Gerrit A1 - Moriondo, Marco A1 - Nendel, Claas A1 - Olesen, Jørgen E. E. A1 - Rötter, Reimund Paul A1 - Ruiz-Ramos, Margarita A1 - Shelia, Vakhtang A1 - Stella, Tommaso A1 - Hoffmann, Munir Paul A1 - Takáč, Jozef A1 - Eitzinger, Josef A1 - Dibari, Camilla A1 - Ferrise, Roberto A1 - Bláhová, Monika A1 - Trnka, Miroslav T1 - Expected effects of climate change on the production and water use of crop rotation management reproduced by crop model ensemble for Czech Republic sites JF - European journal of agronomy N2 - Crop rotation, fertilization and residue management affect the water balance and crop production and can lead to different sensitivities to climate change. To assess the impacts of climate change on crop rotations (CRs), the crop model ensemble (APSIM,AQUACROP, CROPSYST, DAISY, DSSAT, HERMES, MONICA) was used. The yields and water balance of two CRs with the same set of crops (winter wheat, silage maize, spring barley and winter rape) in a continuous transient run from 1961 to 2080 were simulated. CR1 was without cover crops and without manure application. Straw after the harvest was exported from the fields. CR2 included cover crops, manure application and crop residue retention left on field. Simulations were performed using two soil types (Chernozem, Cambisol) within three sites in the Czech Republic, which represent temperature and precipitation gradients for crops in Central Europe. For the description of future climatic conditions, seven climate scenarios were used. Six of them had increasing CO & nbsp;concentrations according RCP 8.5, one had no CO2 increase in the future. The output of an ensemble expected higher productivity by 0.82 t/ha/year and 2.04 t/ha/year for yields and aboveground biomass in the future (2051-2080). However, if the direct effect of a CO2 increase is not considered, the average yields for lowlands will be lower. Compared to CR1, CR2 showed higher average yields of 1.26 t/ha/year for current climatic conditions and 1.41 t/ha/year for future climatic conditions. For the majority of climate change scenarios, the crop model ensemble agrees on the projected yield increase in C3 crops in the future for CR2 but not for CR1. Higher agreement for future yield increases was found for Chernozem, while for Cambisol, lower yields under dry climate scenarios are expected. For silage maize, changes in simulated yields depend on locality. If the same hybrid will be used in the future, then yield reductions should be expected within lower altitudes. The results indicate the potential for higher biomass production from cover crops, but CR2 is associated with almost 120 mm higher evapotranspiration compared to that of CR1 over a 5-year cycle for lowland stations in the future, which in the case of the rainfed agriculture could affect the long-term soil water balance. This could affect groundwater replenishment, especially for locations with fine textured soils, although the findings of this study highlight the potential for the soil water-holding capacity to buffer against the adverse weather conditions. KW - Yields KW - Evapotranspiration KW - Winter wheat KW - Silage maize KW - Spring barley KW - Winter oilseed rape Y1 - 2022 U6 - https://doi.org/10.1016/j.eja.2021.126446 SN - 1161-0301 SN - 1873-7331 VL - 134 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Wang, Enli A1 - He, Di A1 - Wang, Jing A1 - Lilley, Julianne M. A1 - Christy, Brendan A1 - Hoffmann, Munir P. A1 - O'Leary, Garry A1 - Hatfield, Jerry L. A1 - Ledda, Luigi A1 - Deligios, Paola A. A1 - Grant, Brian A1 - Jing, Qi A1 - Nendel, Claas A1 - Kage, Henning A1 - Qian, Budong A1 - Rezaei, Ehsan Eyshi A1 - Smith, Ward A1 - Weymann, Wiebke A1 - Ewert, Frank T1 - How reliable are current crop models for simulating growth and seed yield of canola across global sites and under future climate change? JF - Climatic change N2 - To better understand how climate change might influence global canola production, scientists from six countries have completed the first inter-comparison of eight crop models for simulating growth and seed yield of canola, based on experimental data from six sites across five countries. A sensitivity analysis was conducted with a combination of five levels of atmospheric CO2 concentrations, seven temperature changes, five precipitation changes, together with five nitrogen application rates. Our results were in several aspects different from those of previous model inter-comparison studies for wheat, maize, rice, and potato crops. A partial model calibration only on phenology led to very poor simulation of aboveground biomass and seed yield of canola, even from the ensemble median or mean. A full calibration with additional data of leaf area index, biomass, and yield from one treatment at each site reduced simulation error of seed yield from 43.8 to 18.0%, but the uncertainty in simulation results remained large. Such calibration (with data from one treatment) was not able to constrain model parameters to reduce simulation uncertainty across the wide range of environments. Using a multi-model ensemble mean or median reduced the uncertainty of yield simulations, but the simulation error remained much larger than observation errors, indicating no guarantee that the ensemble mean/median would predict the correct responses. Using multi-model ensemble median, canola yield was projected to decline with rising temperature (2.5-5.7% per degrees C), but to increase with increasing CO2 concentration (4.6-8.3% per 100-ppm), rainfall (2.1-6.1% per 10% increase), and nitrogen rates (1.3-6.0% per 10% increase) depending on locations. Due to the large uncertainty, these results need to be treated with caution. We further discuss the need to collect new data to improve modelling of several key physiological processes of canola for increased confidence in future climate impact assessments. KW - AgMIP KW - Brassica napus L. KW - Model calibration KW - Model improvement; KW - Multimodel ensemble KW - Sensitivity analysis Y1 - 2022 U6 - https://doi.org/10.1007/s10584-022-03375-2 SN - 0165-0009 SN - 1573-1480 VL - 172 IS - 1-2 PB - Springer Nature CY - Dordrecht ER - TY - JOUR A1 - McHuron, Elizabeth A. A1 - Adamczak, Stephanie A1 - Arnould, John P. Y. A1 - Ashe, Erin A1 - Booth, Cormac A1 - Bowen, W. Don A1 - Christiansen, Fredrik A1 - Chudzinska, Magda A1 - Costa, Daniel P. A1 - Fahlman, Andreas A1 - Farmer, Nicholas A. A1 - Fortune, Sarah M. E. A1 - Gallagher, Cara A. A1 - Keen, Kelly A. A1 - Madsen, Peter T. A1 - McMahon, Clive R. A1 - Nabe-Nielsen, Jacob A1 - Noren, Dawn P. A1 - Noren, Shawn R. A1 - Pirotta, Enrico A1 - Rosen, David A. S. A1 - Speakman, Cassie N. A1 - Villegas-Amtmann, Stella A1 - Williams, Rob T1 - Key questions in marine mammal bioenergetics JF - Conservation physiology N2 - Bioenergetic approaches are increasingly used to understand how marine mammal populations could be affected by a changing and disturbed aquatic environment. There remain considerable gaps in our knowledge of marine mammal bioenergetics, which hinder the application of bioenergetic studies to inform policy decisions. We conducted a priority-setting exercise to identify high-priority unanswered questions in marine mammal bioenergetics, with an emphasis on questions relevant to conservation and management. Electronic communication and a virtual workshop were used to solicit and collate potential research questions from the marine mammal bioenergetic community. From a final list of 39 questions, 11 were identified as 'key'questions because they received votes from at least 50% of survey participants. Key questions included those related to energy intake (prey landscapes, exposure to human activities) and expenditure (field metabolic rate, exposure to human activities, lactation, time-activity budgets), energy allocation priorities, metrics of body condition and relationships with survival and reproductive success and extrapolation of data from one species to another. Existing tools to address key questions include labelled water, animal-borne sensors, mark-resight data from long-term research programs, environmental DNA and unmanned vehicles. Further validation of existing approaches and development of new methodologies are needed to comprehensively address some key questions, particularly for cetaceans. The identification of these key questions can provide a guiding framework to set research priorities, which ultimately may yield more accurate information to inform policies and better conserve marine mammal populations. Y1 - 2022 U6 - https://doi.org/10.1093/conphys/coac055 SN - 2051-1434 VL - 10 IS - 1 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Sporbert, Maria A1 - Jakubka, Desiree A1 - Bucher, Solveig Franziska A1 - Hensen, Isabell A1 - Freiberg, Martin A1 - Heubach, Katja A1 - König, Andreas A1 - Nordt, Birgit A1 - Plos, Carolin A1 - Blinova, Ilona A1 - Bonn, Aletta A1 - Knickmann, Barbara A1 - Koubek, Tomáš A1 - Linstädter, Anja A1 - Mašková, Tereza A1 - Primack, Richard B. A1 - Rosche, Christoph A1 - Shah, Manzoor A. A1 - Stevens, Albert-Dieter A1 - Tielbörger, Katja A1 - Träger, Sabrina A1 - Wirth, Christian A1 - Römermann, Christine T1 - Functional traits influence patterns in vegetative and reproductive plant phenology - a multi-botanical garden study JF - New phytologist N2 - Phenology has emerged as key indicator of the biological impacts of climate change, yet the role of functional traits constraining variation in herbaceous species' phenology has received little attention. Botanical gardens are ideal places in which to investigate large numbers of species growing under common climate conditions. We ask whether interspecific variation in plant phenology is influenced by differences in functional traits. We recorded onset, end, duration and intensity of initial growth, leafing out, leaf senescence, flowering and fruiting for 212 species across five botanical gardens in Germany. We measured functional traits, including plant height, absolute and specific leaf area, leaf dry matter content, leaf carbon and nitrogen content and seed mass and accounted for species' relatedness. Closely related species showed greater similarities in timing of phenological events than expected by chance, but species' traits had a high degree of explanatory power, pointing to paramount importance of species' life-history strategies. Taller plants showed later timing of initial growth, and flowered, fruited and underwent leaf senescence later. Large-leaved species had shorter flowering and fruiting durations. Taller, large-leaved species differ in their phenology and are more competitive than smaller, small-leaved species. We assume climate warming will change plant communities' competitive hierarchies with consequences for biodiversity. KW - botanical gardens KW - first flowering day KW - growing season length KW - leaf KW - traits KW - PhenObs phenological network KW - phylogeny Y1 - 2022 U6 - https://doi.org/10.1111/nph.18345 SN - 0028-646X SN - 1469-8137 VL - 235 IS - 6 SP - 2199 EP - 2210 PB - Wiley CY - Hoboken ER - TY - THES A1 - Wojcik, Laurie Anne Myriam T1 - Beyond a single diversity facet: implications for the links between biodiversity, environmental changes and ecosystem functioning T1 - Mehr als eine einzelne Facette der Biodiversität: Auswirkungen auf die Verbindungen zwischen Biodiversität, Umweltveränderungen und der Funktionalität von Ökosystemen N2 - Human activities modify nature worldwide via changes in the environment, biodiversity and the functioning of ecosystems, which in turn disrupt ecosystem services and feed back negatively on humans. A pressing challenge is thus to limit our impact on nature, and this requires detailed understanding of the interconnections between the environment, biodiversity and ecosystem functioning. These three components of ecosystems each include multiple dimensions, which interact with each other in different ways, but we lack a comprehensive picture of their interconnections and underlying mechanisms. Notably, diversity is often viewed as a single facet, namely species diversity, while many more facets exist at different levels of biological organisation (e.g. genetic, phenotypic, functional, multitrophic diversity), and multiple diversity facets together constitute the raw material for adaptation to environmental changes and shape ecosystem functioning. Consequently, investigating the multidimensionality of ecosystems, and in particular the links between multifaceted diversity, environmental changes and ecosystem functions, is crucial for ecological research, management and conservation. This thesis aims to explore several aspects of this question theoretically. I investigate three broad topics in this thesis. First, I focus on how food webs with varying levels of functional diversity across three trophic levels buffer environmental changes, such as a sudden addition of nutrients or long-term changes (e.g. warming or eutrophication). I observed that functional diversity generally enhanced ecological stability (i.e. the buffering capacity of the food web) by increasing trophic coupling. More precisely, two aspects of ecological stability (resistance and resilience) increased even though a third aspect (the inverse of the time required for the system to reach its post-perturbation state) decreased with increasing functional diversity. Second, I explore how several diversity facets served as a raw material for different sources of adaptation and how these sources affected multiple ecosystem functions across two trophic levels. Considering several sources of adaptation enabled the interplay between ecological and evolutionary processes, which affected trophic coupling and thereby ecosystem functioning. Third, I reflect further on the multifaceted nature of diversity by developing an index K able to quantify the facet of functional diversity, which is itself multifaceted. K can provide a comprehensive picture of functional diversity and is a rather good predictor of ecosystem functioning. Finally I synthesise the interdependent mechanisms (complementarity and selection effects, trophic coupling and adaptation) underlying the relationships between multifaceted diversity, ecosystem functioning and the environment, and discuss the generalisation of my findings across ecosystems and further perspectives towards elaborating an operational biodiversity-ecosystem functioning framework for research and conservation. N2 - Menschliche Aktivität verändert die Natur weltweit durch Einflussnahme auf die Umwelt, Biodiversität und Funktionsweise von Ökosystemen, die wiederum Ökosystemdienstleistungen stören und sich negativ auf den Menschen auswirken. Eine dringende Herausforderung besteht daher darin, unsere Wirkung auf die Natur zu begrenzen, was ein tiefgreifendes Verständnis der Zusammenhänge zwischen Umwelt, Biodiversität und dem Funktionalität von Ökosystemen voraussetzt. Diese drei Komponenten von Ökosystemen umfassen jedoch jeweils mehrere Dimensionen, die auf unterschiedliche Weise interagieren, und bisher haben wir kein umfassendes Bild von ihren Zusammenhängen und den zugrundeliegenden Mechanismen. Vor allem Diversität wird oft als eine einzige Facette betrachtet, nämlich als Artendiversität, während es auf verschiedenen biologischen Organisationsebenen viele weitere Facetten gibt, z. B. genetische, phänotypische, funktionelle, multitrophische Diversität, die zusammen mehrere Quellen für Rohmaterial zur die Anpassung an Umweltveränderungen bilden und die Funktionsweise von Ökosystemen beeinflussen. Folglich ist die Untersuchung der Multidimensionalität von Ökosystemen, insbesondere der Zusammenhänge zwischen multifacettierter Diversität, Umweltveränderungen und Ökosystemfunktionen, von entscheidender Bedeutung für Forschung, Management und Naturschutz. In dieser Arbeit sollen mehrere Aspekte dieser Frage theoretisch untersucht werden. In dieser Arbeit untersuche ich drei große Themenbereiche. Erstens konzentriere ich mich auf die Frage, wie Nahrungsnetze mit unterschiedlichem Grad funktioneller Diversität auf drei trophischen Ebenen Umweltveränderungen abpuffern, wie etwa eine plötzliche Zugabe von Nährstoffen oder langfristige Veränderungen (z. B. Erwärmung oder Eutrophierung). Hier habe ich festgestellt, dass die funktionelle Diversität die ökologische Stabilität (d. h. die Pufferkapazität des Nahrungsnetzes) durch eine stärkere trophische Kopplung allgemein erhöht. Im Speziellen nahmen zwei Aspekte der ökologischen Stabilität (Resistenz und Resilienz) zu, obwohl ein dritter Aspekt, der Kehrwert der Zeit, die das System benötigt, um den Post-Störungszustand zu erreichen, mit zunehmender funktioneller Diversität abnahm. Zweitens untersuche ich, wie mehrere Facetten der Diversität als Basis für mehrere Anpassungsprozesse aus verschiedenen Quellen dienten und wie diese Quellen mehrere Ökosystemfunktionen auf zwei trophischen Ebenen beeinflussten. Die Berücksichtigung mehrerer Anpassungsquellen ermöglichte das Zusammenspiel zwischen ökologischen und evolutionären Prozessen, die sich auf die trophische Kopplung und damit auf die Funktionalität des Ökosystems auswirkten. Drittens reflektiere ich weiter über die Facetten der Diversität, indem ich einen Index K entwickle, der die Facette der funktionalen Diversität quantifizieren kann, welche wiederum selbst vielschichtig ist. K kann ein umfassendes Bild der funktionellen Diversität vermitteln und ist ein recht guter Prädiktor für das Funktionieren von Ökosystemen. Schließlich fasse ich die voneinander abhängigen Mechanismen (Komplementarität und Selektionseffekte, trophische Kopplung und Anpassung) zusammen, die den Beziehungen zwischen multi-facettierter Diversität, dem Funktionieren von Ökosystemen und der Umwelt zugrunde liegen, und erörtere die Möglichkeiten zur Verallgemeinerung meiner Ergebnisse über Ökosysteme hinweg sowie Perspektiven für die Ausarbeitung eines operativen Rahmens für der Biodiversität-Ökosystem- Funktionalität für Forscher und Anwender. KW - multifaceted diversity KW - multi-facettierter Diversität KW - perturbation KW - Störung KW - trait-based approaches KW - merkmalsbasierte Ansätze KW - food web models KW - Modelle der Nahrungsnetze KW - ecological stability KW - ökologische Stabilität KW - trait adaptation KW - Anpassung Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-646925 ER - TY - JOUR A1 - Vences, Miguel A1 - Köhler, Jörn A1 - Crottini, Angelica A1 - Hofreiter, Michael A1 - Hutter, Carl R. A1 - du Preez, Louis A1 - Preick, Michaela A1 - Rakotoarison, Andolalao A1 - Rancilhac, Loïs A1 - Raselimanana, Achille P. A1 - Rosa, Gonçalo M. A1 - Scherz, Mark D. A1 - Glaw, Frank T1 - An integrative taxonomic revision and redefinition of Gephyromantis (Laurentomantis) malagasius based on archival DNA analysis reveals four new mantellid frog species from Madagascar JF - Vertebrate zoology N2 - The subgenus Laurentomantis in the genus Gephyromantis contains some of the least known amphibian species of Madagascar. The six currently valid nominal species are rainforest frogs known from few individuals, hampering a full understanding of the species diversity of the clade. We assembled data on specimens collected during field surveys over the past 30 years and integrated analysis of mitochondrial and nuclear-encoded genes of 88 individuals, a comprehensive bioacoustic analysis, and morphological comparisons to delimit a minimum of nine species-level lineages in the subgenus. To clarify the identity of the species Gephyromantis malagasius, we applied a target-enrichment approach to a sample of the 110 year old holotype of Microphryne malagasia Methuen and Hewitt, 1913 to assign this specimen to a lineage based on a mitochondrial DNA barcode. The holotype clustered unambiguously with specimens previously named G. ventrimaculatus. Consequently we propose to consider Trachymantis malagasia ventrimaculatus Angel, 1935 as a junior synonym of Gephyromantis malagasius. Due to this redefinition of G. malagasius, no scientific name is available for any of the four deep lineages of frogs previously subsumed under this name, all characterized by red color ventrally on the hindlimbs. These are here formally named as Gephyromantis fiharimpe sp. nov., G. matsilo sp. nov., G. oelkrugi sp. nov., and G. portonae sp. nov. The new species are distinguishable from each other by genetic divergences of >4% uncorrected pairwise distance in a fragment of the 16S rRNA marker and a combination of morphological and bioacoustic characters. Gephyromantis fiharimpe and G. matsilo occur, respectively, at mid-elevations and lower elevations along a wide stretch of Madagascar's eastern rainforest band, while G. oelkrugi and G. portonae appear to be more range-restricted in parts of Madagascar's North East and Northern Central East regions. Open taxonomic questions surround G. horridus, to which we here assign specimens from Montagne d'Ambre and the type locality Nosy Be; and G. ranjomavo, which contains genetically divergent populations from Marojejy, Tsaratanana, and Ampotsidy. KW - Amphibia KW - Anura KW - archival DNA KW - Mantellidae KW - new species KW - phylogeography Y1 - 2022 U6 - https://doi.org/10.3897/vz.72.e78830 SN - 1864-5755 SN - 2625-8498 VL - 72 SP - 271 EP - 309 PB - Senckenberg Gesellschaft für Naturforschung CY - Frankfurt am Main 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 - Esmaeilishirazifard, Elham A1 - Usher, Louise A1 - Trim, Carol A1 - Denise, Hubert A1 - Sangal, Vartul A1 - Tyson, Gregory H. A1 - Barlow, Axel A1 - Redway, Keith F. A1 - Taylor, John D. A1 - Kremyda-Vlachou, Myrto A1 - Davies, Sam A1 - Loftus, Teresa D. A1 - Lock, Mikaella M. G. A1 - Wright, Kstir A1 - Dalby, Andrew A1 - Snyder, Lori A. S. A1 - Wuster, Wolfgang A1 - Trim, Steve A1 - Moschos, Sterghios A. T1 - Bacterial adaptation to venom in snakes and arachnida JF - Microbiology spectrum N2 - Notwithstanding their 3 to 5% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane-disrupting activity against multidrug-resistant bacteria. However, venomous bite wound infections are common in developing nations. Investigating the envenomation organ and venom microbiota of five snake and two spider species, we observed venom community structures that depend on the host venomous animal species and evidenced recovery of viable microorganisms from black-necked spitting cobra (Naja nigricollis) and Indian ornamental tarantula (Poecilotheria regalis) venoms. Among the bacterial isolates recovered from N. nigricollis, we identified two venom-resistant, novel sequence types of Enterococcus faecalis whose genomes feature 16 virulence genes, indicating infectious potential, and 45 additional genes, nearly half of which improve bacterial membrane integrity. Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds. IMPORTANCE Notwithstanding their 3 to 5% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Here, we provide evidence on venom microbiota across snakes and arachnida and report on the convergent evolution mechanisms that can facilitate adaptation to black-necked cobra venom in two independent E. faecalis strains, easily misidentified by biochemical diagnostics. Therefore, since inoculation with viable and virulence gene-harboring bacteria can occur during envenomation, acute infection risk management following envenomation is warranted, particularly for immunocompromised and malnourished victims in resource-limited settings. These results shed light on how bacteria evolve for survival in one of the most extreme environments on Earth and how venomous bites must be also treated for infections. KW - drug resistance evolution KW - extremophiles KW - genome analysis KW - microbiome KW - multidrug resistance KW - venom Y1 - 2022 U6 - https://doi.org/10.1128/spectrum.02408-21 SN - 2165-0497 VL - 10 IS - 3 PB - American Society for Microbiology CY - Birmingham, Ala. ER - TY - JOUR A1 - Riemann, Lasse A1 - Rahav, Eyal A1 - Passow, Uta A1 - Grossart, Hans-Peter A1 - de Beer, Dirk A1 - Klawonn, Isabell A1 - Eichner, Meri A1 - Benavides, Mar A1 - Bar-Zeev, Edo T1 - Planktonic aggregates as hotspots for heterotrophic diazotrophy: the plot thickens JF - Frontiers in microbiology N2 - Biological dinitrogen (N-2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N-2 fixation by NCDs and propose a conceptual framework for aggregate-associated N-2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments. KW - aggregates KW - nitrogen fixation KW - heterotrophic bacteria KW - marine KW - aquatic KW - NCDs Y1 - 2022 U6 - https://doi.org/10.3389/fmicb.2022.875050 SN - 1664-302X VL - 13 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Schulte, Luise A1 - Meucci, Stefano A1 - Stoof-Leichsenring, Kathleen R. A1 - Heitkam, Tony A1 - Schmidt, Nicola A1 - von Hippel, Barbara A1 - Andreev, Andrei A. A1 - Diekmann, Bernhard A1 - Biskaborn, Boris A1 - Wagner, Bernd A1 - Melles, Martin A1 - Pestryakova, Lyudmila A. A1 - Alsos, Inger G. A1 - Clarke, Charlotte A1 - Krutovsky, Konstantin A1 - Herzschuh, Ulrike T1 - Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA JF - Communications biology N2 - Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate. Using ancient sedimentary DNA from up to 50 kya, dramatic distributional shifts are documented in two dominant boreal larch species, likely guided by environmental changes suggesting climate as a strong determinant of species distribution. Y1 - 2022 U6 - https://doi.org/10.1038/s42003-022-03455-0 SN - 2399-3642 VL - 5 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - López-Sánchez, Aida A1 - Bareth, Georg A1 - Bolten, Andreas A1 - Rose, Laura E. A1 - Mansfeldt, Tim A1 - Sapp, Melanie A1 - Linstädter, Anja T1 - Effects of declining oak vitality on ecosystem multifunctionality BT - lessons from a Spanish oak woodland JF - Forest ecology and management N2 - Mediterranean oak woodlands are currently facing unprecedented degradation threats from oak decline. The Iberian oak decline "Seca", related to Phytophthora infection, causes crown defoliation that may adversely affect ecosystem services (ESs). We aim to improve our understanding of how Seca-induced declines in crown foliation affect the provision of multiple ecosystem services from understory vegetation. We selected holm (Quercus ilex) and cork oak (Q. suber) trees in a Spanish oak woodland and evaluated three proxies of canopy effects. One proxy (crown defoliation) solely captured Seca-dependent effects, one proxy solely captured Seca-independent effects (tree dimensions such as diameter and height), while the third proxy (tree vigor) captured overall canopy effects. We then used the best-performing proxies to assess canopy effects on key ecosystem services (ESs) such as aboveground net primary production (ANPP), grass and legume biomass, species diversity, litter decomposition rates, and a combined index of ecosystem multifunctionality.
We found that both types of canopy effects (i.e. Seca-dependent and Seca-independent effects) were related, indicating that ANPP was disproportionally more affected by Seca when defoliated trees were large. Responses of other ESs were mostly not significant, although lower species diversity was found under trees with intermediate vigor. Our results underline that a Seca-related decline in canopy density triggered a homogenization of ecosystem service delivery on the ecosystem scale. The ecosystem functions (EFs) under trees of low vigor are similar to that in adjacent open microsites indicating that the presence of vigorous (i.e. old and vital) trees is critical for maintaining EFs at a landscape level. Our results also highlight the importance of quantifying not only defoliation but also tree dimensions as both factors jointly and interactively modify canopy effects on ecosystem multifunctionality. KW - ANPP KW - Decomposition KW - Microsite degradation KW - Herb diversity KW - Seca Y1 - 2021 U6 - https://doi.org/10.1016/j.foreco.2021.118927 SN - 0378-1127 SN - 1872-7042 VL - 484 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Dunker, Susanne A1 - Boyd, Matthew A1 - Durka, Walter A1 - Erler, Silvio A1 - Harpole, W. Stanley A1 - Henning, Silvia A1 - Herzschuh, Ulrike A1 - Hornick, Thomas A1 - Knight, Tiffany A1 - Lips, Stefan A1 - Mäder, Patrick A1 - Švara, Elena Motivans A1 - Mozarowski, Steven A1 - Rakosy, Demetra A1 - Römermann, Christine A1 - Schmitt-Jansen, Mechthild A1 - Stoof-Leichsenring, Kathleen A1 - Stratmann, Frank A1 - Treudler, Regina A1 - Virtanen, Risto A1 - Wendt-Potthoff, Katrin A1 - Wilhelm, Christian T1 - The potential of multispectral imaging flow cytometry for environmental monitoring JF - Cytometry part A N2 - Environmental monitoring involves the quantification of microscopic cells and particles such as algae, plant cells, pollen, or fungal spores. Traditional methods using conventional microscopy require expert knowledge, are time-intensive and not well-suited for automated high throughput. Multispectral imaging flow cytometry (MIFC) allows measurement of up to 5000 particles per second from a fluid suspension and can simultaneously capture up to 12 images of every single particle for brightfield and different spectral ranges, with up to 60x magnification. The high throughput of MIFC has high potential for increasing the amount and accuracy of environmental monitoring, such as for plant-pollinator interactions, fossil samples, air, water or food quality that currently rely on manual microscopic methods. Automated recognition of particles and cells is also possible, when MIFC is combined with deep-learning computational techniques. Furthermore, various fluorescence dyes can be used to stain specific parts of the cell to highlight physiological and chemical features including: vitality of pollen or algae, allergen content of individual pollen, surface chemical composition (carbohydrate coating) of cells, DNA- or enzyme-activity staining. Here, we outline the great potential for MIFC in environmental research for a variety of research fields and focal organisms. In addition, we provide best practice recommendations. KW - environmental monitoring KW - imaging flow cytometry KW - plant traits Y1 - 2022 U6 - https://doi.org/10.1002/cyto.a.24658 SN - 1552-4922 SN - 1552-4930 VL - 101 IS - 9 SP - 782 EP - 799 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Groh, Jannis A1 - Diamantopoulos, Efstathios A1 - Duan, Xiaohong A1 - Ewert, Frank A1 - Heinlein, Florian A1 - Herbst, Michael A1 - Holbak, Maja A1 - Kamali, Bahareh A1 - Kersebaum, Kurt-Christian A1 - Kuhnert, Matthias A1 - Nendel, Claas A1 - Priesack, Eckart A1 - Steidl, Jörg A1 - Sommer, Michael A1 - Pütz, Thomas A1 - Vanderborght, Jan A1 - Vereecken, Harry A1 - Wallor, Evelyn A1 - Weber, Tobias K. D. A1 - Wegehenkel, Martin A1 - Weihermüller, Lutz A1 - Gerke, Horst H. T1 - Same soil, different climate: Crop model intercomparison on translocated lysimeters JF - Vadose zone journal N2 - Crop model intercomparison studies have mostly focused on the assessment of predictive capabilities for crop development using weather and basic soil data from the same location. Still challenging is the model performance when considering complex interrelations between soil and crop dynamics under a changing climate. The objective of this study was to test the agronomic crop and environmental flux-related performance of a set of crop models. The aim was to predict weighing lysimeter-based crop (i.e., agronomic) and water-related flux or state data (i.e., environmental) obtained for the same soil monoliths that were taken from their original environment and translocated to regions with different climatic conditions, after model calibration at the original site. Eleven models were deployed in the study. The lysimeter data (2014-2018) were from the Dedelow (Dd), Bad Lauchstadt (BL), and Selhausen (Se) sites of the TERENO (TERrestrial ENvironmental Observatories) SOILCan network. Soil monoliths from Dd were transferred to the drier and warmer BL site and the wetter and warmer Se site, which allowed a comparison of similar soil and crop under varying climatic conditions. The model parameters were calibrated using an identical set of crop- and soil-related data from Dd. Environmental fluxes and crop growth of Dd soil were predicted for conditions at BL and Se sites using the calibrated models. The comparison of predicted and measured data of Dd lysimeters at BL and Se revealed differences among models. At site BL, the crop models predicted agronomic and environmental components similarly well. Model performance values indicate that the environmental components at site Se were better predicted than agronomic ones. The multi-model mean was for most observations the better predictor compared with those of individual models. For Se site conditions, crop models failed to predict site-specific crop development indicating that climatic conditions (i.e., heat stress) were outside the range of variation in the data sets considered for model calibration. For improving predictive ability of crop models (i.e., productivity and fluxes), more attention should be paid to soil-related data (i.e., water fluxes and system states) when simulating soil-crop-climate interrelations in changing climatic conditions. Y1 - 2022 U6 - https://doi.org/10.1002/vzj2.20202 SN - 1539-1663 VL - 21 IS - 4 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Cao, Xianyong A1 - Chen, Jianhui A1 - Tian, Fang A1 - Xu, Qinghai A1 - Herzschuh, Ulrike A1 - Telford, Richard A1 - Huang, Xiaozhong A1 - Zheng, Zhuo A1 - Shen, Caiming A1 - Li, Wenjia T1 - Long-distance modern analogues bias results of pollen-based precipitation reconstructions JF - Science bulletin Y1 - 2022 U6 - https://doi.org/10.1016/j.scib.2022.01.003 SN - 2095-9273 SN - 2095-9281 VL - 67 IS - 11 SP - 1115 EP - 1117 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Sedaghatmehr, Mastoureh A1 - Thirumalaikumar, Venkatesh P. A1 - Kamranfar, Iman A1 - Schulz, Karina A1 - Müller-Röber, Bernd A1 - Sampathkumar, Arun A1 - Balazadeh, Salma T1 - Autophagy complements metalloprotease FtsH6 in degrading plastid heat shock protein HSP21 during heat stress recovery JF - The journal of experimental botany : an official publication of the Society for Experimental Biology and of the Federation of European Societies of Plant Physiology N2 - Moderate and temporary heat stresses prime plants to tolerate, and survive, a subsequent severe heat stress. Such acquired thermotolerance can be maintained for several days under normal growth conditions, and can create a heat stress memory. We recently demonstrated that plastid-localized small heat shock protein 21 ( HSP21) is a key component of heat stress memory in Arabidopsis thaliana. A sustained high abundance of HSP21 during the heat stress recovery phase extends heat stress memory. The level of HSP21 is negatively controlled by plastid-localized metalloprotease FtsH6 during heat stress recovery. Here, we demonstrate that autophagy, a cellular recycling mechanism, exerts additional control over HSP21 degradation. Genetic and chemical disruption of both metalloprotease activity and autophagy trigger superior HSP21 accumulation, thereby improving memory. Furthermore, we provide evidence that autophagy cargo receptor ATG8-INTERACTING PROTEIN1 (ATI1) is associated with heat stress memory. ATI1 bodies co-localize with both autophagosomes and HSP21, and their abundance and transport to the vacuole increase during heat stress recovery. Together, our results provide new insights into the module for control of the regulation of heat stress memory, in which two distinct protein degradation pathways act in concert to degrade HSP21, thereby enabling cells to recover from the heat stress effect at the cost of reducing the heat stress memory. KW - Arabidopsis thaliana KW - ATI1 KW - FtsH6 KW - heat stress KW - HSP21 KW - plastid KW - selective autophagy KW - stress memory KW - stress recovery Y1 - 2021 U6 - https://doi.org/10.1093/jxb/erab304 SN - 0022-0957 SN - 1460-2431 VL - 72 IS - 21 SP - 7498 EP - 7513 PB - Oxford University Press CY - Oxford ER - TY - JOUR A1 - Van den Wyngaert, Silke A1 - Ganzert, Lars A1 - Seto, Kensuke A1 - Rojas-Jimenez, Keilor A1 - Agha, Ramsy A1 - Berger, Stella A. A1 - Woodhouse, Jason A1 - Padisak, Judit A1 - Wurzbacher, Christian A1 - Kagami, Maiko A1 - Grossart, Hans-Peter T1 - Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits JF - ISME journal N2 - Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments. Y1 - 2022 U6 - https://doi.org/10.1038/s41396-022-01267-y SN - 1751-7362 SN - 1751-7370 VL - 16 IS - 9 SP - 2242 EP - 2254 PB - Springer Nature CY - London ER - TY - JOUR A1 - Gorin, Vladislav A. A1 - Scherz, Mark D. A1 - Korost, Dmitry V. A1 - Poyarkov, Nikolay A. T1 - Consequences of parallel miniaturisation in Microhylinae (Anura, Microhylidae), with the description of a new genus of diminutive South East Asian frogs JF - Zoosystematics and evolution : Mitteilungen aus dem Museum für Naturkunde in Berlin N2 - The genus Microhyla Tschudi, 1838 includes 52 species and is one of the most diverse genera of the family Microhylidae, being the most species-rich taxon of the Asian subfamily Microhylinae. The recent, rapid description of numerous new species of Microhyla with complex phylogenetic relationships has made the taxonomy of the group especially challenging. Several recent phylogenetic studies suggested paraphyly of Microhyla with respect to Glyphoglossus Gunther, 1869, and revealed three major phylogenetic lineages of mid-Eocene origin within this assemblage. However, comprehensive works assessing morphological variation among and within these lineages are absent. In the present study we investigate the generic taxonomy of Microhyla-Glyphoglossus assemblage based on a new phylogeny including 57 species, comparative morphological analysis of skeletons from cleared-and-stained specimens for 23 species, and detailed descriptions of generalized osteology based on volume-rendered micro-CT scans for five speciesal-together representing all major lineages within the group. The results confirm three highly divergent and well-supported clades that correspond with external and osteological morphological characteristics, as well as respective geographic distribution. Accordingly, acknowledging ancient divergence between these lineages and their significant morphological differentiation, we propose to consider these three lineages as distinct genera: Microhyla sensu stricto, Glyphoglossus, and a newly described genus, Nanohyla gen. nov. KW - Amphibians KW - integrative taxonomy KW - narrow-mouthed frogs KW - micro-computed tomography KW - Nanohyla gen. nov KW - osteology KW - sexual dimorphism KW - taxonomic revision Y1 - 2021 U6 - https://doi.org/10.3897/zse.97.57968 SN - 1860-0743 SN - 1435-1935 VL - 97 IS - 1 SP - 21 EP - 54 PB - Pensoft Publishers CY - Sofia ER - TY - JOUR A1 - Schmidt, Sabrina A1 - Reil, Daniela A1 - Jeske, Kathrin A1 - Drewes, Stephan A1 - Rosenfeld, Ulrike A1 - Fischer, Stefan A1 - Spierling, Nastasja G. A1 - Labutin, Anton A1 - Heckel, Gerald A1 - Jacob, Jens A1 - Ulrich, Rainer G. A1 - Imholt, Christian T1 - Spatial and temporal dynamics and molecular evolution of Tula orthohantavirus in German vole populations JF - Viruses / Molecular Diversity Preservation International (MDPI) N2 - Tula orthohantavirus (TULV) is a rodent-borne hantavirus with broad geographical distribution in Europe. Its major reservoir is the common vole (Microtus arvalis), but TULV has also been detected in closely related vole species. Given the large distributional range and high amplitude population dynamics of common voles, this host-pathogen complex presents an ideal system to study the complex mechanisms of pathogen transmission in a wild rodent reservoir. We investigated the dynamics of TULV prevalence and the subsequent potential effects on the molecular evolution of TULV in common voles of the Central evolutionary lineage. Rodents were trapped for three years in four regions of Germany and samples were analyzed for the presence of TULV-reactive antibodies and TULV RNA with subsequent sequence determination. The results show that individual (sex) and population-level factors (abundance) of hosts were significant predictors of local TULV dynamics. At the large geographic scale, different phylogenetic TULV clades and an overall isolation-by-distance pattern in virus sequences were detected, while at the small scale (<4 km) this depended on the study area. In combination with an overall delayed density dependence, our results highlight that frequent, localized bottleneck events for the common vole and TULV do occur and can be offset by local recolonization dynamics. KW - rodents KW - hantavirus KW - monitoring KW - population dynamics KW - common vole KW - field vole KW - water vole KW - phylogeny KW - molecular evolution Y1 - 2021 U6 - https://doi.org/10.3390/v13061132 SN - 1999-4915 VL - 13 IS - 6 PB - MDPI CY - Basel ER - TY - JOUR A1 - Belluardo, Francesco A1 - Scherz, Mark D. A1 - Santos, Barbara A1 - Andreone, Franco A1 - Antonelli, Alexandre A1 - Glaw, Frank A1 - Munoz-Pajares, A. Jesus A1 - Randrianirina, Jasmin E. A1 - Raselimanana, Achille P. A1 - Vences, Miguel A1 - Crottini, Angelica T1 - Molecular taxonomic identification and species-level phylogeny of the narrow-mouthed frogs of the genus Rhombophryne (Anura: Microhylidae: Cophylinae) from Madagascar JF - Systematics and biodiversity N2 - The study of diamond frogs (genus Rhombophryne, endemic to Madagascar) has been historically hampered by the paucity of available specimens, because of their low detectability in the field. Over the last 10 years, 13 new taxa have been described, and 20 named species are currently recognized. Nevertheless, undescribed diversity within the genus is probably large, calling for a revision of the taxonomic identification of published records and an update of the known distribution of each lineage. Here we generate DNA sequences of the mitochondrial 16S rRNA gene of all specimens available to us, revise the genetic data from public databases, and report all deeply divergent mitochondrial lineages of Rhombophryne identifiable from these data. We also generate a multi-locus dataset (including five mitochondrial and eight nuclear markers; 9844 bp) to infer a species-level phylogenetic hypothesis for the diversification of this genus and revise the distribution of each lineage. We recognize a total of 10 candidate species, two of which are identified here for the first time. The genus Rhombophryne is here proposed to be divided into six main species groups, and phylogenetic relationships among some of them are not fully resolved. These frogs are primarily distributed in northern Madagascar, and most species are known from only few localities. A previous record of this genus from the Tsingy de Bemaraha (western Madagascar) is interpreted as probably due to a mislabelling and should not be considered further unless confirmed by new data. By generating this phylogenetic hypothesis and providing an updated distribution of each lineage, our findings will facilitate future species descriptions, pave the way for evolutionary studies, and provide valuable information for the urgent conservation of diamond frogs. KW - amphibians KW - candidate species KW - diamond frogs KW - mitochondrial lineages KW - northern Madagascar KW - species-identification KW - systematics Y1 - 2022 U6 - https://doi.org/10.1080/14772000.2022.2039320 SN - 1477-2000 SN - 1478-0933 VL - 20 IS - 1 SP - 1 EP - 13 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Garbulowski, Mateusz A1 - Smolinska, Karolina A1 - Çabuk, Uğur A1 - Yones, Sara A. A1 - Celli, Ludovica A1 - Yaz, Esma Nur A1 - Barrenas, Fredrik A1 - Diamanti, Klev A1 - Wadelius, Claes A1 - Komorowski, Jan T1 - Machine learning-based analysis of glioma grades reveals co-enrichment JF - Cancers N2 - Simple Summary Gliomas are heterogenous types of cancer, therefore the therapy should be personalized and targeted toward specific pathways. We developed a methodology that corrected strong batch effects from The Cancer Genome Atlas datasets and estimated glioma grade-specific co-enrichment mechanisms using machine learning. Our findings created hypotheses for annotations, e.g., pathways, that should be considered as therapeutic targets. Gliomas develop and grow in the brain and central nervous system. Examining glioma grading processes is valuable for improving therapeutic challenges. One of the most extensive repositories storing transcriptomics data for gliomas is The Cancer Genome Atlas (TCGA). However, such big cohorts should be processed with caution and evaluated thoroughly as they can contain batch and other effects. Furthermore, biological mechanisms of cancer contain interactions among biomarkers. Thus, we applied an interpretable machine learning approach to discover such relationships. This type of transparent learning provides not only good predictability, but also reveals co-predictive mechanisms among features. In this study, we corrected the strong and confounded batch effect in the TCGA glioma data. We further used the corrected datasets to perform comprehensive machine learning analysis applied on single-sample gene set enrichment scores using collections from the Molecular Signature Database. Furthermore, using rule-based classifiers, we displayed networks of co-enrichment related to glioma grades. Moreover, we validated our results using the external glioma cohorts. We believe that utilizing corrected glioma cohorts from TCGA may improve the application and validation of any future studies. Finally, the co-enrichment and survival analysis provided detailed explanations for glioma progression and consequently, it should support the targeted treatment. KW - glioma KW - machine learning KW - batch effect KW - TCGA KW - co-enrichment KW - rough sets Y1 - 2022 U6 - https://doi.org/10.3390/cancers14041014 SN - 2072-6694 VL - 14 IS - 4 PB - MDPI CY - Basel ER - TY - JOUR A1 - Agarwal, Saloni A1 - Hamidizadeh, Mojdeh A1 - Bier, Frank Fabian T1 - Detection of reverse transcriptase LAMP-amplified nucleic acid from oropharyngeal viral swab samples using biotinylated DNA probes through a lateral flow assay JF - Biosensors : open access journal N2 - This study focuses on three key aspects: (a) crude throat swab samples in a viral transport medium (VTM) as templates for RT-LAMP reactions; (b) a biotinylated DNA probe with enhanced specificity for LFA readouts; and (c) a digital semi-quantification of LFA readouts. Throat swab samples from SARS-CoV-2 positive and negative patients were used in their crude (no cleaning or pre-treatment) forms for the RT-LAMP reaction. The samples were heat-inactivated but not treated for any kind of nucleic acid extraction or purification. The RT-LAMP (20 min processing time) product was read out by an LFA approach using two labels: FITC and biotin. FITC was enzymatically incorporated into the RT-LAMP amplicon with the LF-LAMP primer, and biotin was introduced using biotinylated DNA probes, specifically for the amplicon region after RT-LAMP amplification. This assay setup with biotinylated DNA probe-based LFA readouts of the RT-LAMP amplicon was 98.11% sensitive and 96.15% specific. The LFA result was further analysed by a smartphone-based IVD device, wherein the T-line intensity was recorded. The LFA T-line intensity was then correlated with the qRT-PCR Ct value of the positive swab samples. A digital semi-quantification of RT-LAMP-LFA was reported with a correlation coefficient of R2 = 0.702. The overall RT-LAMP-LFA assay time was recorded to be 35 min with a LoD of three RNA copies/µL (Ct-33). With these three advancements, the nucleic acid testing-point of care technique (NAT-POCT) is exemplified as a versatile biosensor platform with great potential and applicability for the detection of pathogens without the need for sample storage, transportation, or pre-processing. KW - RT-LAMP KW - LFA KW - NAAT-LFA KW - semi-quantitative KW - surveillance-based diagnostics Y1 - 2023 U6 - https://doi.org/10.3390/bios13110988 SN - 2079-6374 VL - 13 IS - 11 PB - MDPI CY - Basel ER - TY - JOUR A1 - Numberger, Daniela A1 - Zoccarato, Luca A1 - Woodhouse, Jason Nicholas A1 - Ganzert, Lars A1 - Sauer, Sascha A1 - García Márquez, Jaime Ricardo A1 - Domisch, Sami A1 - Grossart, Hans-Peter A1 - Greenwood, Alex T1 - Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - Freshwater ecosystems are characterized by complex and highly dynamic microbial communities that are strongly structured by their local environment and biota. Accelerating urbanization and growing city populations detrimentally alter freshwater environments. To determine differences in freshwater microbial communities associated with urban-ization, full-length 16S rRNA gene PacBio sequencing was performed in a case study from surface waters and sedi-ments from a wastewater treatment plant, urban and rural lakes in the Berlin-Brandenburg region, Northeast Germany. Water samples exhibited highly habitat specific bacterial communities with multiple genera showing clear urban signatures. We identified potentially harmful bacterial groups associated with environmental parameters specific to urban habitats such as Alistipes, Escherichia/Shigella, Rickettsia and Streptococcus. We demonstrate that urban-ization alters natural microbial communities in lakes and, via simultaneous warming and eutrophication and creates favourable conditions that promote specific bacterial genera including potential pathogens. Our findings are evidence to suggest an increased potential for long-term health risk in urbanized waterbodies, at a time of rapidly expanding global urbanization. The results highlight the urgency for undertaking mitigation measures such as targeted lake restoration projects and sustainable water management efforts. KW - Urbanization KW - Urban waters KW - Wastewater KW - Lakes KW - Microbial community KW - composition KW - Humanization KW - Full-length 16S rRNA PacBio sequencing Y1 - 2022 U6 - https://doi.org/10.1016/j.scitotenv.2022.157321 SN - 0048-9697 SN - 1879-1026 VL - 845 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Zavorka, Libor A1 - Blanco, Andreu A1 - Chaguaceda, Fernando A1 - Cucherousset, Julien A1 - Killen, Shaun S. A1 - Lienart, Camilla A1 - Mathieu-Resuge, Margaux A1 - Nemec, Pavel A1 - Pilecky, Matthias A1 - Scharnweber, Inga Kristin A1 - Twining, Cornelia W. A1 - Kainz, Martin J. T1 - The role of vital dietary biomolecules in eco-evo-devo dynamics JF - Trends in ecology and evolution N2 - The physiological dependence of animals on dietary intake of vitamins, amino acids, and fatty acids is ubiquitous. Sharp differences in the availability of these vital dietary biomolecules among different resources mean that consumers must adopt a range of strategies to meet their physiological needs. We review the emerging work on omega-3 long-chain polyunsaturated fatty acids, focusing predominantly on predator-prey interactions, to illustrate that trade-off between capacities to consume resources rich in vital biomolecules and internal synthesis capacity drives differences in phenotype and fitness of consumers. This can then feedback to impact ecosystem functioning. We outline how focus on vital dietary biomolecules in eco-eco-devo dynamics can improve our understanding of anthropogenic changes across multiple levels of biological organization. Y1 - 2023 U6 - https://doi.org/10.1016/j.tree.2022.08.010 SN - 0169-5347 SN - 1872-8383 VL - 38 IS - 1 SP - 72 EP - 84 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Grdseloff, Nastasja A1 - Boulday, Gwenola A1 - Roedel, Claudia J. A1 - Otten, Cecile A1 - Vannier, Daphne Raphaelle A1 - Cardoso, Cecile A1 - Faurobert, Eva A1 - Dogra, Deepika A1 - Tournier-Lasserve, Elisabeth A1 - Abdelilah-Seyfried, Salim T1 - Impaired retinoic acid signaling in cerebral cavernous malformations JF - Scientific reports N2 - The capillary-venous pathology cerebral cavernous malformation (CCM) is caused by loss of CCM1/Krev interaction trapped protein 1 (KRIT1), CCM2/MGC4607, or CCM3/PDCD10 in some endothelial cells. Mutations of CCM genes within the brain vasculature can lead to recurrent cerebral hemorrhages. Pharmacological treatment options are urgently needed when lesions are located in deeply-seated and in-operable regions of the central nervous system. Previous pharmacological suppression screens in disease models of CCM led to the discovery that treatment with retinoic acid improved CCM phenotypes. This finding raised a need to investigate the involvement of retinoic acid in CCM and test whether it has a curative effect in preclinical mouse models. Here, we show that components of the retinoic acid synthesis and degradation pathway are transcriptionally misregulated across disease models of CCM. We complemented this analysis by pharmacologically modifying retinoic acid levels in zebrafish and human endothelial cell models of CCM, and in acute and chronic mouse models of CCM. Our pharmacological intervention studies in CCM2-depleted human umbilical vein endothelial cells (HUVECs) and krit1 mutant zebrafish showed positive effects when retinoic acid levels were increased. However, therapeutic approaches to prevent the development of vascular lesions in adult chronic murine models of CCM were drug regiment-sensitive, possibly due to adverse developmental effects of this hormone. A treatment with high doses of retinoic acid even worsened CCM lesions in an adult chronic murine model of CCM. This study provides evidence that retinoic acid signaling is impaired in the CCM pathophysiology and suggests that modification of retinoic acid levels can alleviate CCM phenotypes. KW - Developmental biology KW - Molecular medicine Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-31905-0 SN - 2045-2322 VL - 13 IS - 1 PB - Nature Portfolio CY - Berlin ER - TY - JOUR A1 - Stübler, Sabine A1 - Kloft, Charlotte A1 - Huisinga, Wilhelm T1 - Cell-level systems biology model to study inflammatory bowel diseases and their treatment options JF - CPT: pharmacometrics & systems pharmacology N2 - To help understand the complex and therapeutically challenging inflammatory bowel diseases (IBDs), we developed a systems biology model of the intestinal immune system that is able to describe main aspects of IBD and different treatment modalities thereof. The model, including key cell types and processes of the mucosal immune response, compiles a large amount of isolated experimental findings from literature into a larger context and allows for simulations of different inflammation scenarios based on the underlying data and assumptions. In the context of a large and diverse virtual IBD population, we characterized the patients based on their phenotype (in contrast to healthy individuals, they developed persistent inflammation after a trigger event) rather than on a priori assumptions on parameter differences to a healthy individual. This allowed to reproduce the enormous diversity of predispositions known to lead to IBD. Analyzing different treatment effects, the model provides insight into characteristics of individual drug therapy. We illustrate for anti-TNF-alpha therapy, how the model can be used (i) to decide for alternative treatments with best prospects in the case of nonresponse, and (ii) to identify promising combination therapies with other available treatment options. Y1 - 2023 U6 - https://doi.org/10.1002/psp4.12932 SN - 2163-8306 VL - 12 IS - 5 SP - 690 EP - 705 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Derežanin, Lorena A1 - Blažytė, Asta A1 - Dobrynin, Pavel A1 - Duchêne, David A. A1 - Grau, José Horacio A1 - Jeon, Sungwon A1 - Kliver, Sergei A1 - Koepfli, Klaus-Peter A1 - Meneghini, Dorina A1 - Preick, Michaela A1 - Tomarovsky, Andrey A1 - Totikov, Azamat A1 - Fickel, Jörns A1 - Förster, Daniel W. T1 - Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae JF - Molecular ecology N2 - Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance. KW - adaptation KW - gene family evolution KW - genomics KW - mustelids KW - positive KW - selection KW - structural variation Y1 - 2022 U6 - https://doi.org/10.1111/mec.16443 SN - 0962-1083 SN - 1365-294X VL - 31 IS - 10 SP - 2898 EP - 2919 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Abdelilah-Seyfried, Salim A1 - Iruela-Arispe, M. Luisa A1 - Penninger, Josef M. A1 - Tournier-Lasserve, Elisabeth A1 - Vikkula, Miikka A1 - Cleaver, Ondine T1 - Recalibrating vascular malformations and mechanotransduction by pharmacological intervention JF - Journal of clinical investigation Y1 - 2022 U6 - https://doi.org/10.1172/JCI160227 SN - 0021-9738 SN - 1558-8238 VL - 132 IS - 8 PB - American Society for Clinical Investigation CY - Ann Arbor ER - TY - JOUR A1 - Cao, Xianyong A1 - Tian, Fang A1 - Herzschuh, Ulrike A1 - Ni, Jian A1 - Xu, Qinghai A1 - Li, Wenjia A1 - Zhang, Yanrong A1 - Luo, Mingyu A1 - Chen, Fahu T1 - Human activities have reduced plant diversity in eastern China over the last two millennia JF - Global change biology N2 - Understanding the history and regional singularities of human impact on vegetation is key to developing strategies for sustainable ecosystem management. In this study, fossil and modern pollen datasets from China are employed to investigate temporal changes in pollen composition, analogue quality, and pollen diversity during the Holocene. Anthropogenic disturbance and vegetation's responses are also assessed. Results reveal that pollen assemblages from non-forest communities fail to provide evidence of human impact for the western part of China (annual precipitation less than 400 mm and/or elevation more than 3000 m.a.s.l.), as inferred from the stable quality of modern analogues, principal components, and diversity of species and communities throughout the Holocene. For the eastern part of China, the proportion of fossil pollen spectra with good modern analogues increases from ca. 50% to ca. 80% during the last 2 millennia, indicating an enhanced intensity of anthropogenic disturbance on vegetation. This disturbance has caused the pollen spectra to become taxonomically less diverse over space (reduced abundances of arboreal taxa and increased abundances of herbaceous taxa), highlighting a reduced south-north differentiation and divergence from past vegetation between regions in the eastern part of China. We recommend that care is taken in eastern China when basing the development of ecosystem management strategies on vegetation changes in the region during the last 2000 years, since humans have significantly disturbed the vegetation during this period. KW - analogue quality KW - human-vegetation interaction KW - land use KW - latitudinal KW - zonation KW - plant diversity KW - pollen Y1 - 2022 U6 - https://doi.org/10.1111/gcb.16274 SN - 1354-1013 SN - 1365-2486 VL - 28 IS - 16 SP - 4962 EP - 4976 PB - Wiley CY - Hoboken ER - TY - THES A1 - Montulet, Orianne T1 - Functional characterization of putative interactors of the Cellulose Synthase Complex T1 - Funktionelle Charakterisierung von mutmaßlichen Interaktoren des Cellulose-Synthase-Komplexes N2 - The plant cell wall plays several crucial roles during plant development with its integrity acting as key signalling component for growth regulation during biotic and abiotic stresses. Cellulose microfibrils, the principal load-bearing components is the major component of the primary cell wall, whose synthesis is mediated by microtubule-associated CELLULOSE SYNTHASE (CESA) COMPLEXES (CSC). Previous studies have shown that CSC interacting proteins COMPANION OF CELLULOSE SYNTHASE (CC) facilitate sustained cellulose synthesis during salt stress by promoting repolymerization of cortical microtubules. However, our understanding of cellulose synthesis during salt stress remains incomplete. In this study, a pull-down of CC1 protein led to the identification of a novel interactor, termed LEA-like. Phylogenetic analysis revealed that LEA-like belongs to the LATE EMBRYOGENESIS ABUNDANT (LEA) protein family, specifically to the LEA_2 subgroup, showing a close relationship with the CC proteins. Roots of the double mutants lea-like and its closest homolog emb3135 exhibited hypersensitivity when grown on cellulose synthesis inhibitors. Further analysis of higher-order mutants of lea-like, emb3135, and cesa6 demonstrated a genetic interaction between them indicating a significant role in cellulose synthesis. Live-cell imaging revealed that both LEA-like and EMB3135 migrated with the CSC at the plasma membrane along microtubule tracks in control and oryzalin-treated conditions which destabilize microtubules, suggesting a tight interaction. Investigation of fluorescently labeled lines of different domains of the LEA-like protein revealed that the N-terminal cytosolic domain of LEA-like colocalizes with microtubules, suggesting a physical association between the two. Considering the established role of LEA proteins in abiotic stress tolerance, we performed phenotypic analysis of the mutant under various stresses. Growth of double mutants of lea-like and emb3135 on NaCl containing media resulted in swelling of root cell indicating a putative role in salt stress tolerance. Supportive of this the quadruple mutant, lacking LEA-like, EMB3135, CC1, and CC2 proteins, exhibited a severe root growth defect on NaCl media compared to control conditions. Live-cell imaging revealed that under salt stress, the LEA-like protein forms aggregates in the plasma membrane. In conclusion, this study has unveiled two novel interactors of the CSC that act with the CC proteins that regulate plant growth in response to salt stress providing new insights into the intricate regulation of cellulose synthesis, particularly under such conditions. N2 - Die pflanzliche Zellwand spielt während der Pflanzenentwicklung mehrere entscheidende Rollen, wobei ihre Integrität als zentrale Signalkomponente für die Wachstumsregulierung bei biotischem und abiotischem Stress fungiert. Zellulose-Mikrofibrillen, die wichtigsten tragenden Komponenten, sind der Hauptbestandteil der primären Zellwand, deren Synthese durch Mikrotubuli assoziierte CELLULOSE SYNTHASE (CESA) Komplexe (CSC) vermittelt wird. Frühere Studien haben gezeigt, dass die mit den CSC interagierenden Proteinen COMPANION OF CELLULOSE SYNTHASE (CC) die anhaltende Zellulosesynthese bei Salzstress erleichtern, indem sie die Repolymerisation der kortikalen Mikrotubuli fördern. Unser Verständnis der Zellulosesynthese bei Salzstress ist jedoch noch unvollständig. In dieser Studie führte ein Pull-down des CC1-Proteins zur Identifizierung eines neuen Interaktors, der als LEA-like bezeichnet wird. Eine phylogenetische Analyse ergab, dass LEA-like zur Late Embryogenesis Abundant (LEA)-Proteinfamilie gehört, insbesondere zur LEA_2-Untergruppe, die eine enge Beziehung zu den CC-Proteinen aufweist. Die Wurzeln der Doppelmutanten lea-like und seines engsten Homologen emb3135 zeigten eine Überempfindlichkeit, wenn sie auf Zellulose-Synthese-Inhibitoren wuchsen. Weitere Analysen von Mutanten höherer Ordnung von lea-like, emb3135 und cesa6 zeigten eine genetische Interaktion zwischen ihnen, die auf eine bedeutende Rolle bei der Zellulosesynthese hinweist. Die Bildgebung in lebenden Zellen zeigte, dass sowohl LEA-like als auch EMB3135 mit dem CSC an der Plasmamembran entlang von Mikrotubuli-Spuren wandern, und zwar sowohl unter Kontrollbedingungen als auch unter Oryzalin-Behandlung, die die Mikrotubuli destabilisiert, was auf eine enge Interaktion hindeutet. Die Untersuchung von fluoreszenzmarkierten Linien verschiedener Domänen des LEA-like-Proteins ergab, dass die N-terminale zytosolische Domäne von LEA-like mit Mikrotubuli kolokalisiert, was auf eine physische Verbindung zwischen den beiden hindeutet. In Anbetracht der bekannten Rolle der LEA-Proteine bei der abiotischen Stresstoleranz haben wir eine phänotypische Analyse der Mutante unter verschiedenen Stressbedingungen durchgeführt. Das Wachstum von Doppelmutanten von lea-like und emb3135 auf NaCl-haltigen Medien führte zu einem Anschwellen der Wurzelzellen, was auf eine mutmaßliche Rolle bei der Salzstresstoleranz hindeutet. Die Vierfachmutante, der die Proteine LEA-like, EMB3135, CC1 und CC2 fehlen, wies im Vergleich zu den Kontrollbedingungen auf NaCl-Medien einen schweren Wachstumsdefekt der Wurzeln auf. Die Bildgebung in lebenden Zellen zeigte, dass das LEA-like-Protein unter Salzstress Aggregate in der Plasmamembran bildet. Zusammenfassend lässt sich sagen, dass diese Studie zwei neue Interaktoren des CSC aufgedeckt hat, die mit den CC-Proteinen zusammenwirken und das Pflanzenwachstum als Reaktion auf Salzstress regulieren. KW - cell wall KW - cellulose KW - salt stress KW - cellulose synthase complex KW - Arabidopsis KW - Zellwand KW - zellulose, Salzstress KW - Cellulose-Synthese-Complex KW - Arabidopsis Y1 - 2024 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 - 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 - Hagemann, Justus T1 - On the molecular evolution of sengis (Macroscelidea) N2 - This thesis focuses on the molecular evolution of Macroscelidea, commonly referred to as sengis. Sengis are a mammalian order belonging to the Afrotherians, one of the four major clades of placental mammals. Sengis currently consist of twenty extant species, all of which are endemic to the African continent. They can be separated in two families, the soft-furred sengis (Macroscelididae) and the giant sengis (Rhynchocyonidae). While giant sengis can be exclusively found in forest habitats, the different soft-furred sengi species dwell in a broad range of habitats, from tropical rain-forests to rocky deserts. Our knowledge on the evolutionary history of sengis is largely incomplete. The high level of superficial morphological resemblance among different sengi species (especially the soft-furred sengis) has for example led to misinterpretations of phylogenetic relationships, based on morphological characters. With the rise of DNA based taxonomic inferences, multiple new genera were defined and new species described. Yet, no full taxon molecular phylogeny exists, hampering the answering of basic taxonomic questions. This lack of knowledge can be to some extent attributed to the limited availability of fresh-tissue samples for DNA extraction. The broad African distribution, partly in political unstable regions and low population densities complicate contemporary sampling approaches. Furthermore, the DNA information available usually covers only short stretches of the mitochondrial genome and thus a single genetic locus with limited informational content. Developments in DNA extraction and library protocols nowadays offer the opportunity to access DNA from museum specimens, collected over the past centuries and stored in natural history museums throughout the world. Thus, the difficulties in fresh-sample acquisition for molecular biological studies can be overcome by the application of museomics, the research field which emerged from those laboratory developments. This thesis uses fresh-tissue samples as well as a vast collection museum specimens to investigate multiple aspects about the macroscelidean evolutionary history. Chapter 4 of this thesis focuses on the phylogenetic relationships of all currently known sengi species. By accessing DNA information from museum specimens in combination of fresh tissue samples and publicly available genetic resources it produces the first full taxon molecular phylogeny of sengis. It confirms the monophyly of the genus Elephantulus and discovers multiple deeply divergent lineages within different species, highlighting the need for species specific approaches. The study furthermore focuses on the evolutionary time frame of sengis by evaluating the impact of commonly varied parameters on tree dating. The results of the study show, that the mitochondrial information used in previous studies to temporal calibrate the Macroscelidean phylogeny led to an overestimation of node ages within sengis. Especially soft-furred sengis are thus much younger than previously assumed. The refined knowledge of nodes ages within sengis offer the opportunity to link e.g. speciation events to environmental changes. Chapter 5 focuses on the genus Petrodromus with its single representative Petrodromus tetradactylus. It again exploits the opportunities of museomics and gathers a comprehensive, multi-locus genetic dataset of P. tetradactylus individuals, distributed across most the known range of this species. It reveals multiple deeply divergent lineages within Petrodromus, whereby some could possibly be associated to previously described sub-species, at least one was formerly unknown. It underscores the necessity for a revision of the genus Petrodromus through the integration of both molecular and morphological evidence. The study, furthermore identifies changing forest distributions through climatic oscillations as main factor shaping the genetic structure of Petrodromus. Chapter 6 uses fresh tissue samples to extent the genomic resources of sengis by thirteen new nuclear genomes, of which two were de-novo assembled. An extensive dataset of more than 8000 protein coding one-to-one orthologs allows to further refine and confirm the temporal time frame of sengi evolution found in Chapter 4. This study moreover investigates the role of gene-flow and incomplete lineage sorting (ILS) in sengi evolution. In addition it identifies clade specific genes of possible outstanding evolutionary importance and links them to potential phenotypic traits affected. A closer investigation of olfactory receptor proteins reveals clade specific differences. A comparison of the demographic past of sengis to other small African mammals does not reveal a sengi specific pattern. N2 - Diese Dissertation untersucht die molekulare Evolution von Macroscelidea, auch als Sengis oder Rüsselspringer bezeichnet. Sengis sind eine Ordnung der Afrotheria, einer der vier Hauptkladen der plazentalen Säugetiere. Aktuell gibt es zwanzig beschriebene Sengiarten, die alle ausschließlich auf dem afrikanischen Kontinent vorkommen. Sengis können in zwei Familien unterteilt werden: die Elephantenspitzmäuse zusammen mit den Rüsselratten bilden die Macroscelididae und die Rüsselhündchen die Rhynchocyonidae. Während Rhynchocyonidae ausschließlich in Waldhabitaten zu finden sind, bewohnen verschiedene Macroscelididaearten ein breites Spektrum von Lebensräumen, von tropischen Regenwäldern bis zu felsigen Wüsten. Unser Wissen über die evolutionäre Geschichte der Sengis ist äußerst unvollständig. Der hohe Grad an morphologischer Ähnlichkeit zwischen verschiedenen Sengiarten (insbesondere innerhalb der Macroscelididae) hat beispielsweise zu Fehlinterpretationen phylogenetischer Beziehungen auf der Grundlage morphologischer Merkmale geführt. Mit dem Aufkommen DNA-basierter taxonomischer Forschung wurden mehrere neue Gattungen definiert und neue Arten beschrieben. Dennoch existiert derzeit keine vollständige molekulare Phylogenie, was die Beantwortung grundlegender taxonomischer Fragen und tiefergehende evolutionsbiologische Analysen erschwert. Dieser Mangel an Wissen kann zum Teil auf die begrenzte Verfügbarkeit von frischen Gewebeproben für die DNA-Extraktion zurückgeführt werden. Die weite Verbreitung in Afrika, teilweise in politisch instabilen Regionen und geringe Populationssdichten von Sengis erschweren das Sammeln von frischem Probenmaterial, was für die Extraktion von DNA genutzt werden kann. Darüber hinaus deckt die bis jetzt verfügbare DNA-Information über Sengis häufig nur kurze Abschnitte des mitochondrialen Genoms ab und damit einen einzelnen genetischen Lokus mit begrenztem Informationsgehalt. Fortentwicklungen von DNA-Extraktions-Protokollen und Library-Protokollen bieten heutzutage die Möglichkeit, auf DNA von Museumsexemplaren zuzugreifen, die über die letzten Jahrhunderte gesammelt und in Naturkundemuseen weltweit aufbewahrt werden. Somit können die Schwierigkeiten bei der Beschaffung von Frischproben für molekularbiologische Studien überwunden werden. Diese Dissertation verwendet sowohl Frischgewebeproben als auch eine umfangreiche Sammlung von Museumssproben, um verschiedene Aspekte der evolutionären Geschichte der Sengis molekularbiologisch zu untersuchen. Kapitel 4 dieser Dissertation konzentriert sich auf die phylogenetischen Beziehungen aller derzeit bekannten Sengiarten. Durch das Generieren von DNA-Information aus Museumsexemplaren in Kombination mit Frischgewebeproben und öffentlich verfügbaren genetischen Ressourcen wird die erste vollständige molekulare Phylogenie aller Rüsselspringer erzeugt. Die Studie bestätigt die Monophylie der Gattung Elephantulus und entdeckt mehrere tief divergente Linien innerhalb verschiedener Arten, was die Notwendigkeit speziesbezogener Ansätze verdeutlicht. Die Studie konzentriert sich außerdem auf den Zeitrahmen der Sengi-Evolution, indem sie die Auswirkungen häufig variierter Parameter auf die Datierung von Stammbäumen untersucht. Die Ergebnisse zeigen, dass die mitochondriale Information, die in früheren Studien zur zeitlichen Kalibrierung der Macroscelidean-Phylogenie verwendet wurde, zu einer Überschätzung des Alters von Arttrennungen innerhalb der Rüsselspringer geführt hat. Insbesondere die Macroscelididae sind daher viel jünger als zuvor angenommen. Das präzisere Wissen über das evolutionäre Alter von Rüsselspringern bietet die Möglichkeit, beispielsweise Artaufspaltungen mit Umweltveränderungen zu verknüpfen. Kapitel 5 konzentriert sich auf die Gattung Petrodromus mit ihrem einzigen Vertreter Petrodromus tetradactylus. Es nutzt erneut die Museomics und sammelt einen umfassenden, genetischen Datensatz von P. tetradactylus-Individuen, die über den größten Teil des bekannten Verbreitungsgebiets dieser Art verteilt sind. Es zeigt mehrere tief divergente Linien innerhalb von Petrodromus auf, wobei einige mit zuvor beschriebenen Unterarten in Verbindung gebracht werden könnten, mindestens eine aber zuvor unbekannt war. Die Ergebnisse verdeutlichen die Notwendigkeit einer taxonomischen Überarbeitung der Gattung Petrodromus durch das Zusammenführen sowohl molekularer als auch morphologischer Indizien. Die Studie identifizier außerdem sich ändernde Waldverteilungen durch klimatische Schwankungen als Hauptfaktor, der die genetische Struktur von Petrodromus formt. Kapitel 6 verwendet Frischgewebeproben, um die genomischen Ressourcen der Rüsselspringer durch dreizehn neue nukleare Genome zu erweitern, von denen zwei de-novo assembliert wurden. Ein umfangreicher Datensatz von mehr als 8000 protein-kodierenden 1:1-Orthologen ermöglicht es, den zeitlichen Rahmen der Rüsselspringerevolution, der in Kapitel 4 gefunden wurde, weiter zu verfeinern und zu bestätigen. Diese Studie untersucht außerdem die Rolle von Genfluss auf die Evolution der Rüsselspringer. Darüber hinaus identifiziert sie für bestimmte Kladen spezifische Gene von möglicherweise herausragender evolutionärer Bedeutung und verknüpft diese mit potenziell betroffenen phänotypischen Merkmalen. Eine genauere Untersuchung von Geruchsrezeptorproteinen zeigt kladespezifische Unterschiede auf. KW - sengis KW - evolution KW - molecular dating KW - biogeography KW - comparative genomics KW - Biogeographie KW - vergleichende Genomik KW - Evolution KW - molekulare Datierung KW - Sengis Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-641975 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 - Cheng, Feng A1 - Dennis, Alice B. A1 - Osuoha, Josephine Ijeoma A1 - Canitz, Julia A1 - Kirschbaum, Frank A1 - Tiedemann, Ralph T1 - A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha JF - BMC genomics N2 - Background Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus Campylomormyrus is mostly endemic to the Congo Basin. Campylomormyrus serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome assembly and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorpha fish in general and of electric fish in particular. Results A high-quality weakly electric fish (C. compressirostris) genome was produced from a single individual with a genome size of 862 Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of Paramormyrops kingsleyae and Scleropages formosus. A Computational Analysis of gene Family Evolution (CAFE5) comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (Cyprinus carpio and Oncorhynchus mykiss). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of C. compressirostris. Conclusions We present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appear to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among Campylomormyrus species. KW - Campylomormyrus KW - Pacbio sequencing KW - Gene family KW - Osteoglossomorpha KW - Kv1 Y1 - 2023 U6 - https://doi.org/10.1186/s12864-023-09196-6 SN - 1471-2164 VL - 24 IS - 1 PB - BMC CY - London ER - TY - JOUR A1 - Peter, Lena A1 - Wendering, Désirée Jacqueline A1 - Schlickeiser, Stephan A1 - Hoffmann, Henrike A1 - Noster, Rebecca A1 - Wagner, Dimitrios Laurin A1 - Zarrinrad, Ghazaleh A1 - Münch, Sandra A1 - Picht, Samira A1 - Schulenberg, Sarah A1 - Moradian, Hanieh A1 - Mashreghi, Mir-Farzin A1 - Klein, Oliver A1 - Gossen, Manfred A1 - Roch, Toralf A1 - Babel, Nina A1 - Reinke, Petra A1 - Volk, Hans-Dieter A1 - Amini, Leila A1 - Schmueck-Henneresse, Michael T1 - Tacrolimus-resistant SARS-CoV-2-specific T cell products to prevent and treat severe COVID-19 in immunosuppressed patients JF - Molecular therapy methods and clinical development N2 - Solid organ transplant (SOT) recipients receive therapeutic immunosuppression that compromises their immune response to infections and vaccines. For this reason, SOT patients have a high risk of developing severe coronavirus disease 2019 (COVID-19) and an increased risk of death from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Moreover, the efficiency of immunotherapies and vaccines is reduced due to the constant immunosuppression in this patient group. Here, we propose adoptive transfer of SARS-CoV-2-specific T cells made resistant to a common immunosuppressant, tacrolimus, for optimized performance in the immunosuppressed patient. Using a ribonucleoprotein approach of CRISPR-Cas9 technology, we have generated tacrolimus-resistant SARS-CoV-2-specific T cell products from convalescent donors and demonstrate their specificity and function through characterizations at the single-cell level, including flow cytometry, single-cell RNA (scRNA) Cellular Indexing of Transcriptomes and Epitopes (CITE), and T cell receptor (TCR) sequencing analyses. Based on the promising results, we aim for clinical validation of this approach in transplant recipients. Additionally, we propose a combinatory approach with tacrolimus, to prevent an overshooting immune response manifested as bystander T cell activation in the setting of severe COVID-19 immunopathology, and tacrolimus-resistant SARS-CoV-2-specific T cell products, allowing for efficient clearance of viral infection. Our strategy has the potential to prevent severe COVID-19 courses in SOT or autoimmunity settings and to prevent immunopathology while providing viral clearance in severe non-transplant COVID-19 cases. Y1 - 2022 U6 - https://doi.org/10.1016/j.omtm.2022.02.012 SN - 2329-0501 VL - 25 SP - 52 EP - 73 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Tomowski, Maxi A1 - Lozada-Gobilard, Sissi Donna A1 - Jeltsch, Florian A1 - Tiedemann, Ralph T1 - Recruitment and migration patterns reveal a key role for seed banks in the meta-population dynamics of an aquatic plant JF - Scientific reports N2 - Progressive habitat fragmentation threatens plant species with narrow habitat requirements. While local environmental conditions define population growth rates and recruitment success at the patch level, dispersal is critical for population viability at the landscape scale. Identifying the dynamics of plant meta-populations is often confounded by the uncertainty about soil-stored population compartments. We combined a landscape-scale assessment of an amphibious plant's population structure with measurements of dispersal complexity in time to track dispersal and putative shifts in functional connectivity. Using 13 microsatellite markers, we analyzed the genetic structure of extant Oenanthe aquatica populations and their soil seed banks in a kettle hole system to uncover hidden connectivity among populations in time and space. Considerable spatial genetic structure and isolation-by-distance suggest limited gene flow between sites. Spatial isolation and patch size showed minor effects on genetic diversity. Genetic similarity found among extant populations and their seed banks suggests increased local recruitment, despite some evidence of migration and recent colonization. Results indicate stepping-stone dispersal across adjacent populations. Among permanent and ephemeral demes the resulting meta-population demography could be determined by source-sink dynamics. Overall, these spatiotemporal connectivity patterns support mainland-island dynamics in our system, highlighting the importance of persistent seed banks as enduring sources of genetic diversity. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-37974-5 SN - 2045-2322 VL - 13 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - Arend, Marius A1 - Zimmer, David A1 - Xu, Rudan A1 - Sommer, Frederik A1 - Mühlhaus, Timo A1 - Nikoloski, Zoran T1 - Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale JF - Nature Communications N2 - Metabolic engineering of microalgae offers a promising solution for sustainable biofuel production, and rational design of engineering strategies can be improved by employing metabolic models that integrate enzyme turnover numbers. However, the coverage of turnover numbers for Chlamydomonas reinhardtii, a model eukaryotic microalga accessible to metabolic engineering, is 17-fold smaller compared to the heterotrophic cell factory Saccharomyces cerevisiae. Here we generate quantitative protein abundance data of Chlamydomonas covering 2337 to 3708 proteins in various growth conditions to estimate in vivo maximum apparent turnover numbers. Using constrained-based modeling we provide proxies for in vivo turnover numbers of 568 reactions, representing a 10-fold increase over the in vitro data for Chlamydomonas. Integration of the in vivo estimates instead of in vitro values in a metabolic model of Chlamydomonas improved the accuracy of enzyme usage predictions. Our results help in extending the knowledge on uncharacterized enzymes and improve biotechnological applications of Chlamydomonas. KW - Computational models KW - Enzymes KW - Proteomics Y1 - 2023 U6 - https://doi.org/10.1038/s41467-023-40498-1 SN - 2041-1723 VL - 14 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - Ferreira, Clara Mendes A1 - Dammhahn, Melanie A1 - Eccard, Jana T1 - So many choices, so little time BT - food preference and movement vary with the landscape of fear JF - Ecology and evolution N2 - Spatial and temporal variation in perceived predation risk is an important determinant of movement and foraging activity of animals. Foraging in this landscape of fear, individuals need to decide where and when to move, and what resources to choose. Foraging theory predicts the outcome of these decisions based on energetic trade-offs, but complex interactions between perceived predation risk and preferences of foragers for certain functional traits of their resources are rarely considered. Here, we studied the interactive effects of perceived predation risk on food trait preferences and foraging behavior in bank voles (Myodes glareolus) in experimental landscapes. Individuals (n = 19) were subjected for periods of 24 h to two extreme, risk-uniform landscapes (either risky or safe), containing 25 discrete food patches, filled with seeds of four plant species in even amounts. Seeds varied in functional traits: size, nutrients, and shape. We evaluated whether and how risk modifies forager preference for functional traits. We also investigated whether perceived risk and distance from shelter affected giving-up density (GUD), time in patches, and number of patch visits. In safe landscapes, individuals increased time spent in patches, lowered GUD and visited distant patches more often compared to risky landscapes. Individuals preferred bigger seeds independent of risk, but in the safe treatment they preferred fat-rich over carb-rich seeds. Thus, higher densities of resource levels remained in risky landscapes, while in safe landscapes resource density was lower and less diverse due to selective foraging. Our results suggest that the interaction of perceived risk and dietary preference adds an additional layer to the cascading effects of a landscape of fear which affects biodiversity at resource level. KW - foraging behavior KW - functional traits KW - giving-up density KW - myodes glareolus KW - perceived predation risk KW - seed ecology Y1 - 2023 U6 - https://doi.org/10.1002/ece3.10330 SN - 2045-7758 VL - 13 IS - 7 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Petrich, Annett A1 - Aji, Amit Koikkarah A1 - Dunsing, Valentin A1 - Chiantia, Salvatore T1 - Benchmarking of novel green fluorescent proteins for the quantification of protein oligomerization in living cells JF - PLoS one N2 - Protein-protein-interactions play an important role in many cellular functions. Quantitative non-invasive techniques are applied in living cells to evaluate such interactions, thereby providing a broader understanding of complex biological processes. Fluorescence fluctuation spectroscopy describes a group of quantitative microscopy approaches for the characterization of molecular interactions at single cell resolution. Through the obtained molecular brightness, it is possible to determine the oligomeric state of proteins. This is usually achieved by fusing fluorescent proteins (FPs) to the protein of interest. Recently, the number of novel green FPs has increased, with consequent improvements to the quality of fluctuation-based measurements. The photophysical behavior of FPs is influenced by multiple factors (including photobleaching, protonation-induced "blinking" and long-lived dark states). Assessing these factors is critical for selecting the appropriate fluorescent tag for live cell imaging applications. In this work, we focus on novel green FPs that are extensively used in live cell imaging. A systematic performance comparison of several green FPs in living cells under different pH conditions using Number & Brightness (N & B) analysis and scanning fluorescence correlation spectroscopy was performed. Our results show that the new FP Gamillus exhibits higher brightness at the cost of lower photostability and fluorescence probability (pf), especially at lower pH. mGreenLantern, on the other hand, thanks to a very high pf, is best suited for multimerization quantification at neutral pH. At lower pH, mEGFP remains apparently the best choice for multimerization investigation. These guidelines provide the information needed to plan quantitative fluorescence microscopy involving these FPs, both for general imaging or for protein-protein-interactions quantification via fluorescence fluctuation-based methods. Y1 - 2023 U6 - https://doi.org/10.1371/journal.pone.0285486 SN - 1932-6203 VL - 18 IS - 8 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Xu, Huizhen A1 - Giannetti, Alessandro A1 - Sugiyama, Yuki A1 - Zheng, Wenna A1 - Schneider, René A1 - Watanabe, Yoichiro A1 - Oda, Yoshihisa A1 - Persson, Staffan T1 - Secondary cell wall patterning-connecting the dots, pits and helices JF - Open biology N2 - All plant cells are encased in primary cell walls that determine plant morphology, but also protect the cells against the environment. Certain cells also produce a secondary wall that supports mechanically demanding processes, such as maintaining plant body stature and water transport inside plants. Both these walls are primarily composed of polysaccharides that are arranged in certain patterns to support cell functions. A key requisite for patterned cell walls is the arrangement of cortical microtubules that may direct the delivery of wall polymers and/or cell wall producing enzymes to certain plasma membrane locations. Microtubules also steer the synthesis of cellulose-the load-bearing structure in cell walls-at the plasma membrane. The organization and behaviour of the microtubule array are thus of fundamental importance to cell wall patterns. These aspects are controlled by the coordinated effort of small GTPases that probably coordinate a Turing's reaction-diffusion mechanism to drive microtubule patterns. Here, we give an overview on how wall patterns form in the water-transporting xylem vessels of plants. We discuss systems that have been used to dissect mechanisms that underpin the xylem wall patterns, emphasizing the VND6 and VND7 inducible systems, and outline challenges that lay ahead in this field. KW - plant cell wall KW - microtubules KW - xylem KW - cell wall patterning KW - cellulose Y1 - 2022 U6 - https://doi.org/10.1098/rsob.210208 SN - 2046-2441 VL - 12 IS - 5 PB - Royal Society CY - London ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Compart, Julia A1 - Fettke, Jörg T1 - Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield JF - Frontiers in plant science N2 - The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches. KW - starch KW - oil yield KW - fruit development KW - gene expression KW - RNA-seq KW - and palm KW - oil KW - Elaeis guineensis Jacq Y1 - 2023 U6 - https://doi.org/10.3389/fpls.2023.1220237 SN - 1664-462X VL - 14 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Berry, Paul E. A1 - Dammhahn, Melanie A1 - Blaum, Niels T1 - Keeping cool on hot days BT - activity responses of African antelope to heat extremes JF - Frontiers in ecology and evolution N2 - Long-lived organisms are likely to respond to a rapidly changing climate with behavioral flexibility. Animals inhabiting the arid parts of southern Africa face a particularly rapid rise in temperature which in combination with food and water scarcity places substantial constraints on the ability of animals to tolerate heat. We investigated how three species of African antelope-springbok Antidorcas marsupialis, kudu Tragelaphus strepsiceros and eland T. oryx-differing in body size, habitat preference and movement ecology, change their activity in response to extreme heat in an arid savanna. Serving as a proxy for activity, dynamic body acceleration data recorded every five minutes were analyzed for seven to eight individuals per species for the three hottest months of the year. Activity responses to heat during the hottest time of day (the afternoons) were investigated and diel activity patterns were compared between hot and cool days. Springbok, which prefer open habitat, are highly mobile and the smallest of the species studied, showed the greatest decrease in activity with rising temperature. Furthermore, springbok showed reduced mean activity over the 24 h cycle on hot days compared to cool days. Large-bodied eland seemed less affected by afternoon heat than springbok. While eland also reduced diurnal activity on hot days compared to cool days, they compensated for this by increasing nocturnal activity, possibly because their predation risk is lower. Kudu, which are comparatively sedentary and typically occupy shady habitat, seemed least affected during the hottest time of day and showed no appreciable difference in diel activity patterns between hot and cool days. The interplay between habitat preference, body size, movement patterns, and other factors seems complex and even sub-lethal levels of heat stress have been shown to impact an animal's long-term survival and reproduction. Thus, differing heat tolerances among species could result in a shift in the composition of African herbivore communities as temperatures continue to rise, with significant implications for economically important wildlife-based land use and conservation. KW - springbok KW - kudu KW - eland KW - dynamic body acceleration KW - tri-axial accelerometers KW - behavioral flexibility KW - climate change KW - savanna ecology Y1 - 2023 U6 - https://doi.org/10.3389/fevo.2023.1172303 SN - 2296-701X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Compart, Julia A1 - Singh, Aakanksha A1 - Fettke, Jörg A1 - Apriyanto, Ardha T1 - Customizing starch properties BT - a review of starch modifications and their applications JF - Polymers N2 - Starch has been a convenient, economically important polymer with substantial applications in the food and processing industry. However, native starches present restricted applications, which hinder their industrial usage. Therefore, modification of starch is carried out to augment the positive characteristics and eliminate the limitations of the native starches. Modifications of starch can result in generating novel polymers with numerous functional and value-added properties that suit the needs of the industry. Here, we summarize the possible starch modifications in planta and outside the plant system (physical, chemical, and enzymatic) and their corresponding applications. In addition, this review will highlight the implications of each starch property adjustment. KW - starch KW - starch modification KW - in planta modification KW - physical modification KW - chemical modification KW - enzymatic modification KW - starch application Y1 - 2023 U6 - https://doi.org/10.3390/polym15163491 SN - 2073-4360 VL - 15 IS - 16 PB - MDPI CY - Basel ER - TY - JOUR A1 - Kappel, Christian A1 - Friedrich, Thomas A1 - Oberkofler, Vicky A1 - Jiang, Li A1 - Crawford, Tim A1 - Lenhard, Michael A1 - Bäurle, Isabel T1 - Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis JF - Genome biology : biology for the post-genomic era N2 - Background Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq. Results HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. Conclusions Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior. KW - Transcriptional memory KW - Priming KW - Heat stress KW - HSFA2 KW - HSFA3 KW - Arabidopsis thaliana KW - Histone H3K4 trimethylation KW - ChIP-seq Y1 - 2023 U6 - https://doi.org/10.1186/s13059-023-02970-5 SN - 1474-760X VL - 24 IS - 1 PB - BioMed Central CY - London ER - TY - JOUR A1 - Tabatabaei, Iman A1 - Alseekh, Saleh A1 - Shahid, Mohammad A1 - Leniak, Ewa A1 - Wagner, Mateusz A1 - Mahmoudi, Henda A1 - Thushar, Sumitha A1 - Fernie, Alisdair A1 - Murphy, Kevin M. A1 - Schmöckel, Sandra M. A1 - Tester, Mark A1 - Müller-Röber, Bernd A1 - Skirycz, Aleksandra A1 - Balazadeh, Salma T1 - The diversity of quinoa morphological traits and seed metabolic composition JF - Scientific data N2 - Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa. Y1 - 2022 U6 - https://doi.org/10.1038/s41597-022-01399-y SN - 2052-4463 VL - 9 IS - 1 PB - Nature Research CY - Berlin ER - TY - JOUR A1 - Stiegler, Jonas A1 - Pahl, Janice A1 - Guillen, Rafael Arce A1 - Ullmann, Wiebke A1 - Blaum, Niels T1 - The heat is on BT - impacts of rising temperature on the activity of a common European mammal JF - Frontiers in Ecology and Evolution N2 - Climate conditions severely impact the activity and, consequently, the fitness of wildlife species across the globe. Wildlife can respond to new climatic conditions, but the pace of human-induced change limits opportunities for adaptation or migration. Thus, how these changes affect behavior, movement patterns, and activity levels remains unclear. In this study, we investigate how extreme weather conditions affect the activity of European hares (Lepus europaeus) during their peak reproduction period. When hares must additionally invest energy in mating, prevailing against competitors, or lactating, we investigated their sensitivities to rising temperatures, wind speed, and humidity. To quantify their activity, we used the overall dynamic body acceleration (ODBA) calculated from tri-axial acceleration measurements of 33 GPS-collared hares. Our analysis revealed that temperature, humidity, and wind speed are important in explaining changes in activity, with a strong response for high temperatures above 25 & DEG;C and the highest change in activity during temperature extremes of over 35 & DEG;C during their inactive period. Further, we found a non-linear relationship between temperature and activity and an interaction of activity changes between day and night. Activity increased at higher temperatures during the inactive period (day) and decreased during the active period (night). This decrease was strongest during hot tropical nights. At a stage of life when mammals such as hares must substantially invest in reproduction, the sensitivity of females to extreme temperatures was particularly pronounced. Similarly, both sexes increased their activity at high humidity levels during the day and low wind speeds, irrespective of the time of day, while the effect of humidity was stronger for males. Our findings highlight the importance of understanding the complex relationships between extreme weather conditions and mammal behavior, critical for conservation and management. With ongoing climate change, extreme weather events such as heat waves and heavy rainfall are predicted to occur more often and last longer. These events will directly impact the fitness of hares and other wildlife species and hence the population dynamics of already declining populations across Europe. KW - activity KW - ODBA KW - animal tracking KW - European hare KW - extreme weather events KW - climate change Y1 - 2023 U6 - https://doi.org/10.3389/fevo.2023.1193861 SN - 2296-701X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Schwieder, Marcel A1 - Wesemeyer, Maximilian A1 - Frantz, David A1 - Pfoch, Kira A1 - Erasmi, Stefan A1 - Pickert, Jürgen A1 - Nendel, Claas A1 - Hostert, Patrick T1 - Mapping grassland mowing events across Germany based on combined Sentinel-2 and Landsat 8 time series JF - Remote sensing of environment N2 - Spatially explicit knowledge on grassland extent and management is critical to understand and monitor the impact of grassland use intensity on ecosystem services and biodiversity. While regional studies allow detailed insights into land use and ecosystem service interactions, information on a national scale can aid biodiversity assessments. However, for most European countries this information is not yet widely available. We used an analysis-ready-data cube that contains dense time series of co-registered Sentinel-2 and Landsat 8 data, covering the extent of Germany. We propose an algorithm that detects mowing events in the time series based on residuals from an assumed undisturbed phenology, as an indicator of grassland use intensity. A self-adaptive ruleset enabled to account for regional variations in land surface phenology and non-stationary time series on a pixelbasis. We mapped mowing events for the years from 2017 to 2020 for permanent grassland areas in Germany. The results were validated on a pixel level in four of the main natural regions in Germany based on reported mowing events for a total of 92 (2018) and 78 (2019) grassland parcels. Results for 2020 were evaluated with combined time series of Landsat, Sentinel-2 and PlanetScope data. The mean absolute percentage error between detected and reported mowing events was on average 40% (2018), 36% (2019) and 35% (2020). Mowing events were on average detected 11 days (2018), 7 days (2019) and 6 days (2020) after the reported mowing. Performance measures varied between the different regions of Germany, and lower accuracies were found in areas that are revisited less frequently by Sentinel-2. Thus, we assessed the influence of data availability and found that the detection of mowing events was less influenced by data availability when at least 16 cloud-free observations were available in the grassland season. Still, the distribution of available observations throughout the season appeared to be critical. On a national scale our results revealed overall higher shares of less intensively mown grasslands and smaller shares of highly intensively managed grasslands. Hotspots of the latter were identified in the alpine foreland in Southern Germany as well as in the lowlands in the Northwest of Germany. While these patterns were stable throughout the years, the results revealed a tendency to lower management intensity in the extremely dry year 2018. Our results emphasize the ability of the approach to map the intensity of grassland management throughout large areas despite variations in data availability and environmental conditions. KW - Analysis-ready data KW - Big data KW - Large-area mapping KW - Germany KW - Common agricultural policy KW - Time series KW - Land use intensity KW - Optical remote sensing KW - Multi-spectral data KW - PlanetScope Y1 - 2022 U6 - https://doi.org/10.1016/j.rse.2021.112795 SN - 0034-4257 SN - 1879-0704 VL - 269 PB - Elsevier CY - New York ER - TY - JOUR A1 - Alshareef, Nouf Owdah A1 - Otterbach, Sophie L. A1 - Allu, Annapurna Devi A1 - Woo, Yong H. A1 - de Werk, Tobias A1 - Kamranfar, Iman A1 - Müller-Röber, Bernd A1 - Tester, Mark A1 - Balazadeh, Salma A1 - Schmöckel, Sandra M. T1 - NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis JF - Scientific reports N2 - Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. 'Thermomemory' is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/ CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Ara bidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like atafl, anac055 mutants show improved thermomemory, revealing a potential co-control of both NACTFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-14429-x SN - 2045-2322 VL - 12 IS - 1 PB - Nature Research CY - Berlin ER - TY - JOUR A1 - Hoang, Yen A1 - Gryzik, Stefanie A1 - Hoppe, Ines A1 - Rybak, Alexander A1 - Schädlich, Martin A1 - Kadner, Isabelle A1 - Walther, Dirk A1 - Vera, Julio A1 - Radbruch, Andreas A1 - Groth, Detlef A1 - Baumgart, Sabine A1 - Baumgrass, Ria T1 - PRI: Re-analysis of a public mass cytometry dataset reveals patterns of effective tumor treatments JF - Frontiers in immunology N2 - Recently, mass cytometry has enabled quantification of up to 50 parameters for millions of cells per sample. It remains a challenge to analyze such high-dimensional data to exploit the richness of the inherent information, even though many valuable new analysis tools have already been developed. We propose a novel algorithm "pattern recognition of immune cells (PRI)" to tackle these high-dimensional protein combinations in the data. PRI is a tool for the analysis and visualization of cytometry data based on a three or more-parametric binning approach, feature engineering of bin properties of multivariate cell data, and a pseudo-multiparametric visualization. Using a publicly available mass cytometry dataset, we proved that reproducible feature engineering and intuitive understanding of the generated bin plots are helpful hallmarks for re-analysis with PRI. In the CD4(+)T cell population analyzed, PRI revealed two bin-plot patterns (CD90/CD44/CD86 and CD90/CD44/CD27) and 20 bin plot features for threshold-independent classification of mice concerning ineffective and effective tumor treatment. In addition, PRI mapped cell subsets regarding co-expression of the proliferation marker Ki67 with two major transcription factors and further delineated a specific Th1 cell subset. All these results demonstrate the added insights that can be obtained using the non-cluster-based tool PRI for re-analyses of high-dimensional cytometric data. KW - multi-parametric analysis KW - re-analysis KW - combinatorial protein KW - expression KW - high-dimensional cytometry data KW - mass cytometry data KW - pattern perception Y1 - 2022 U6 - https://doi.org/10.3389/fimmu.2022.849329 SN - 1664-3224 VL - 13 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Tian, Fang A1 - Qin, Wen A1 - Zhang, Ran A1 - Herzschuh, Ulrike A1 - Ni, Jian A1 - Zhang, Chengjun A1 - Mischke, Steffen A1 - Cao, Xianyong T1 - Palynological evidence for the temporal stability of the plant community in the Yellow River Source Area over the last 7,400 years JF - Vegetation history and archaeobotany N2 - The terrestrial ecosystem in the Yellow River Source Area (YRSA) is sensitive to climate change and human impacts, although past vegetation change and the degree of human disturbance are still largely unknown. A 170-cm-long sediment core covering the last 7,400 years was collected from Lake Xingxinghai (XXH) in the YRSA. Pollen, together with a series of other environmental proxies (including grain size, total organic carbon (TOC) and carbonate content), were analysed to explore past vegetation and environmental changes for the YRSA. Dominant and common pollen components-Cyperaceae, Poaceae, Artemisia, Chenopodiaceae and Asteraceae-are stable throughout the last 7,400 years. Slight vegetation change is inferred from an increasing trend of Cyperaceae and decreasing trend of Poaceae, suggesting that alpine steppe was replaced by alpine meadow at ca. 3.5 ka cal bp. The vegetation transformation indicates a generally wetter climate during the middle and late Holocene, which is supported by increased amounts of TOC and Pediastrum (representing high water-level) and is consistent with previous past climate records from the north-eastern Tibetan Plateau. Our results find no evidence of human impact on the regional vegetation surrounding XXH, hence we conclude the vegetation change likely reflects the regional climate signal. KW - Pollen KW - Lake Xingxinghai KW - Tibetan Plateau KW - Holocene KW - Vegetation change KW - Regional climate Y1 - 2022 U6 - https://doi.org/10.1007/s00334-022-00870-5 SN - 0939-6314 SN - 1617-6278 VL - 31 IS - 6 SP - 549 EP - 558 PB - Springer CY - New York ER - TY - JOUR A1 - Vatova, Mariyana A1 - Rubin, Conrad A1 - Grossart, Hans-Peter A1 - Goncalves, Susana C. A1 - Schmidt, Susanne I. A1 - Jarić, Ivan T1 - Aquatic fungi: largely neglected targets for conservation JF - Frontiers in ecology and the environment Y1 - 2022 U6 - https://doi.org/10.1002/fee.2495 SN - 1540-9295 SN - 1540-9309 VL - 20 IS - 4 SP - 207 EP - 209 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Glückler, Ramesh A1 - Geng, Rongwei A1 - Grimm, Lennart A1 - Baisheva, Izabella A1 - Herzschuh, Ulrike A1 - Stoof-Leichsenring, Kathleen R. A1 - Kruse, Stefan A1 - Andreev, Andrej Aleksandrovic A1 - Pestryakova, Luidmila A1 - Dietze, Elisabeth T1 - Holocene wildfire and vegetation dynamics in Central Yakutia, Siberia, reconstructed from lake-sediment proxies JF - Frontiers in Ecology and Evolution N2 - Wildfires play an essential role in the ecology of boreal forests. In eastern Siberia, fire activity has been increasing in recent years, challenging the livelihoods of local communities. Intensifying fire regimes also increase disturbance pressure on the boreal forests, which currently protect the permafrost beneath from accelerated degradation. However, long-term relationships between changes in fire regime and forest structure remain largely unknown. We assess past fire-vegetation feedbacks using sedimentary proxy records from Lake Satagay, Central Yakutia, Siberia, covering the past c. 10,800 years. Results from macroscopic and microscopic charcoal analyses indicate high amounts of burnt biomass during the Early Holocene, and that the present-day, low-severity surface fire regime has been in place since c. 4,500 years before present. A pollen-based quantitative reconstruction of vegetation cover and a terrestrial plant record based on sedimentary ancient DNA metabarcoding suggest a pronounced shift in forest structure toward the Late Holocene. Whereas the Early Holocene was characterized by postglacial open larch-birch woodlands, forest structure changed toward the modern, mixed larch-dominated closed-canopy forest during the Mid-Holocene. We propose a potential relationship between open woodlands and high amounts of burnt biomass, as well as a mediating effect of dense larch forest on the climate-driven intensification of fire regimes. Considering the anticipated increase in forest disturbances (droughts, insect invasions, and wildfires), higher tree mortality may force the modern state of the forest to shift toward an open woodland state comparable to the Early Holocene. Such a shift in forest structure may result in a positive feedback on currently intensifying wildfires. These new long-term data improve our understanding of millennial-scale fire regime changes and their relationships to changes of vegetation in Central Yakutia, where the local population is already being confronted with intensifying wildfire seasons. KW - fire KW - larch KW - boreal KW - forest KW - Russia KW - charcoal KW - pollen KW - ancient DNA Y1 - 2022 U6 - https://doi.org/10.3389/fevo.2022.962906 SN - 2296-701X VL - 10 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Welke, Robert-William A1 - Sperber, Hannah Sabeth A1 - Bergmann, Ronny A1 - Koikkarah, Amit A1 - Menke, Laura A1 - Sieben, Christian A1 - Krüger, Detlev H. A1 - Chiantia, Salvatore A1 - Herrmann, Andreas A1 - Schwarzer, Roland T1 - Characterization of hantavirus N protein intracellular dynamics and localization JF - Viruses N2 - Hantaviruses are enveloped viruses that possess a tri-segmented, negative-sense RNA genome. The viral S-segment encodes the multifunctional nucleocapsid protein (N), which is involved in genome packaging, intracellular protein transport, immunoregulation, and several other crucial processes during hantavirus infection. In this study, we generated fluorescently tagged N protein constructs derived from Puumalavirus (PUUV), the dominant hantavirus species in Central, Northern, and Eastern Europe. We comprehensively characterized this protein in the rodent cell line CHO-K1, monitoring the dynamics of N protein complex formation and investigating co-localization with host proteins as well as the viral glycoproteins Gc and Gn. We observed formation of large, fibrillar PUUV N protein aggregates, rapidly coalescing from early punctate and spike-like assemblies. Moreover, we found significant spatial correlation of N with vimentin, actin, and P-bodies but not with microtubules. N constructs also co-localized with Gn and Gc albeit not as strongly as the glycoproteins associated with each other. Finally, we assessed oligomerization of N constructs, observing efficient and concentration-dependent multimerization, with complexes comprising more than 10 individual proteins. KW - hantavirus KW - N protein KW - oligomerization KW - actin KW - P-bodies KW - vimentin KW - Number and Brightness KW - Puumalavirus KW - macromolecular assemblies Y1 - 2022 U6 - https://doi.org/10.3390/v14030457 SN - 1999-4915 VL - 14 IS - 3 PB - MDPI CY - Basel ER - TY - JOUR A1 - Kamali, Bahareh A1 - Jahanbakhshi, Farshid A1 - Dogaru, Diana A1 - Dietrich, Jörg A1 - Nendel, Claas A1 - AghaKouchak, Amir T1 - Probabilistic modeling of crop-yield loss risk under drought: a spatial showcase for sub-Saharan Africa JF - Environmental research letters N2 - Assessing the risk of yield loss in African drought-affected regions is key to identify feasible solutions for stable crop production. Recent studies have demonstrated that Copula-based probabilistic methods are well suited for such assessment owing to reasonably inferring important properties in terms of exceedance probability and joint dependence of different characterization. However, insufficient attention has been given to quantifying the probability of yield loss and determining the contribution of climatic factors. This study applies the Copula theory to describe the dependence between drought and crop yield anomalies for rainfed maize, millet, and sorghum crops in sub-Saharan Africa (SSA). The environmental policy integrated climate model, calibrated with Food and Agriculture Organization country-level yield data, was used to simulate yields across SSA (1980-2012). The results showed that the severity of yield loss due to drought had a higher magnitude than the severity of drought itself. Sensitivity analysis to identify factors contributing to drought and high-temperature stresses for all crops showed that the amount of precipitation during vegetation and grain filling was the main driver of crop yield loss, and the effect of temperature was stronger for sorghum than for maize and millet. The results demonstrate the added value of probabilistic methods for drought-impact assessment. For future studies, we recommend looking into factors influencing drought and high-temperature stresses as individual/concurrent climatic extremes. KW - Copula theory KW - crop model KW - drought stress KW - joint probability KW - risk Y1 - 2022 U6 - https://doi.org/10.1088/1748-9326/ac4ec1 SN - 1748-9326 VL - 17 IS - 2 PB - IOP Publishing CY - Bristol ER - TY - JOUR A1 - Kamali, Bahareh A1 - Lorite, Ignacio J. A1 - Webber, Heidi A. A1 - Rezaei, Ehsan Eyshi A1 - Gabaldon-Leal, Clara A1 - Nendel, Claas A1 - Siebert, Stefan A1 - Ramirez-Cuesta, Juan Miguel A1 - Ewert, Frank A1 - Ojeda, Jonathan J. T1 - Uncertainty in climate change impact studies for irrigated maize cropping systems in southern Spain JF - Scientific reports N2 - This study investigates the main drivers of uncertainties in simulated irrigated maize yield under historical conditions as well as scenarios of increased temperatures and altered irrigation water availability. Using APSIM, MONICA, and SIMPLACE crop models, we quantified the relative contributions of three irrigation water allocation strategies, three sowing dates, and three maize cultivars to the uncertainty in simulated yields. The water allocation strategies were derived from historical records of farmer's allocation patterns in drip-irrigation scheme of the Genil-Cabra region, Spain (2014-2017). By considering combinations of allocation strategies, the adjusted R-2 values (showing the degree of agreement between simulated and observed yields) increased by 29% compared to unrealistic assumptions of considering only near optimal or deficit irrigation scheduling. The factor decomposition analysis based on historic climate showed that irrigation strategies was the main driver of uncertainty in simulated yields (66%). However, under temperature increase scenarios, the contribution of crop model and cultivar choice to uncertainty in simulated yields were as important as irrigation strategy. This was partially due to different model structure in processes related to the temperature responses. Our study calls for including information on irrigation strategies conducted by farmers to reduce the uncertainty in simulated yields at field scale. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-08056-9 SN - 2045-2322 VL - 12 IS - 1 PB - Macmillan Publishers Limited, CY - London ER - TY - JOUR A1 - Tolomeev, Aleksandr P. A1 - Dubovskaya, Olga P. A1 - Kirillin, Georgiy A1 - Buseva, Zhanna A1 - Kolmakova, Olesya A1 - Grossart, Hans-Peter A1 - Tang, Kam W. A1 - Gladyšev, Michail I. T1 - Degradation of dead cladoceran zooplankton and their contribution to organic carbon cycling in stratified lakes BT - field observation and model prediction JF - Journal of plankton research N2 - The contribution of dead zooplankton biomass to carbon cycle in aquatic ecosystems is practically unknown. Using abundance data of zooplankton in water column and dead zooplankton in sediment traps in Lake Stechlin, an ecological-mathematical model was developed to simulate the abundance and sinking of zooplankton carcasses and predict the related release of labile organic matter (LOM) into the water column. We found species-specific differences in mortality rate of the dominant zooplankton: Daphnia cucullata, Bosmina coregoni and Diaphanosoma brachyurum (0.008, 0.129 and 0.020 day(-1), respectively) and differences in their carcass sinking velocities in metalimnion (and hypolimnion): 2.1 (7.64), 14.0 (19.5) and 1.1 (5.9) m day(-1), respectively. Our model simulating formation and degradation processes of dead zooplankton predicted a bimodal distribution of the released LOM: epilimnic and metalimnic peaks of comparable intensity, ca. 1 mg DW m(-3) day(-1). Maximum degradation of carcasses up to ca. 1.7 mg DW m(-3) day(-1) occurred in the density gradient zone of metalimnion. LOM released from zooplankton carcasses into the surrounding water may stimulate microbial activity and facilitate microbial degradation of more refractory organic matter; therefore, dead zooplankton are expected to be an integral part of water column carbon source/sink dynamics in stratified lakes. KW - zooplankton carcasses KW - non-predatory mortality KW - sinking velocities KW - microbial degradation KW - Lake Stechlin KW - simulation modeling Y1 - 2022 U6 - https://doi.org/10.1093/plankt/fbac023 SN - 0142-7873 SN - 1464-3774 VL - 44 IS - 3 SP - 386 EP - 400 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Leong, Jia Xuan A1 - Raffeiner, Margot A1 - Spinti, Daniela A1 - Langin, Gautier A1 - Franz-Wachtel, Mirita A1 - Guzman, Andrew R. A1 - Kim, Jung-Gun A1 - Pandey, Pooja A1 - Minina, Alyona E. A1 - Macek, Boris A1 - Hafren, Anders A1 - Bozkurt, Tolga O. A1 - Mudgett, Mary Beth A1 - Börnke, Frederik A1 - Hofius, Daniel A1 - Uestuen, Suayib T1 - A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component JF - The EMBO journal N2 - Beyond its role in cellular homeostasis, autophagy plays anti- and promicrobial roles in host-microbe interactions, both in animals and plants. One prominent role of antimicrobial autophagy is to degrade intracellular pathogens or microbial molecules, in a process termed xenophagy. Consequently, microbes evolved mechanisms to hijack or modulate autophagy to escape elimination. Although well-described in animals, the extent to which xenophagy contributes to plant-bacteria interactions remains unknown. Here, we provide evidence that Xanthomonas campestris pv. vesicatoria (Xcv) suppresses host autophagy by utilizing type-III effector XopL. XopL interacts with and degrades the autophagy component SH3P2 via its E3 ligase activity to promote infection. Intriguingly, XopL is targeted for degradation by defense-related selective autophagy mediated by NBR1/Joka2, revealing a complex antagonistic interplay between XopL and the host autophagy machinery. Our results implicate plant antimicrobial autophagy in the depletion of a bacterial virulence factor and unravel an unprecedented pathogen strategy to counteract defense-related autophagy in plant-bacteria interactions. KW - autophagy KW - effectors KW - immunity KW - ubiquitination KW - xenophagy Y1 - 2022 U6 - https://doi.org/10.15252/embj.2021110352 SN - 1460-2075 VL - 41 IS - 13 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Agne, Stefanie A1 - Naylor, Gavin J. P. A1 - Preick, Michaela A1 - Yang, Lei A1 - Thiel, Ralf A1 - Weigmann, Simon A1 - Paijmans, Johanna L. A. A1 - Barlow, Axel A1 - Hofreiter, Michael A1 - Straube, Nicolas T1 - Taxonomic identification of two poorly known lantern shark species based on mitochondrial DNA from wet-collection paratypes JF - Frontiers in Ecology and Evolution N2 - Etmopteridae (lantern sharks) is the most species-rich family of sharks, comprising more than 50 species. Many species are described from few individuals, and re-collection of specimens is often hindered by the remoteness of their sampling sites. For taxonomic studies, comparative morphological analysis of type specimens housed in natural history collections has been the main source of evidence. In contrast, DNA sequence information has rarely been used. Most lantern shark collection specimens, including the types, were formalin fixed before long-term storage in ethanol solutions. The DNA damage caused by both fixation and preservation of specimens has excluded these specimens from DNA sequence-based phylogenetic analyses so far. However, recent advances in the field of ancient DNA have allowed recovery of wet-collection specimen DNA sequence data. Here we analyse archival mitochondrial DNA sequences, obtained using ancient DNA approaches, of two wet-collection lantern shark paratype specimens, namely Etmopterus litvinovi and E. pycnolepis, for which the type series represent the only known individuals. Target capture of mitochondrial markers from single-stranded DNA libraries allows for phylogenetic placement of both species. Our results suggest synonymy of E. benchleyi with E. litvinovi but support the species status of E. pycnolepis. This revised taxonomy is helpful for future conservation and management efforts, as our results indicate a larger distribution range of E. litvinovi. This study further demonstrates the importance of wet-collection type specimens as genetic resource for taxonomic research. KW - type specimens KW - Etmopterus litvinovi KW - Etmopterus pycnolepis KW - deep-sea KW - sharks KW - archival DNA Y1 - 2022 U6 - https://doi.org/10.3389/fevo.2022.910009 SN - 2296-701X VL - 10 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Havermann, Felix A1 - Ghirardo, Andrea A1 - Schnitzler, Jörg-Peter A1 - Nendel, Claas A1 - Hoffmann, Mathias A1 - Kraus, David A1 - Grote, Rüdiger T1 - Modeling intra- and interannual variability of BVOC emissions from maize, oil-seed rape, and ryegrass JF - Journal of advances in modeling earth systems N2 - Air chemistry is affected by the emission of biogenic volatile organic compounds (BVOCs), which originate from almost all plants in varying qualities and quantities. They also vary widely among different crops, an aspect that has been largely neglected in emission inventories. In particular, bioenergy-related species can emit mixtures of highly reactive compounds that have received little attention so far. For such species, long-term field observations of BVOC exchange from relevant crops covering different phenological phases are scarcely available. Therefore, we measured and modeled the emission of three prominent European bioenergy crops (maize, ryegrass, and oil-seed rape) for full rotations in north-eastern Germany. Using a proton transfer reaction-mass spectrometer combined with automatically moving large canopy chambers, we were able to quantify the characteristic seasonal BVOC flux dynamics of each crop species. The measured BVOC fluxes were used to parameterize and evaluate the BVOC emission module (JJv) of the physiology-oriented LandscapeDNDC model, which was enhanced to cover de novo emissions as well as those from plant storage pools. Parameters are defined for each compound individually. The model is used for simulating total compound-specific reactivity over several years and also to evaluate the importance of these emissions for air chemistry. We can demonstrate substantial differences between the investigated crops with oil-seed rape having 37-fold higher total annual emissions than maize. However, due to a higher chemical reactivity of the emitted blend in maize, potential impacts on atmospheric OH-chemistry are only 6-fold higher. KW - biogenic volatile organic compounds KW - process-based modeling KW - Zea mays KW - Brassica napus KW - Lolium multiflorum KW - plant ontogenetic stage Y1 - 2022 U6 - https://doi.org/10.1029/2021MS002683 SN - 1942-2466 VL - 14 IS - 3 PB - American Geophysical Union CY - Washington ER - TY - JOUR A1 - Rosso, Pablo A1 - Nendel, Claas A1 - Gilardi, Nicolas A1 - Udroiu, Cosmin A1 - Chlebowski, Florent T1 - Processing of remote sensing information to retrieve leaf area index in barley BT - a comparison of methods JF - Precision agriculture N2 - Leaf area index (LAI) is a key variable in understanding and modeling crop-environment interactions. With the advent of increasingly higher spatial resolution satellites and sensors mounted on remotely piloted aircrafts (RPAs), the use of remote sensing in precision agriculture is becoming more common. Since also the availability of methods to retrieve LAI from image data have also drastically expanded, it is necessary to test simultaneously as many methods as possible to understand the advantages and disadvantages of each approach. Ground-based LAI data from three years of barley experiments were related to remote sensing information using vegetation indices (VI), machine learning (ML) and radiative transfer models (RTM), to assess the relative accuracy and efficacy of these methods. The optimized soil adjusted vegetation index and a modified version of the Weighted Difference Vegetation Index performed slightly better than any other retrieval method. However, all methods yielded coefficients of determination of around 0.7 to 0.9. The best performing machine learning algorithms achieved higher accuracies when four Sentinel-2 bands instead of 12 were used. Also, the good performance of VIs and the satisfactory performance of the 4-band RTM, strongly support the synergistic use of satellites and RPAs in precision agriculture. One of the methods used, Sen2-Agri, an open source ML-RTM-based operational system, was also able to accurately retrieve LAI, although it is restricted to Sentinel-2 and Landsat data. This study shows the benefits of testing simultaneously a broad range of retrieval methods to monitor crops for precision agriculture. KW - leaf area index KW - vegetation indices KW - machine learning KW - radiative transfer models Y1 - 2022 U6 - https://doi.org/10.1007/s11119-022-09893-4 SN - 1385-2256 SN - 1573-1618 VL - 23 IS - 4 SP - 1449 EP - 1472 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Straube, Nicolas A1 - Preick, Michaela A1 - Naylor, Gavin J. P. A1 - Hofreiter, Michael T1 - Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae) JF - Royal Society Open Science N2 - After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus, in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy. KW - museum specimens KW - archival DNA KW - deep-sea sharks KW - Etmopterus pusillus KW - Etmopterus joungi KW - taxonomy Y1 - 2021 U6 - https://doi.org/10.1098/rsos.210474 SN - 2054-5703 VL - 8 IS - 9 PB - Royal Society CY - London ER - TY - JOUR A1 - Andreev, Andrei A1 - Raschke, Elena A1 - Biskaborn, Boris A1 - Vyse, Stuart Andrew A1 - Courtin, Jérémy A1 - Böhmer, Thomas A1 - Stoof-Leichsenring, Kathleen R. A1 - Kruse, Stefan A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - Late Pleistocene to Holocene vegetation and climate changes in northwestern Chukotka (Far East Russia) deduced from lakes Ilirney and Rauchuagytgyn pollen records JF - Boreas : an international journal of quaternary research N2 - This paper presents two new pollen records and quantitative climate reconstructions from northern Chukotka documenting environmental changes over the last 27.9 ka. Open tundra- and steppe-like habitats dominated between 27.9 and 18.7 cal. ka BP. Betula and Alnus shrubs might have grown in sheltered microhabitats but disappeared after 18.7 cal. ka BP. Although the climate was rather harsh, local herb-dominated communities supported herbivores as is evident by the presence of coprophilous spores in the sediments. The increase in Salix and Cyperaceae similar to 16.1 cal. ka BP suggests climate amelioration. Shrub Betula appeared similar to 15.9 cal. ka BP, and became dominant after similar to 15.52 cal. ka BP, whilst typical steppe communities drastically reduced. Very high presence of Botryococcus in the Lateglacial sediments reflects widespread shallow habitats, probably due to lake level increase. Shrub Alnus became common after similar to 13 cal. ka BP reflecting further climate amelioration. Simultaneously, herb communities gradually decreased in the vegetation reaching a minimum similar to 11.8 cal. ka BP. A gradual decrease of algae remains suggests a reduction of shallow-water habitats. Shrubby and graminoid tundra was dominant similar to 11.8-11.1 cal. ka BP, later Salix stands significantly decreased. The forest-tundra ecotone established in the Early Holocene, shortly after 11.1 cal. ka BP. Low contents of green algae in the Early Holocene sediments likely reflect deeper aquatic conditions. The most favourable climate conditions were between similar to 10.6 and 7 cal. ka BP. Vegetation became similar to the modern after similar to 7 cal. ka BP but Pinus pumila came to the Ilirney area at about 1.2 cal. ka BP. It is important to emphasize that the study area provided refugia for Betula and Alnus during MIS 2. It is also notable that our records do not reflect evidence of Younger Dryas cooling, which is inconsistent with some regional environmental records but in good accordance with some others. Y1 - 2021 U6 - https://doi.org/10.1111/bor.12521 SN - 0300-9483 SN - 1502-3885 VL - 50 IS - 3 SP - 652 EP - 670 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - JOUR A1 - Zhang, Naimeng A1 - Cao, Xianyong A1 - Xu, Qinghai A1 - Huang, Xiaozhong A1 - Herzschuh, Ulrike A1 - Shen, Zhongwei A1 - Peng, Wei A1 - Liu, Sisi A1 - Wu, Duo A1 - Wang, Jian A1 - Xia, Huan A1 - Zhang, Dongju A1 - Chen, Fahu T1 - Vegetation change and human-environment interactions in the Qinghai Lake Basin, northeastern Tibetan Plateau, since the last deglaciation JF - Catena N2 - The nature of the interaction between prehistoric humans and their environment, especially the vegetation, has long been of interest. The Qinghai Lake Basin in North China is well-suited to exploring the interactions between prehistoric humans and vegetation in the Tibetan Plateau, because of the comparatively dense distribution of archaeological sites and the ecologically fragile environment. Previous pollen studies of Qinghai Lake have enabled a detailed reconstruction of the regional vegetation, but they have provided relatively little information on vegetation change within the Qinghai Lake watershed. To address the issue we conducted a pollen-based vegetation reconstruction for an archaeological site (YWY), located on the southern shore of Qinghai Lake. We used high temporal-resolution pollen records from the YWY site and from Qinghai Lake, spanning the interval since the last deglaciation (15.3 kyr BP to the present) to quantitatively reconstruct changes in the local and regional vegetation using Landscape Reconstruction Algorithm models. The results show that, since the late glacial, spruce forest grew at high altitudes in the surrounding mountains, while the lakeshore environment was occupied mainly by shrub-steppe. From the lateglacial to the middle Holocene, coniferous woodland began to expand downslope and reached the YWY site at 7.1 kyr BP. The living environment of the local small groups of Paleolithic-Epipaleolithic humans (during 15.3-13.1 kyr BP and 9-6.4 kyr BP) changed from shrub-steppe to coniferous forest-steppe. The pollen record shows no evidence of pronounced changes in the vegetation community corresponding to human activity. However, based on a comparison of the local and regional vegetation reconstructions, low values of biodiversity and a significant increase in two indicators of vegetation degradation, Chenopodiaceae and Rosaceae, suggest that prehistoric hunters-gatherers likely disturbed the local vegetation during 9.0-6.4 kyr BP. Our findings are a preliminary attempt to study human-environment interactions at Paleolithic-Epipaleolithic sites in the region, and they contribute to ongoing environmental archaeology research in the Tibetan Plateau. KW - Quantitative vegetation reconstruction KW - Local and regional vegetation KW - dynamics KW - Paleolithic-Epipaleolithic human-environment  KW - interactions KW - Northeastern Tibetan Plateau Y1 - 2022 U6 - https://doi.org/10.1016/j.catena.2021.105892 SN - 0341-8162 SN - 1872-6887 VL - 210 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Schittko, Conrad A1 - Onandia, Gabriela A1 - Bernard-Verdier, Maud A1 - Heger, Tina A1 - Jeschke, Jonathan M. A1 - Kowarik, Ingo A1 - Maaß, Stefanie A1 - Joshi, Jasmin T1 - Biodiversity maintains soil multifunctionality and soil organic carbon in novel urban ecosystems JF - Journal of ecology N2 - Biodiversity in urban ecosystems has the potential to increase ecosystem functions and support a suite of services valued by society, including services provided by soils. Specifically, the sequestration of carbon in soils has often been advocated as a solution to mitigate the steady increase in CO2 concentration in the atmosphere as a key driver of climate change. However, urban ecosystems are also characterized by an often high level of ecological novelty due to profound human-mediated changes, such as the presence of high numbers of non-native species, impervious surfaces or other disturbances. Yet it is poorly understood whether and how biodiversity affects ecosystem functioning and services of urban soils under these novel conditions. In this study, we assessed the influence of above- and below-ground diversity, as well as urbanization and plant invasions, on multifunctionality and organic carbon stocks of soils in non-manipulated grasslands along an urbanization gradient in Berlin, Germany. We focused on plant diversity (measured as species richness and functional trait diversity) and, in addition, on soil organism diversity as a potential mediator for the relationship of plant species diversity and ecosystem functioning. Our results showed positive effects of plant diversity on soil multifunctionality and soil organic carbon stocks along the entire gradient. Structural equation models revealed that plant diversity enhanced soil multifunctionality and soil organic carbon by increasing the diversity of below-ground organisms. These positive effects of plant diversity on soil multifunctionality and soil fauna were not restricted to native plant species only, but were also exerted by non-native species, although to a lesser degree. Synthesis. We conclude that enhancing diversity in plants and soil fauna of urban grasslands can increase the multifunctionality of urban soils and also add to their often underestimated but very valuable role in mitigating effects of climate change. KW - Anthropocene KW - biological invasions KW - ecosystem function and services; KW - functional diversity KW - global change KW - non-native species KW - novel KW - ecosystems KW - urbanization Y1 - 2022 U6 - https://doi.org/10.1111/1365-2745.13852 SN - 0022-0477 SN - 1365-2745 VL - 110 IS - 4 SP - 916 EP - 934 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Ionescu, Danny A1 - Bizic, Mina A1 - Karnatak, Rajat A1 - Musseau, Camille L. A1 - Onandia, Gabriela A1 - Kasada, Minoru A1 - Berger, Stella A. A1 - Nejstgaard, Jens Christian A1 - Ryo, Masahiro A1 - Lischeid, Gunnar A1 - Gessner, Mark O. A1 - Wollrab, Sabine A1 - Grossart, Hans-Peter T1 - From microbes to mammals: Pond biodiversity homogenization across different land-use types in an agricultural landscape JF - Ecological monographs N2 - Local biodiversity patterns are expected to strongly reflect variation in topography, land use, dispersal boundaries, nutrient supplies, contaminant spread, management practices, and other anthropogenic influences. Contrary to this expectation, studies focusing on specific taxa revealed a biodiversity homogenization effect in areas subjected to long-term intensive industrial agriculture. We investigated whether land use affects biodiversity levels and community composition (alpha- and beta-diversity) in 67 kettle holes (KH) representing small aquatic islands embedded in the patchwork matrix of a largely agricultural landscape comprising grassland, forest, and arable fields. These KH, similar to millions of standing water bodies of glacial origin, spread across northern Europe, Asia, and North America, are physico-chemically diverse and differ in the degree of coupling with their surroundings. We assessed aquatic and sediment biodiversity patterns of eukaryotes, Bacteria, and Archaea in relation to environmental features of the KH, using deep-amplicon-sequencing of environmental DNA (eDNA). First, we asked whether deep sequencing of eDNA provides a representative picture of KH aquatic biodiversity across the Bacteria, Archaea, and eukaryotes. Second, we investigated if and to what extent KH biodiversity is influenced by the surrounding land use. We hypothesized that richness and community composition will greatly differ in KH from agricultural land use compared with KH in grasslands and forests. Our data show that deep eDNA amplicon sequencing is useful for in-depth assessments of cross-domain biodiversity comprising both micro- and macro-organisms, but has limitations with respect to single-taxa conservation studies. Using this broad method, we show that sediment eDNA, integrating several years to decades, depicts the history of agricultural land-use intensification. Aquatic biodiversity was best explained by seasonality, whereas land-use type explained little of the variation. We concluded that, counter to our hypothesis, land use intensification coupled with landscape wide nutrient enrichment (including atmospheric deposition), groundwater connectivity between KH and organismal (active and passive) dispersal in the tight network of ponds, resulted in a biodiversity homogenization in the KH water, leveling off today's detectable differences in KH biodiversity between land-use types. These findings have profound implications for measures and management strategies to combat current biodiversity loss in agricultural landscapes worldwide. KW - biodiversity homogenization KW - eDNA KW - intensive agriculture KW - kettle hole; KW - land use Y1 - 2022 U6 - https://doi.org/10.1002/ecm.1523 SN - 0012-9615 SN - 1557-7015 VL - 92 IS - 3 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Mehner, Thomas A1 - Attermeyer, Katrin A1 - Brauns, Mario A1 - Brothers, Soren A1 - Hilt, Sabine A1 - Scharnweber, Inga Kristin A1 - Dorst, Renee Minavan A1 - Vanni, Michael J. A1 - Gaedke, Ursula T1 - Trophic transfer efficiency in lakes JF - Ecosystems N2 - Trophic transfer efficiency (TTE) is usually calculated as the ratio of production rates between two consecutive trophic levels. Although seemingly simple, TTE estimates from lakes are rare. In our review, we explore the processes and structures that must be understood for a proper lake TTE estimate. We briefly discuss measurements of production rates and trophic positions and mention how ecological efficiencies, nutrients (N, P) and other compounds (fatty acids) affect energy transfer between trophic levels and hence TTE. Furthermore, we elucidate how TTE estimates are linked with size-based approaches according to the Metabolic Theory of Ecology, and how food-web models can be applied to study TTE in lakes. Subsequently, we explore temporal and spatial heterogeneity of production and TTE in lakes, with a particular focus on the links between benthic and pelagic habitats and between the lake and the terrestrial environment. We provide an overview of TTE estimates from lakes found in the published literature. Finally, we present two alternative approaches to estimating TTE. First, TTE can be seen as a mechanistic quantity informing about the energy and matter flow between producer and consumer groups. This approach is informative with respect to food-web structure, but requires enormous amounts of data. The greatest uncertainty comes from the proper consideration of basal production to estimate TTE of omnivorous organisms. An alternative approach is estimating food-chain and food-web efficiencies, by comparing the heterotrophic production of single consumer levels or the total sum of all heterotrophic production including that of heterotrophic bacteria to the total sum of primary production. We close the review by pointing to a few research questions that would benefit from more frequent and standardized estimates of TTE in lakes. KW - stoichiometry KW - production rates KW - trophic position KW - fatty acids KW - land-water coupling KW - food-web models Y1 - 2022 U6 - https://doi.org/10.1007/s10021-022-00776-3 SN - 1432-9840 SN - 1435-0629 VL - 25 IS - 8 SP - 1628 EP - 1652 PB - Springer CY - New York ER - TY - JOUR A1 - Zappa, Luca A1 - Schlaffer, Stefan A1 - Brocca, Luca A1 - Vreugdenhil, Mariette A1 - Nendel, Claas A1 - Dorigo, Wouter T1 - How accurately can we retrieve irrigation timing and water amounts from (satellite) soil moisture? JF - International journal of applied earth observation and geoinformation N2 - While ensuring food security worldwide, irrigation is altering the water cycle and generating numerous environmental side effects. As detailed knowledge about the timing and the amounts of water used for irrigation over large areas is still lacking, remotely sensed soil moisture has proved potential to fill this gap. However, the spatial resolution and revisit time of current satellite products represent a major limitation to accurately estimating irrigation. This work aims to systematically quantify their impact on the retrieved irrigation information, hence assessing the value of satellite soil moisture for estimating irrigation timing and water amounts. In a real-world experiment, we modeled soil moisture using actual irrigation and meteorological data, obtained from farmers and weather stations, respectively. Modeled soil moisture was compared against various remotely sensed products differing in terms of spatio-temporal resolution to test the hypothesis that high-resolution observations can disclose the irrigation signal from individual fields while coarse-scale satellite products cannot. Then, in a synthetic experiment, we systematically investigated the effect of soil moisture spatial and temporal resolution on the accuracy of irrigation estimates. The analysis was further elaborated by considering different irrigation scenarios and by adding realistic amounts of random errors in the soil moisture time series. We show that coarse-scale remotely sensed soil moisture products achieve higher correlations with rainfed simulations, while high-resolution satellite observations agree significantly better with irrigated simulations, suggesting that high-resolution satellite soil moisture can inform on field-scale (similar to 40 ha) irrigation. A thorough analysis of the synthetic dataset showed that satisfactory results, both in terms of detection (F-score > 0.8) and quantification (Pearson's correlation > 0.8), are found for noise-free soil moisture observations either with a temporal sampling up to 3 days or if at least one-third of the pixel covers the irrigated field(s). However, irrigation water amounts are systematically underestimated for temporal samplings of more than one day, and decrease proportionally to the spatial resolution, i.e., coarsening the pixel size leads to larger irrigation underestimations. Although lower spatial and temporal resolutions decrease the detection and quantification accuracies (e.g., R between 0.6 and 1 depending on the irrigation rate and spatio-temporal resolution), random errors in the soil moisture time series have a stronger negative impact (Pearson R always smaller than 0.85). As expected, better performances are found for higher irrigation rates, i.e. when more water is supplied during an irrigation event. Despite the potentially large underestimations, our results suggest that high-resolution satellite soil moisture has the potential to track and quantify irrigation, especially over regions where large volumes of irrigation water are applied to the fields, and given that low errors affect the soil moisture observations. KW - remote sensing KW - soil moisture KW - irrigation KW - detection KW - quantification KW - sentinel-1 Y1 - 2022 U6 - https://doi.org/10.1016/j.jag.2022.102979 SN - 1569-8432 SN - 1872-826X VL - 113 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Hagberg, Linda A1 - Celemin, Enrique A1 - Irisarri, Iker A1 - Hawlitschek, Oliver A1 - Bella, Jose L. A1 - Mott, Tami A1 - Pereira, Ricardo J. T1 - Extensive introgression at late stages of species formation BT - insights from grasshopper hybrid zones JF - Molecular ecology N2 - The process of species formation is characterized by the accumulation of multiple reproductive barriers. The evolution of hybrid male sterility, or Haldane's rule, typically characterizes later stages of species formation, when reproductive isolation is strongest. Yet, understanding how quickly reproductive barriers evolve and their consequences for maintaining genetic boundaries between emerging species remains a challenging task because it requires studying taxa that hybridize in nature. Here, we address these questions using the meadow grasshopper Pseudochorthippus parallelus, where populations that show multiple reproductive barriers, including hybrid male sterility, hybridize in two natural hybrid zones. Using mitochondrial data, we infer that such populations diverged some 100,000 years ago, at the beginning of the last glacial cycle in Europe. Nuclear data show that contractions at multiple glacial refugia, and post-glacial expansions have facilitated genetic differentiation between lineages that today interact in hybrid zones. We find extensive introgression throughout the sampled species range, irrespective of the current strength of reproductive isolation. Populations exhibiting hybrid male sterility in two hybrid zones show repeatable patterns of genomic differentiation, consistent with shared genomic constraints affecting ancestral divergence or with the role of those regions in reproductive isolation. Together, our results suggest that reproductive barriers that characterize late stages of species formation can evolve relatively quickly, particularly when associated with strong demographic changes. Moreover, we show that such barriers persist in the face of extensive gene flow, allowing future studies to identify associated genomic regions. KW - Haldane's rule KW - hybridization KW - Pseudochorthippus parallelus KW - speciation KW - sterility Y1 - 2022 U6 - https://doi.org/10.1111/mec.16406 SN - 0962-1083 SN - 1365-294X VL - 31 IS - 8 SP - 2384 EP - 2399 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Moradian, Hanieh A1 - Roch, Toralf A1 - Anthofer, Larissa A1 - Lendlein, Andreas A1 - Gossen, Manfred T1 - Chemical modification of uridine modulates mRNA-mediated proinflammatory and antiviral response in primary human macrophages JF - Molecular therapy N2 - In vitro transcribed (IVT)-mRNA has been accepted as a promising therapeutic modality. Advances in facile and rapid production technologies make IVT-mRNA an appealing alternative to protein- or virus-based medicines. Robust expression levels, lack of genotoxicity, and their manageable immunogenicity benefit its clinical applicability. We postulated that innate immune responses of therapeutically relevant human cells can be tailored or abrogated by combinations of 5'-end and internal IVT-mRNA modifications. Using primary human macrophages as targets, our data show the particular importance of uridine modifications for IVT-mRNA performance. Among five nucleotide modification schemes tested, 5-methoxy-uridine outperformed other modifications up to 4-fold increased transgene expression, triggering moderate proinflammatory and non-detectable antiviral responses. Macrophage responses against IVT-mRNAs exhibiting high immunogenicity (e.g., pseudouridine) could be minimized upon HPLC purification. Conversely, 5'-end modifications had only modest effects on mRNA expression and immune responses. Our results revealed how the uptake of chemically modified IVT-mRNA impacts human macrophages, responding with distinct patterns of innate immune responses concomitant with increased transient transgene expression. We anticipate our findings are instrumental to predictively address specific cell responses required for a wide range of therapeutic applications from eliciting controlled immunogenicity in mRNA vaccines to, e.g., completely abrogating cell activation in protein replacement therapies. Y1 - 2022 U6 - https://doi.org/10.1016/j.omtn.2022.01.004 SN - 2162-2531 VL - 27 SP - 854 EP - 869 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Kamali, Bahareh A1 - Stella, Tommaso A1 - Berg-Mohnicke, Michael A1 - Pickert, Jürgen A1 - Groh, Jannis A1 - Nendel, Claas T1 - Improving the simulation of permanent grasslands across Germany by using multi-objective uncertainty-based calibration of plant-water dynamics JF - European journal of agronomy N2 - The dynamics of grassland ecosystems are highly complex due to multifaceted interactions among their soil, water, and vegetation components. Precise simulations of grassland productivity therefore rely on accurately estimating a variety of parameters that characterize different processes of these systems. This study applied three calibration schemes - a Single-Objective (SO-SUFI2), a Multi-Objective Pareto (MO-Pareto), and, a novel Uncertainty-Based Multi-Objective (MO-SUFI2) - to estimate the parameters of MONICA (Model for Nitrogen and Carbon Simulation) agro-ecosystem model in grassland ecosystems across Germany. The MO-Pareto model is based on a traditional Pareto optimality concept, while the MO-SUFI2 optimizes multiple target variables considering their level of prediction uncertainty. We used measurements of leaf area index, aboveground biomass, and soil moisture from experimental data at five sites with different intensities of cutting regimes (from two to five cutting events per season) to evaluate model performance. Both MO-Pareto and MO-SUFI2 outperformed SO-SUFI2 during calibration and validation. The comparison of the two MO approaches shows that they do not necessarily conflict with each other, but MO-SUFI2 provides complementary information for better estimations of model parameter uncertainty. We used the obtained parameter ranges to simulate grassland productivity across Germany under different cutting regimes and quantified the uncertainty associated with estimated productivity across regions. The results showed higher uncertainty in intensively managed grasslands compared to extensively managed grasslands, partially due to a lack of high-resolution input information concerning cutting dates. Furthermore, the additional information on the quantified uncertainty provided by our proposed MO-SUFI2 method adds deeper insights on confidence levels of estimated productivity. Benefiting from additional management data collected at high resolution and ground measurements on the composition of grassland species mixtures appear to be promising solutions to reduce uncertainty and increase model reliability. KW - intensively managed grasslands KW - extensively managed grasslands KW - grassland productivity KW - pareto optimality Y1 - 2022 U6 - https://doi.org/10.1016/j.eja.2022.126464 SN - 1161-0301 SN - 1873-7331 VL - 134 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Zielhofer, Christoph A1 - Schmidt, Johannes A1 - Reiche, Niklas A1 - Tautenhahn, Marie A1 - Ballasus, Helen A1 - Burkart, Michael A1 - Linstädter, Anja A1 - Dietze, Elisabeth A1 - Kaiser, Knut A1 - Mehler, Natascha T1 - The lower Havel River Region (Brandenburg, Germany) BT - a 230-Year-Long historical map record indicates a decrease in surface water areas and groundwater levels JF - Water N2 - Instrumental data show that the groundwater and lake levels in Northeast Germany have decreased over the past decades, and this process has accelerated over the past few years. In addition to global warming, the direct influence of humans on the local water balance is suspected to be the cause. Since the instrumental data usually go back only a few decades, little is known about the multidecadal to centennial-scale trend, which also takes long-term climate variation and the long-term influence by humans on the water balance into account. This study aims to quantitatively reconstruct the surface water areas in the Lower Havel Inner Delta and of adjacent Lake Gulpe in Brandenburg. The analysis includes the calculation of surface water areas from historical and modern maps from 1797 to 2020. The major finding is that surface water areas have decreased by approximately 30% since the pre-industrial period, with the decline being continuous. Our data show that the comprehensive measures in Lower Havel hydro-engineering correspond with groundwater lowering that started before recent global warming. Further, large-scale melioration measures with increasing water demands in the upstream wetlands beginning from the 1960s to the 1980s may have amplified the decline in downstream surface water areas. KW - long-term hydrological changes KW - historical maps KW - review of written KW - sources KW - preindustrial to industrial period KW - hydro-engineering history; KW - effects of global warming KW - drying trend KW - wetlands KW - drainage works to KW - create cropland KW - Lower Havel River Region KW - Brandenburg KW - Germany Y1 - 2022 U6 - https://doi.org/10.3390/w14030480 SN - 2073-4441 VL - 14 IS - 3 PB - MDPI CY - Basel ER - TY - JOUR A1 - Stelbrink, Björn A1 - von Rintelen, Thomas A1 - Richter, Kirsten A1 - Finstermeier, Knut A1 - Frahnert, Sylke A1 - Cracraft, Joel A1 - Hofreiter, Michael T1 - Insights into the geographical origin and phylogeographical patterns of Paradisaea birds-of-paradise JF - Zoological journal of the Linnean Society N2 - Birds-of-paradise represent a textbook example for geographical speciation and sexual selection. Perhaps the most iconic genus is Paradisaea, which is restricted to New Guinea and a few surrounding islands. Although several species concepts have been applied in the past to disentangle the different entities within this genus, no attempt has been made so far to uncover phylogeographical patterns based on a genetic dataset that includes multiple individuals per species. Here, we applied amplicon sequencing for the mitochondrial fragment Cytb for a total of 69 museum specimens representing all seven Paradisaea species described and inferred both phylogenetic relationships and colonization pathways across the island. Our analyses show that the most recent common ancestor of the diverging lineages within Paradisaea probably originated in the Late Miocene in the eastern part of the Central Range and suggest that tectonic processes played a key role in shaping the diversification and distribution of species. All species were recovered as monophyletic, except for those within the apoda-minor-raggiana clade, which comprises the allopatric and parapatric species P. apoda, P. minor and P. raggiana. The comparatively young divergence times, together with possible instances of mitochondrial introgression and incomplete lineage sorting, suggest recent speciation in this clade. KW - amplicon sequencing KW - Cytb KW - historical DNA KW - molecular clock KW - molecular phylogeny KW - museomics KW - New Guinea KW - Paradisaeidae Y1 - 2022 U6 - https://doi.org/10.1093/zoolinnean/zlac010 SN - 0024-4082 SN - 1096-3642 VL - 196 IS - 4 SP - 1394 EP - 1407 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Andreev, Andrei A1 - Nazarova, Larisa B. A1 - Lenz, Marlene M. A1 - Böhmer, Thomas A1 - Syrykh, Ludmila A1 - Wagner, Bernd A1 - Melles, Martin A1 - Pestryakova, Luidmila A. A1 - Herzschuh, Ulrike T1 - Late Quaternary paleoenvironmental reconstructions from sediments of Lake Emanda (Verkhoyansk Mountains, East Siberia) JF - Journal of quaternary science : JQS N2 - Continuous pollen and chironomid records from Lake Emanda (65 degrees 17'N, 135 degrees 45'E) provide new insights into the Late Quaternary environmental history of the Yana Highlands (Yakutia). Larch forest with shrubs (alders, pines, birches) dominated during the deposition of the lowermost sediments suggesting its Early Weichselian [Marine Isotope Stage (MIS) 5] age. Pollen- and chironomid-based climate reconstructions suggest July temperatures (T-July) slightly lower than modern. Gradually increasing amounts of herb pollen and cold stenotherm chironomid head capsules reflect cooler and drier environments, probably during the termination of MIS 5. T-July dropped to 8 degrees C. Mostly treeless vegetation is reconstructed during MIS 3. Tundra and steppe communities dominated during MIS 2. Shrubs became common after similar to 14.5 ka BP but herb-dominated habitats remained until the onset of the Holocene. Larch forests with shrub alder and dwarf birch dominated after the Holocene onset, ca. 11.7 ka BP. Decreasing amounts of shrub pollen during the Lateglacial are assigned to the Older Dryas and Younger Dryas with T-July similar to 7.5 degrees C. T-July increased up to 13 degrees C. Shrub stone pine was present after similar to 7.5 ka BP. The vegetation has been similar to modern since ca. 5.8 ka BP. Chironomid diversity and concentration in the sediments increased towards the present day, indicating the development of richer hydrobiological communities in response to the Holocene thermal maximum. KW - chironomids KW - environmental reconstructions KW - Late Quaternary KW - pollen Y1 - 2022 U6 - https://doi.org/10.1002/jqs.3419 SN - 0267-8179 SN - 1099-1417 VL - 37 IS - 5 SP - 884 EP - 899 PB - Wiley CY - New York, NY [u.a.] ER - TY - JOUR A1 - Souto-Veiga, Rodrigo A1 - Groeneveld, Juergen A1 - Enright, Neal J. A1 - Fontaine, Joseph B. A1 - Jeltsch, Florian T1 - Declining pollination success reinforces negative climate and fire change impacts in a serotinous, fire-killed plant JF - Plant ecology : an international journal N2 - Climate change projections predict that Mediterranean-type ecosystems (MTEs) are becoming hotter and drier and that fires will become more frequent and severe. While most plant species in these important biodiversity hotspots are adapted to hot, dry summers and recurrent fire, the Interval Squeeze framework suggests that reduced seed production (demographic shift), reduced seedling establishment after fire (post fire recruitment shift), and reduction in the time between successive fires (fire interval shift) will threaten fire killed species under climate change. One additional potential driver of accelerated species decline, however, has not been considered so far: the decrease in pollination success observed in many ecosystems worldwide has the potential to further reduce seed accumulation and thus population persistence also in these already threatened systems. Using the well-studied fire-killed and serotinous shrub species Banksia hookeriana as an example, we apply a new spatially implicit population simulation model to explore population dynamics under past (1988-2002) and current (2003-2017) climate conditions, deterministic and stochastic fire regimes, and alternative scenarios of pollination decline. Overall, model results suggest that while B. hookeriana populations were stable under past climate conditions, they will not continue to persist under current (and prospective future) climate. Negative effects of climatic changes and more frequent fires are reinforced by the measured decline in seed set leading to further reduction in the mean persistence time by 12-17%. These findings clearly indicate that declining pollination rates can be a critical factor that increases further the pressure on the persistence of fire-killed plants. Future research needs to investigate whether other fire-killed species are similarly threatened, and if local population extinction may be compensated by recolonization events, facilitating persistence in spatially structured meta-communities. KW - climate change KW - fire frequency KW - interval squeeze KW - pollination KW - process-based simulation model KW - mediterranean-type ecosystem Y1 - 2022 U6 - https://doi.org/10.1007/s11258-022-01244-7 SN - 1385-0237 SN - 1573-5052 VL - 223 IS - 7 SP - 863 EP - 881 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Blickensdörfer, Lukas A1 - Schwieder, Marcel A1 - Pflugmacher, Dirk A1 - Nendel, Claas A1 - Erasmi, Stefan A1 - Hostert, Patrick T1 - Mapping of crop types and crop sequences with combined time series of Sentinel-1, Sentinel-2 and Landsat 8 data for Germany JF - Remote sensing of environment : an interdisciplinary journal N2 - Monitoring agricultural systems becomes increasingly important in the context of global challenges like climate change, biodiversity loss, population growth, and the rising demand for agricultural products. High-resolution, national-scale maps of agricultural land are needed to develop strategies for future sustainable agriculture. However, the characterization of agricultural land cover over large areas and for multiple years remains challenging due to the locally diverse and temporally variable characteristics of cultivated land. We here propose a workflow for generating national agricultural land cover maps on a yearly basis that accounts for varying environmental conditions. We tested the approach by mapping 24 agricultural land cover classes in Germany for the three years 2017, 2018, and 2019, in which the meteorological conditions strongly differed. We used a random forest classifier and dense time series data from Sentinel-2 and Landsat 8 in combination with monthly Sentinel-1 composites and environmental data and evaluated the relative importance of optical, radar, and environmental data. Our results show high overall accuracy and plausible class accuracies for the most dominant crop types across different years despite the strong inter-annual meteorological variability and the presence of drought and nondrought years. The maps show high spatial consistency and good delineation of field parcels. Combining optical, SAR, and environmental data increased overall accuracies by 6% to 10% compared to single sensor approaches, in which optical data outperformed SAR. Overall accuracy ranged between 78% and 80%, and the mapped areas aligned well with agricultural statistics at the regional and national level. Based on the multi-year dataset we mapped major crop sequences of cereals and leaf crops. Most crop sequences were dominated by winter cereals followed by summer cereals. Monocultures of summer cereals were mainly revealed in the Northwest of Germany. We showcased that high spatial and thematic detail in combination with annual mapping will stimulate research on crop cycles and studies to assess the impact of environmental policies on management decisions. Our results demonstrate the capabilities of integrated optical time series and SAR data in combination with variables describing local and seasonal environmental conditions for annual large-area crop type mapping. KW - agricultural land cover KW - analysis-ready data KW - time series KW - large-area mapping KW - optical remote sensing KW - SAR KW - big data KW - multi-sensor Y1 - 2022 U6 - https://doi.org/10.1016/j.rse.2021.112831 SN - 0034-4257 SN - 1879-0704 VL - 269 PB - Elsevier CY - New York ER - TY - JOUR A1 - Hu, Ting-Li A1 - Cheng, Feng A1 - Xu, Zhen A1 - Chen, Zhong-Zheng A1 - Yu, Lei A1 - Ban, Qian A1 - Li, Chun-Lin A1 - Pan, Tao A1 - Zhang, Bao-Wei T1 - Molecular and morphological evidence for a new species of the genus Typhlomys (Rodentia: Platacanthomyidae) JF - Zoological research : ZR = Dongwuxue-yanjiu : jikan / published by Kunming Institute of Zoology, Chinese Academy of Sciences, Zhongguo Kexueyuan Kunming Dongwu Yanjiusuo zhuban, Dongwuxue-yanjiu Bianji Weiyuanhui bianji N2 - In this study, we reassessed the taxonomic position of Typhlomys (Rodentia: Platacanthomyidae) from Huangshan, Anhui, China, based on morphological and molecular evidence. Results suggested that Typhlomys is comprised of up to six species, including four currently recognized species ( Typhlomys cinereus, T. chapensis, T. daloushanensis, and T. nanus), one unconfirmed candidate species, and one new species ( Typhlomys huangshanensis sp. nov.). Morphological analyses further supported the designation of the Huangshan specimens found at mid-elevations in the southern Huangshan Mountains (600 m to 1 200 m a.s.l.) as a new species. KW - Morphology KW - Phylogenetics KW - Species delimitation KW - Taxonomy Y1 - 2021 U6 - https://doi.org/10.24272/j.issn.2095-8137.2020.132 SN - 2095-8137 VL - 42 IS - 1 SP - 100 EP - 107 PB - Yunnan Renmin Chubanshe CY - Kunming ER - TY - JOUR A1 - Tung, Wing Tai A1 - Sun, Xianlei A1 - Wang, Weiwei A1 - Xu, Xun A1 - Ma, Nan A1 - Lendlein, Andreas T1 - Structure, mechanical properties and degradation behavior of electrospun PEEU fiber meshes and films JF - MRS advances : a journal of the Materials Research Society (MRS) N2 - The capability of a degradable implant to provide mechanical support depends on its degradation behavior. Hydrolytic degradation was studied for a polyesteretherurethane (PEEU70), which consists of poly(p-dioxanone) (PPDO) and poly(epsilon-caprolactone) (PCL) segments with a weight ratio of 70:30 linked by diurethane junction units. PEEU70 samples prepared in the form of meshes with average fiber diameters of 1.5 mu m (mesh1.5) and 1.2 mu m (mesh1.2), and films were sterilized and incubated in PBS at 37 degrees C with 5 vol% CO2 supply for 1 to 6 weeks. Degradation features, such as cracks or wrinkles, became apparent from week 4 for all samples. Mass loss was found to be 11 wt%, 6 wt%, and 4 wt% for mesh1.2, mesh1.5, and films at week 6. The elongation at break decreased to under 20% in two weeks for mesh1.2. In case of the other two samples, this level of degradation was achieved after 4 weeks. The weight average molecular weight of both PEEU70 mesh and film samples decreased to below 30 kg/mol when elongation at break dropped below 20%. The time period of sustained mechanical stability of PEEU70-based meshes depends on the fiber diameter and molecular weight. Y1 - 2021 U6 - https://doi.org/10.1557/s43580-020-00001-0 SN - 2059-8521 VL - 6 IS - 10 SP - 276 EP - 282 PB - Springer Nature Switzerland AG CY - Cham ER - TY - JOUR A1 - Xu, Xun A1 - Nie, Yan A1 - Wang, Weiwei A1 - Ullah, Imran A1 - Tung, Wing Tai A1 - Ma, Nan A1 - Lendlein, Andreas T1 - Generation of 2.5D lung bud organoids from human induced pluripotent stem cells JF - Clinical hemorheology and microcirculation : blood flow and vessels N2 - Human induced pluripotent stem cells (hiPSCs) are a promising cell source to generate the patient-specific lung organoid given their superior differentiation potential. However, the current 3D cell culture approach is tedious and time-consuming with a low success rate and high batch-to-batch variability. Here, we explored the establishment of lung bud organoids by systematically adjusting the initial confluence levels and homogeneity of cell distribution. The efficiency of single cell seeding and clump seeding was compared. Instead of the traditional 3D culture, we established a 2.5D organoid culture to enable the direct monitoring of the internal structure via microscopy. It was found that the cell confluence and distribution prior to induction were two key parameters, which strongly affected hiPSC differentiation trajectories. Lung bud organoids with positive expression of NKX 2.1, in a single-cell seeding group with homogeneously distributed hiPSCs at 70% confluence (SC 70% hom) or a clump seeding group with heterogeneously distributed cells at 90% confluence (CL 90% het), can be observed as early as 9 days post induction. These results suggest that a successful lung bud organoid formation with single-cell seeding of hiPSCs requires a moderate confluence and homogeneous distribution of cells, while high confluence would be a prominent factor to promote the lung organoid formation when seeding hiPSCs as clumps. 2.5D organoids generated with defined culture conditions could become a simple, efficient, and valuable tool facilitating drug screening, disease modeling and personalized medicine. KW - lung organoid KW - human induced pluripotent stem cell KW - cell culture Y1 - 2021 U6 - https://doi.org/10.3233/CH-219111 SN - 1386-0291 SN - 1875-8622 VL - 79 IS - 1 SP - 217 EP - 230 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - Malacrinò, Antonino A1 - Abdelfattah, Ahmed A1 - Berg, Gabriele A1 - Benitez, Maria-Soledad A1 - Bennett, Alison E. A1 - Böttner, Laura A1 - Xu, Shuqing A1 - Schena, Leonardo T1 - Exploring microbiomes for plant disease management JF - Biological control : theory and application in pest management N2 - Microbiome science is revolutionizing many concepts of plant biology, ecology, and evolution. Understanding plant microbiomes is key to developing solutions that protect crop health without impacting the environment. In this perspective article, we highlight the importance of both the structure and functions of plant-associated microbial communities in protecting their host from pathogens. These new findings have a high potential to aid biocontrol programs and to replace traditional chemical products, guiding the transition towards a sustainable production. KW - microbiota KW - metagenomics KW - plant pathogen KW - plant protection Y1 - 2022 U6 - https://doi.org/10.1016/j.biocontrol.2022.104890 SN - 1049-9644 SN - 1090-2112 VL - 169 PB - Academic Press CY - San Diego, Calif. ER - TY - JOUR A1 - Rutschmann, Sereina A1 - Chen, Ping A1 - Zhou, Changfa A1 - Monaghan, Michael T. T1 - Three mitochondrial genomes of early-winged insects (Ephemeroptera: Baetidae and Leptophlebiidae) JF - Mitochondrial DNA Part B N2 - Mayflies (Ephemeroptera) are a semi-aquatic insect order with comparatively few genomic data available despite their phylogenetic position at the root of the winged-insects and possession of ancestral traits. Here, we provide three mitochondrial genomes (mtgenomes) from representatives of the two most species-rich families, Baetis rutilocylindratus and Cloeon dipterum (Baetidae), and Habrophlebiodes zijinensis (Leptophlebiidae). All mtgenomes had a complete set of 13 protein-coding genes and a conserved orientation except for two inverted tRNAs in H. zijinensis. Phylogenetic reconstructions using 21 mayfly mtgenomes and representatives of seven additional orders recovered both Baetidae and Leptophlebiidae as well supported monophyletic clades, with Ephemeroptera as the sister-taxon to all other winged insects (i.e. Odonata and Neoptera). KW - Baetis KW - Cloeon KW - Habrophlebiodes KW - mayfly KW - mitochondrial phylogeny Y1 - 2021 U6 - https://doi.org/10.1080/23802359.2021.1974966 SN - 2380-2359 VL - 6 IS - 10 SP - 2969 EP - 2971 PB - Routledge, Taylor & Francis Group CY - Abingdon ER -