Refine
Year of publication
- 2018 (326) (remove)
Document Type
- Article (222)
- Doctoral Thesis (34)
- Postprint (30)
- Review (20)
- Other (16)
- Habilitation Thesis (3)
- Conference Proceeding (1)
Keywords
- Arabidopsis (6)
- nitrogen deposition (5)
- plasticity (5)
- Arabidopsis thaliana (4)
- adaptation (4)
- ancient DNA (4)
- biodiversity (4)
- climate change (4)
- competition (4)
- inheritance (4)
Institute
- Institut für Biochemie und Biologie (326) (remove)
Plants encounter biotic and abiotic stresses many times during their life cycle and this limits their productivity. Moderate heat stress (HS) primes a plant to survive higher temperatures that are lethal in the naïve state. Once temperature stress subsides, the memory of the priming event is actively retained for several days preparing the plant to better cope with recurring HS. Recently, chromatin regulation at different levels has been implicated in HS memory. Here, we report that the chromatin protein BRUSHY1 (BRU1)/TONSOKU/MGOUN3 plays a role in the HS memory in Arabidopsis thaliana. BRU1 is also involved in transcriptional gene silencing and DNA damage repair. This corresponds with the functions of its mammalian orthologue TONSOKU‐LIKE/NFΚBIL2. During HS memory, BRU1 is required to maintain sustained induction of HS memory‐associated genes, whereas it is dispensable for the acquisition of thermotolerance. In summary, we report that BRU1 is required for HS memory in A. thaliana, and propose a model where BRU1 mediates the epigenetic inheritance of chromatin states across DNA replication and cell division.
Thigmomorphogenesis
(2018)
Controlled regulation of plant growth is a general prerequisite for the production of marketable ornamental plants. Consumers as well as retailers prefer stronger, more compact plants with greener leaves as these not only better meet a certain desired visual quality but also allow for a maximization of production per unit area as well as facilitation of packaging and transport. The same applies for the production of young vegetable plants. Special attention is paid to solid, compact and resilient plants that survive transport and planting without any problems. During the last decades plant growth control has mainly been achieved through the application of chemical plant growth regulators that generally interfere with the function of growth regulating hormones. However, there is an increasing demand to replace chemical treatments by other means such as the modulation of growth conditions, including temperature, light and fertilization. Alternatively, the application of mechanical stimulation has been shown to induce plant responses that yield some of the commercially relevant phenotypes including increased compactness, higher girth, darker leaves and a delay in flowering. The ability of plants to sense and respond to mechanical stimuli is an adaptive trait associated with increased fitness in many environmental settings. Mechanical stimulation in nature occurs e.g. through wind, rain, neighboring plants or predatory animals and induces a range of morphogenic responses that have been summarized under the term thigmomorphogenesis. We are only just about to begin to understand the molecular mechanisms underlying mechanosensing and the associated morphogenic changes in plants. However, a number of examples suggest that mechanical stimulation applied in a greenhouse setting can be used to alter plant growth in order to produce marketable plants. In this review will briefly summarize the current knowledge concerning the biological principles of thigmomorphogenesis and discuss the potential of mechanical growth regulation in commercial plant production especially with respect to organic horticulture.
Remote sensing, which is a common method to examine land-use/land-cover (LULC) changes, could be useful in the analysis of livestock ecosystem transformations. In the last two decades, before Landsat images were free, developing countries could not afford monitoring through remote sensing because of the high cost of acquiring satellite imagery and commercial software. However, Landsat time series nowadays allows the characterization of changes in vegetation across large areas over time. The aim of this study is to analyse the LULC changes affecting forest frontiers and traditional silvopastoral systems (TSPS) in a representative livestock area of Nicaragua. Nearly cloud-free Landsat scenes - a Landsat 5 Thematic Mapper (TM) scene from 1986 and a Landsat 8 Operational Land Imager (OLI) scene from 2015 - have been the data sets used in the study. A process chain following a four-step definition of the remote-sensing process was conceptually developed and implemented based onfree open source software components and by applying the random forest (RF) algorithm. A conceptual LULC classification scheme representing TSPS was developed. Although the imagery shows a heterogeneous surface cover and mixed pixels, it is possible to achieve promising classification results with the RF algorithm with out-of-the-bag (OOB) errors below 13% for both images along with an overall accuracy level of 85.9% for the 2015 subset and 85.2% for the 1986 subset. The classification shows that from 1986 to 2015 (29years) the intervened secondary forest (ISF) increased 2.6 times, whereas the degraded pastures decreased by 34.5%. The livestock landscape in Matiguas is in a state of constant transformation, but the main changes head towards the positive direction of tree-cover recovery and an increased number of areas of natural regeneration.
The plant cell wall surrounds and protects the cells. To divide, plant cells must synthesize a new cell wall to separate the two daughter cells. The cell plate is a transient polysaccharide-based compartment that grows between daughter cells and gives rise to the new cell wall. Cellulose constitutes a key component of the cell wall, and mutants with defects in cellulose synthesis commonly share phenotypes with cytokinesis-defective mutants. However, despite the importance of cellulose in the cell plate and the daughter cell wall, many open questions remain regarding the timing and regulation of cellulose synthesis during cell division. These questions represent a critical gap in our knowledge of cell plate assembly, cell division and growth. Here, we review what is known about cellulose synthesis at the cell plate and in the newly formed cross-wall and pose key questions about the molecular mechanisms that govern these processes. We further provide an outlook discussing outstanding questions and possible future directions for this field of research.
Manganese (Mn) is an essential nutrient for intracellular activities; it functions as a cofactor for a variety of enzymes, including arginase, glutamine synthetase (GS), pyruvate carboxylase and Mn superoxide dismutase (Mn-SOD). Through these metalloproteins, Mn plays critically important roles in development, digestion, reproduction, antioxidant defense, energy production, immune response and regulation of neuronal activities. Mn deficiency is rare. In contrast Mn poisoning may be encountered upon overexposure to this metal. Excessive Mn tends to accumulate in the liver, pancreas, bone, kidney and brain, with the latter being the major target of Mn intoxication. Hepatic cirrhosis, polycythemia, hypermanganesemia, dystonia and Parkinsonism-like symptoms have been reported in patients with Mn poisoning. In recent years, Mn has come to the forefront of environmental concerns due to its neurotoxicity. Molecular mechanisms of Mn toxicity include oxidative stress, mitochondrial dysfunction, protein misfolding, endoplasmic reticulum (ER) stress, autophagy dysregulation, apoptosis, and disruption of other metal homeostasis. The mechanisms of Mn homeostasis are not fully understood. Here, we will address recent progress in Mn absorption, distribution and elimination across different tissues, as well as the intracellular regulation of Mn homeostasis in cells. We will conclude with recommendations for future research areas on Mn metabolism.
Second harmonic generation (SHG) is a nonlinear optical process that inherently generates signal in non-centrosymmetric materials, such as starch granules, and therefore can be used for label-free imaging. Both intensity and polarization of SHG are determined by material properties that are characterized by the nonlinear susceptibility tensor, ((2)). Examination of the tensor is performed for each focal volume of the image by measuring the outgoing polarization state of the SHG signal for a set of incoming laser beam polarizations. Mapping of nonlinear properties expressed as the susceptibility ratio reveals structural features including the organization of crystalline material within a single starch granule, and the distribution of structural properties in a population of granules. Isolated granules, as well as in situ starch, can be analyzed using polarimetric SHG microscopy. Due to the fast sample preparation and short imaging times, polarimetric SHG microscopy allows for a quick assessment of starch structure and permits rapid feedback for bioengineering applications. This article presents the basics of SHG theory and microscopy applications for starch-containing materials. Quantification of ultrastructural features within individual starch granules is described. New results obtained by polarization resolved SHG microscopy of starch granules are presented for various maize genotypes revealing heterogeneity within a single starch particle and between various granules.
Intraspecific trait variation (ITV) is thought to play a significant role in community assembly, but the magnitude and direction of its influence are not well understood. Although it may be critical to better explain population persistence, species interactions, and therefore biodiversity patterns, manipulating ITV in experiments is challenging. We therefore incorporated ITV into a trait‐ and individual‐based model of grassland community assembly by adding variation to the plants’ functional traits, which then drive life‐history tradeoffs. Varying the amount of ITV in the simulation, we examine its influence on pairwise‐coexistence and then on the species diversity in communities of different initial sizes. We find that ITV increases the ability of the weakest species to invade most, but that this effect does not scale to the community level, where the primary effect of ITV is to increase the persistence and abundance of the competitively‐average species. Diversity of the initial community is also of critical importance in determining ITV's efficacy; above a threshold of interspecific diversity, ITV does not increase diversity further. For communities below this threshold, ITV mainly helps to increase diversity in those communities that would otherwise be low‐diversity. These findings suggest that ITV actively maintains diversity by helping the species on the margins of persistence, but mostly in habitats of relatively low alpha and beta diversity.
Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics
(2018)
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.
Pace-of-life syndromes
(2018)
This introduction to the topical collection on Pace-of-life syndromes: a framework for the adaptive integration of behaviour, physiology, and life history provides an overview of conceptual, theoretical, methodological, and empirical progress in research on pace-of-life syndromes (POLSs) over the last decade. The topical collection has two main goals. First, we briefly describe the history of POLS research and provide a refined definition of POLS that is applicable to various key levels of variation (genetic, individual, population, species). Second, we summarise the main lessons learned from current POLS research included in this topical collection. Based on an assessment of the current state of the theoretical foundations and the empirical support of the POLS hypothesis, we propose (i) conceptual refinements of theory, particularly with respect to the role of ecology in the evolution of (sexual dimorphism in) POLS, and (ii) methodological and statistical approaches to the study of POLS at all major levels of variation. This topical collection further holds (iii) key empirical examples demonstrating how POLS structures may be studied in wild populations of (non) human animals, and (iv) a modelling paper predicting POLS under various ecological conditions. Future POLS research will profit from the development of more explicit theoretical models and stringent empirical tests of model assumptions and predictions, increased focus on how ecology shapes (sex-specific) POLS structures at multiple hierarchical levels, and the usage of appropriate statistical tests and study designs. Significance statement As an introduction to the topical collection, we summarise current conceptual, theoretical, methodological and empirical progress in research on pace-of-life syndromes (POLSs), a framework for the adaptive integration of behaviour, physiology and life history at multiple hierarchical levels of variation (genetic, individual, population, species). Mixed empirical support of POLSs, particularly at the within-species level, calls for an evaluation and refinement of the hypothesis. We provide a refined definition of POLSs facilitating testable predictions. Future research on POLSs will profit from the development of more explicit theoretical models and stringent empirical tests of model assumptions and predictions, increased focus on how ecology shapes (sex-specific) POLSs structures at multiple hierarchical levels and the usage of appropriate statistical tests and study designs.
Die Folgen einer lebensmittelbedingten Erkrankung sind zum Teil gravierend, insbesondere für Kinder und immunsupprimierte Menschen. Hierbei gehören Salmonella und Campylobacter zu den häufigsten Erregern, die verantwortlich für gastrointestinale Erkrankungen in Deutschland sind. Trotz umfassender Maßnahmen der EU zur Prävention und Bekämpfung von Salmonellen in Geflügelbeständen und der Lebensmittel-Industrie, wird von einem stagnierenden Trend von Infektionszahlen berichtet. Zoonose-Erreger wie Salmonellen können über Nutztiere in die Nahrungskette des Menschen gelangen, wodurch sich Infektionsherde schnell ausbreiten können. Dabei sind bestehende Präventionsstrategien für Geflügel vorhanden, die aber nicht auf den Menschen übertragbar sind. Folglich sind Diagnostik und Prävention in der Lebensmittelindustrie essentiell. Deshalb besteht ein hoher Bedarf für spezifische, sensitive und zuverlässige Nachweismethoden, die eine Point-of-care Diagnostik gewährleisten. Durch ein wachsendes Verständnis der wirtsspezifischen Faktoren von S. enterica Serovaren kann die Entwicklung sowohl neuartiger diagnostischer Methoden, als auch neuartiger Therapien und Impfstoffe maßgeblich vorangetrieben werden.
Infolgedessen wurde in dieser Arbeit ein infektionsähnliches in vitro Modell für S. Enteritidis etabliert und darauf basierend eine umfassende Untersuchung zur Identifizierung neuer Zielstrukturen für den Erreger durchgeführt. Während einer Salmonellen-Infektion ist die erste zelluläre Barriere im Wirt die Epithelschicht. Dementsprechend wurde eine humane Zelllinie (CaCo 2, Darmepithel) für die Pathogen-Wirt-Studie ausgewählt. Das Salmonellen-Transkriptom und morphologische Eigenschaften der Epithelzellen wurden in verschiedenen Phasen der Salmonellen-Infektion untersucht und mit bereits gut beschriebenen Virulenzfaktoren und Beobachtungen in Bezug gesetzt. Durch dieses Infektionsmodell konnte ein spezifischer Phänotyp für die intrazellulären Salmonellen in den Epithelzellen nachgewiesen werden. Zudem wurde aufgezeigt, dass bereits die Kultivierung in Flüssigmedium einen invasionsaktiven Zustand der Salmonellen erzeugt. Allerdings wurde durch die Kokultivierung mit Epithelzellen eine zusätzliche Expression relevanter Gene induziert, um eine effiziente Adhäsion und Transmembran-Transport zu gewährleisten. Letzterer ist charakteristisch für die intrazelluläre Limitierung von Nährstoffen und prägt den infektionsrelevanten Status. Unter Berücksichtigung dieser Faktoren ergab sich ein Phänotyp, der eindeutig Mechanismen zur Wirtsadaptation und möglicherweise auch Pathogenese aufzeigt. Die intrazellulären Bakterien müssen vom Wirt separiert werden, was ein wesentlicher Schritt für Pathogen-bestimmende Analysen ist. Hierbei wurde mithilfe einer Detergenz-basierten Lyse der eukaryotischen Zellmembran und differentieller Zentrifugation, der eukaryotische Eintrag minimal gehalten. Unter Verwendung der Virulenz-adaptierten Salmonellen wurden Untersuchungen in Hinblick auf die Identifizierung neuer Zielstrukturen für S. Enteritidis durchgeführt. Mithilfe eines immunologischen Screenings wurden neue potentielle Antigene entdeckt. Zu diesem Zweck wurden bakterielle cDNA-basierte Expressionsbibliotheken hergestellt, die durch eine vereinfachte Microarray-Anwendung ein Hochdurchsatzscreening von Proteinen als potentielle Binder ermöglichen. Folglich konnten neue unbeschriebene Proteine identifiziert werden, die sich durch eine Salmonella-Spezifität oder Membranständigkeit auszeichnen. Ebenso wurde ein Vergleich der im Screening identifizierten Proteine mit der Regulation der kodierenden Gene im infektionsähnlichen Modell durchgeführt. Dabei wurde deutlich, dass die Häufigkeit von Transkripten einen Einfluss auf die Verfügbarkeit in der cDNA-Bibliothek und folglich auch auf die Expressionsbibliothek nimmt. Angesichts eines Ungleichgewichts zwischen der Gesamtzahl protein-kodierender Gene in S. Enteritidis zu möglichen Klonen, die während des Microarray-Screenings untersucht werden können, besteht der Bedarf einer Anreicherung von Proteinen in der Expressionsbibliothek. Das infektionsähnliche Modell zeigte, dass nicht nur Virulenz-assoziierte, sondern auch Stress- und Metabolismus-relevante Gene hochreguliert werden. Durch die Konstruktion dieser spezifischen cDNA-Bibliotheken ist die Erkennung von charakteristischen molekularen Markern gegeben.
Weiterhin wurden anhand der Transkriptomanalyse spezifisch hochregulierte Gene identifiziert, die relevant für das intrazelluläre Überleben von S. Enteritidis in humanen Epithelzellen sind. Hiervon wurden drei Gene näher untersucht, indem ihr Einfluss im infektionsähnlichen Modell mittels entsprechender Gen-Knockout-Stämme analysiert wurde. Dabei wurde für eine dieser Mutanten ein reduziertes Wachstum in der späten intrazellulären Phase nachgewiesen. Weiterführende in vitro Analysen sind für die Charakterisierung des Knockout-Stamms notwendig, um den Einsatz als potenzielles Therapeutikum zu verifizieren.
Zusammenfassend wurde ein in vitro Infektionsmodell für S. Enteritidis etabliert, wodurch neue Zielstrukturen des Erregers identifiziert wurden. Diese sind für diagnostische oder therapeutische Anwendungen interessant. Das Modell lässt sich ebenso für andere intrazelluläre Pathogene übertragen und gewährleistet eine zuverlässige Identifizierung von potentiellen Antigenen.
1. Global pressures on freshwater ecosystems are high and rising. Viewed primarily as a resource for humans, current practices of water use have led to catastrophic declines in freshwater species and the degradation of freshwater ecosystems, including their genetic and functional diversity. Approximately three-quarters of the world's inland wetlands have been lost, one-third of the 28 000 freshwater species assessed for the International Union for Conservation of Nature (IUCN) Red List are threatened with extinction, and freshwater vertebrate populations are undergoing declines that are more rapid than those of terrestrial and marine species. This global loss continues unchecked, despite the importance of freshwater ecosystems as a source of clean water, food, livelihoods, recreation, and inspiration.
2. The causes of these declines include hydrological alterations, habitat degradation and loss, overexploitation, invasive species, pollution, and the multiple impacts of climate change. Although there are policy initiatives that aim to protect freshwater life, these are rarely implemented with sufficient conviction and enforcement. Policies that focus on the development and management of fresh waters as a resource for people almost universally neglect the biodiversity that they contain.
3. Here we introduce the Alliance for Freshwater Life, a global initiative, uniting specialists in research, data synthesis, conservation, education and outreach, and policymaking. This expert network aims to provide the critical mass required for the effective representation of freshwater biodiversity at policy meetings, to develop solutions balancing the needs of development and conservation, and to better convey the important role freshwater ecosystems play in human well-being. Through this united effort we hope to reverse this tide of loss and decline in freshwater biodiversity. We introduce several short- and medium-term actions as examples for making positive change, and invite individuals, organizations, authorities, and governments to join the Alliance for Freshwater Life.
Bridging metabolomics with plant phenotypic responses is challenging. Multivariate analyses account for the existing dependencies among metabolites, and regression models in particular capture such dependencies in search for association with a given trait. However, special care should be undertaken with metabolomics data. Here we propose a modeling workflow that considers all caveats imposed by such large data sets.
Maize is the cereal crop with the highest production worldwide, and its oil is a key energy resource. Improving the quantity and quality of maize oil requires a better understanding of lipid metabolism. To predict the function of maize genes involved in lipid biosynthesis, we assembled transcriptomic and lipidomic data sets from leaves of B73 and the high-oil line By804 in two distinct time-series experiments. The integrative analysis based on high-dimensional regularized regression yielded lipid-transcript associations indirectly validated by Gene Ontology and promoter motif enrichment analyses. The co-localization of lipid-transcript associations using the genetic mapping of lipid traits in leaves and seedlings of a B73 x By804 recombinant inbred line population uncovered 323 genes involved in the metabolism of phospholipids, galactolipids, sulfolipids and glycerolipids. The resulting association network further supported the involvement of 50 gene candidates in modulating levels of representatives from multiple acyl-lipid classes. Therefore, the proposed approach provides high-confidence candidates for experimental testing in maize and model plant species.
Maize (Zea mays L.) is a staple food whose production relies on seed stocks that largely comprise hybrid varieties. Therefore, knowledge about the molecular determinants of hybrid performance (HP) in the field can be used to devise better performing hybrids to address the demands for sustainable increase in yield. Here, we propose and test a classification-driven framework that uses metabolic profiles from in vitro grown young roots of parental lines from the Dent x Flint maize heterotic pattern to predict field HP. We identify parental analytes that best predict the metabolic inheritance patterns in 328 hybrids. We then demonstrate that these analytes are also predictive of field HP (0.64 >= r >= 0.79) and discriminate hybrids of good performance (accuracy of 87.50%). Therefore, our approach provides a cost-effective solution for hybrid selection programs.
Atmospheric nitrogen deposition on petals enhances seed quality of the forest herb Anemone nemorosa
(2018)
Elevated atmospheric input of nitrogen (N) is currently affecting plant biodiversity and ecosystem functioning. The growth and survival of numerous plant species is known to respond strongly to N fertilisation. Yet, few studies have assessed the effects of N deposition on seed quality and reproductive performance, which is an important life-history stage of plants. Here we address this knowledge gap by assessing the effects of atmospheric N deposition on seed quality of the ancient forest herb Anemone nemorosa using two complementary approaches. By taking advantage of the wide spatiotemporal variation in N deposition rates in pan-European temperate and boreal forests over 2years, we detected positive effects of N deposition on the N concentration (percentage N per unit seed mass, increased from 2.8% to 4.1%) and N content (total N mass per seed more than doubled) of A.nemorosa seeds. In a complementary experiment, we applied ammonium nitrate to aboveground plant tissues and the soil surface to determine whether dissolved N sources in precipitation could be incorporated into seeds. Although the addition of N to leaves and the soil surface had no effect, a concentrated N solution applied to petals during anthesis resulted in increased seed mass, seed N concentration and N content. Our results demonstrate that N deposition on the petals enhances bioaccumulation of N in the seeds of A.nemorosa. Enhanced atmospheric inputs of N can thus not only affect growth and population dynamics via root or canopy uptake, but can also influence seed quality and reproduction via intake through the inflorescences.
Understorey plant communities play a key role in the functioning of forest ecosystems. Under favourable environmental conditions, competitive understorey species may develop high abundances and influence important ecosystem processes such as tree regeneration. Thus, understanding and predicting the response of competitive understorey species as a function of changing environmental conditions is important for forest managers. In the absence of sufficient temporal data to quantify actual vegetation changes, space-for-time (SFT) substitution is often used, i.e. studies that use environmental gradients across space to infer vegetation responses to environmental change over time. Here we assess the validity of such SFT approaches and analysed 36 resurvey studies from ancient forests with low levels of recent disturbances across temperate Europe to assess how six competitive understorey plant species respond to gradients of overstorey cover, soil conditions, atmospheric N deposition and climatic conditions over space and time. The combination of historical and contemporary surveys allows (i) to test if observed contemporary patterns across space are consistent at the time of the historical survey, and, crucially, (ii) to assess whether changes in abundance over time given recorded environmental change match expectations from patterns recorded along environmental gradients in space. We found consistent spatial relationships at the two periods: local variation in soil variables and overstorey cover were the best predictors of individual species’ cover while interregional variation in coarse-scale variables, i.e. N deposition and climate, was less important. However, we found that our SFT approach could not accurately explain the large variation in abundance changes over time. We thus recommend to be cautious when using SFT substitution to infer species responses to temporal changes.
Eco-physiological processes are expressing the interaction of organisms within an environmental context of their habitat and their degree of adaptation, level of resistance as well as the limits of life in a changing environment. The present study focuses on observations achieved by methods used in this scientific discipline of “Ecophysiology” and to enlarge the scientific context in a broader range of understanding with universal character. The present eco-physiological work is building the basis for classifying and exploring the degree of habitability of another planet like Mars by a bio-driven experimentally approach. It offers also new ways of identifying key-molecules which are playing a specific role in physiological processes of tested organisms to serve as well as potential biosignatures in future space exploration missions with the goal to search for life. This has important implications for the new emerging scientific field of Astrobiology. Astrobiology addresses the study of the origin, evolution, distribution and future of life in the universe. The three fundamental questions which are hidden behind this definition are: how does life begin and evolve? Is there life beyond Earth and, if so, how can we detect it? What is the future of life on Earth and in the universe? It means that this multidisciplinary field encompasses the search for habitable environments in our Solar System and habitable planets outside our Solar System. It comprises the search for the evidence of prebiotic chemistry and life on Mars and other bodies in our Solar System like the icy moons of the Jovian and Saturnian system, laboratory and field research into the origins and early evolution of life on Earth, and studies of the potential for life to adapt to challenges on Earth and in space. For this purpose an integrated research strategy was applied, which connects field research, laboratory research allowing planetary simulation experiments with investigation enterprises performed in space (particularly performed in the low Earth Orbit.
Multivalent flexible nanogels exhibit broad-spectrum antiviral activity by blocking virus entry
(2018)
The entry process of viruses into host cells is complex and involves stable but transient multivalent interactions with different cell surface receptors. The initial contact of several viruses begins with attachment to heparan sulfate (HS) proteoglycans on the cell surface, which results in a cascade of events that end up with virus entry. The development of antiviral agents based on multivalent interactions to shield virus particles and block initial interactions with cellular receptors has attracted attention in antiviral research. Here, we designed nanogels with different degrees of flexibility based on dendritic polyglycerol sulfate to mimic cellular HS. The designed nanogels are nontoxic and broad-spectrum, can multivalently interact with viral glycoproteins, shield virus surfaces, and efficiently block infection. We also visualized virus-nanogel interactions as well as the uptake of nanogels by the cells through clathrin-mediated endocytosis using confocal microscopy. As many human viruses attach to the cells through HS moieties, we introduce our flexible nanogels as robust inhibitors for these viruses.
In einem rund 2.200 ha großen Waldgebiet bei Magdeburgerforth (Fläming, Sachsen-Anhalt) wurden 1948 bis 1950 von Harro Passarge 120 Vegetationsaufnahmen sowie eine Vegetationskartierung erstellt. Das Gebiet zeichnet sich durch eine große Vielfalt an Waldtypen aus den Verbänden Agrostio-Quercion petraeae, Alnion glutinosae, Alnion incanae, Carpinion betuli, Dicrano-Pinion und Quercion roboris aus. Daher und weil viele der heute in Wäldern wirksamen Prozesse (z. B. Stickstoffeintrag,
Klimawandel) vor 60 Jahren noch nicht spürbar waren, bietet sich das Gebiet für eine Wiederholungsuntersuchung besonders an. Da die Aufnahmeflächen von Passarge nicht punktgenau verortet waren, wurden im Jahr 2014 in einem über die Forstabteilungen und die Vegetationskarte definierten Suchraum immer die der Erstaufnahme ähnlichsten Waldbestände erfasst. Insgesamt konnten 97 (81 %) der Aufnahmen wiederholt werden. Vegetationsveränderungen werden mithilfe einer NMDS-Ordination, der Gegenüberstellung von α -Diversität, Zeigerwerten und Waldbindungskategorien für die beiden
Aufnahmezeitpunkte sowie über die Identifikation von Gewinner- und Verlierer-Arten analysiert.
Auch wenn methodenbedingt bei der Wiederholungsuntersuchung nur die jeweils geringstmögliche
Vegetationsveränderung abgebildet wird, konnten Ergebnisse erzielt werden, die mit denen quasi permanenter Plots übereinstimmen. Die beobachteten allgemeinen Trends (Eutrophierung, Sukzession nach Nutzungswandel, Verlust lichtliebender und magerkeitszeigender Arten, Ausbreitung von stickstoffliebenden Arten und mesophilen Waldarten, Einwanderung von Neophyten, keine generelle Abnahme der Artenzahl) stimmen gut mit den in zahlreichen Studien aus mitteleuropäischen Wäldern festgestellten überein. Durch das von nassen bis trockenen sowie von bodensauer-nährstoffarmen bis zu relativ basenreichen Böden reichende Standortsspektrum innerhalb des Untersuchungsgebietes konnte aber – deutlicher als in den meisten bisherigen Fallstudien – gezeigt werden, dass sich die Resilienz der
Wälder gegenüber Vegetationsveränderung je nach Ausgangsgesellschaft stark unterscheidet und jeweils unterschiedliche Treiber wirksam sind. Stellario-Carpinetum und Luzulo-Quercetum erwiesen
sich als relativ stabil, und auch in den Feuchtwäldern des Circaeo-Alnetum gab es trotz eines Artenwechsels wenig Hinweise auf Umweltveränderungen. Dagegen wiesen die Wälder nährstoffarmer Standorte (Sphagno-Alnetum, Betulo-Quercetum, Dicrano-Pinion) viele Verliererarten und eine starke Eutrophierungstendenz auf. Die in besonderem Maße von historischen Waldnutzungsformen abhängigen thermophilen Wälder und die Flechten-Kiefernwälder gingen weitgehend verloren.
In einem rund 2.200 ha großen Waldgebiet bei Magdeburgerforth (Fläming, Sachsen-Anhalt) wur-den 1948 bis 1950 von Harro Passarge 120 Vegetationsaufnahmen sowie eine Vegetationskartierung erstellt. Das Gebiet zeichnet sich durch eine große Vielfalt an Waldtypen aus den Verbänden Agrostio-Quercion petraeae, Alnion glutinosae, Alnion incanae, Carpinion betuli, Dicrano-Pinion und Quercion roboris aus. Daher und weil viele der heute in Wäldern wirksamen Prozesse (z. B. Stickstoffeintrag, Klimawandel) vor 60 Jahren noch nicht spürbar waren, bietet sich das Gebiet für eine Wiederholungs-untersuchung besonders an. Da die Aufnahmeflächen von Passarge nicht punktgenau verortet waren, wurden im Jahr 2014 in einem über die Forstabteilungen und die Vegetationskarte definierten Such-raum immer die der Erstaufnahme ähnlichsten Waldbestände erfasst. Insgesamt konnten 97 (81 %) der Aufnahmen wiederholt werden. Vegetationsveränderungen werden mithilfe einer NMDS-Ordination, der Gegenüberstellung von α-Diversität, Zeigerwerten und Waldbindungskategorien für die beiden Aufnahmezeitpunkte sowie über die Identifikation von Gewinner- und Verlierer-Arten analysiert.Auch wenn methodenbedingt bei der Wiederholungsuntersuchung nur die jeweils geringstmögliche Vegetationsveränderung abgebildet wird, konnten Ergebnisse erzielt werden, die mit denen quasi-permanenter Plots übereinstimmen. Die beobachteten allgemeinen Trends (Eutrophierung, Sukzession nach Nutzungswandel, Verlust lichtliebender und magerkeitszeigender Arten, Ausbreitung von stick-stoffliebenden Arten und mesophilen Waldarten, Einwanderung von Neophyten, keine generelle Ab-nahme der Artenzahl) stimmen gut mit den in zahlreichen Studien aus mitteleuropäischen Wäldern festgestellten überein. Durch das von nassen bis trockenen sowie von bodensauer-nährstoffarmen bis zu relativ basenreichen Böden reichende Standortsspektrum innerhalb des Untersuchungsgebietes konnte aber – deutlicher als in den meisten bisherigen Fallstudien – gezeigt werden, dass sich die Resilienz der Wälder gegenüber Vegetationsveränderung je nach Ausgangsgesellschaft stark unterscheidet und jeweils unterschiedliche Treiber wirksam sind. Stellario-Carpinetum und Luzulo-Quercetum erwiesen sich als relativ stabil, und auch in den Feuchtwäldern des Circaeo-Alnetum gab es trotz eines Arten-wechsels wenig Hinweise auf Umweltveränderungen. Dagegen wiesen die Wälder nährstoffarmer Standorte (Sphagno-Alnetum, Betulo-Quercetum, Dicrano-Pinion) viele Verliererarten und eine starke Eutrophierungstendenz auf. Die in besonderem Maße von historischen Waldnutzungsformen abhängi-gen thermophilen Wälder und die Flechten-Kiefernwälder gingen weitgehend verloren.
Heg1 and Ccm1/2 proteins control endocardial mechanosensitivity during zebrafish valvulogenesis
(2018)
Endothelial cells respond to different levels of fluid shear stress through adaptations of their mechanosensitivity. Currently, we lack a good understanding of how this contributes to sculpting of the cardiovascular system. Cerebral cavernous malformation (CCM) is an inherited vascular disease that occurs when a second somatic mutation causes a loss of CCM1/KRIT1, CCM2, or CCM3 proteins. Here, we demonstrate that zebrafish Krit1 regulates the formation of cardiac valves. Expression of heg1, which encodes a binding partner of Krit1, is positively regulated by blood-flow. In turn, Heg1 stabilizes levels of Krit1 protein, and both Heg1 and Krit1 dampen expression levels of klf2a, a major mechanosensitive gene. Conversely, loss of Krit1 results in increased expression of klf2a and notch1b throughout the endocardium and prevents cardiac valve leaflet formation. Hence, the correct balance of blood-flow-dependent induction and Krit1 protein mediated repression of klf2a and notch1b ultimately shapes cardiac valve leaflet morphology.
Fluorescence fluctuation spectroscopy has become a popular toolbox for non-disruptive analysis of molecular interactions in living cells. The quantification of protein oligomerization in the native cellular environment is highly relevant for a detailed understanding of complex biological processes. An important parameter in this context is the molecular brightness, which serves as a direct measure of oligomerization and can be easily extracted from temporal or spatial fluorescence fluctuations. However, fluorescent proteins (FPs) typically used in such studies suffer from complex photophysical transitions and limited maturation, inducing non-fluorescent states. Here, we show how these processes strongly affect molecular brightness measurements. We perform a systematic characterization of non-fluorescent states for commonly used FPs and provide a simple guideline for accurate, unbiased oligomerization measurements in living cells. Further, we focus on novel red FPs and demonstrate that mCherry2, an mCherry variant, possesses superior properties with regards to precise quantification of oligomerization.
The Amyloid-precursor-like protein 1 (APLP1) is a neuronal type I transmembrane protein which plays a role in synaptic adhesion and synaptogenesis. Past investigations indicated that APLP1 is involved in the formation of protein-protein complexes that bridge the junctions between neighboring cells. Nevertheless, APLP1-APLP1 trans interactions have never been directly observed in higher eukaryotic cells. Here, we investigate APLP1 interactions and dynamics directly in living human embryonic kidney (HEK) cells, using fluorescence fluctuation spectroscopy techniques, namely cross-correlation scanning fluorescence correlation spectroscopy (sFCS) and Number&Brightness (N&B). Our results show that APLP1 forms homotypic trans complexes at cell-cell contacts. In the presence of zinc ions, the protein forms macroscopic clusters, exhibiting an even higher degree of trans binding and strongly reduced dynamics. Further evidence from Giant Plasma Membrane Vesicles and live cell actin staining suggests that the presence of an intact cortical cytoskeleton is required for zinc-induced cis multimerization. Subsequently, large adhesion platforms bridging interacting cells are formed through APLP1-APLP1 direct trans interactions. Taken together, our results provide direct evidence that APLP1 functions as a neuronal zinc-dependent adhesion protein and provide a more detailed understanding of the molecular mechanisms driving the formation of APLP1 adhesion platforms. Further, they show that fluorescence fluctuation spectroscopy techniques are useful tools for the investigation of protein-protein interactions at cell-cell adhesion sites.
The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress-and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast-and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senescence, also was down-regulated. In response to darkness, most of the photosynthesis-and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degradation. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglycerol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chlorophyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness.
The killing of young by unrelated males is widespread in the animal kingdom. In short-lived small rodents, females can mate immediately after delivery (post-partum oestrus) and invest in future reproduction, but infanticide may put the nestlings, their current reproductive investment, at risk. Here, we investigated the behavioural trade-offs between mating interest and nest protection in an arena experiment with bank voles (Myodes glareolus). Non-gravid females (n=33) were housed at one end of a large structured arena with their nestlings. Different scents (cage bedding) were presented to each female in a replicated design. Three combinations of mating opportunities and male-female familiarity were simulated using different scent donors: mating opportunity with the sire of the nestlings with whom the female was familiar; mating opportunity with a male unrelated to the offspring and unfamiliar to the female, thus posing a higher risk to the offspring; and neither risk nor mating opportunity (clean control). Most females investigated male scents, regardless of familiarity, leaving their litter unprotected. During control treatment, females with larger litters spent less time at the scent area, indicating increasing nursing demands or better protection. Females with older litters visited scents more often, suggesting an increased interest in reproduction while they are non-gravid alongside the decreased risk of infanticide for older young. In the presence of unfamiliar scents, females spent more time protecting their nests, supporting the perceived association of unfamiliarity with infanticide risk. Thus, rodent females flexibly allocate time spent between searching for a mate and protecting their nest, which is modulated by their familiarity with a potential intruder.Significance statementInfanticide by conspecific males is an extreme form of sexual conflict and has large costs on females, abolishing their investment into current offspring. In an experimental approach, we exposed lactating female bank voles to different combinations of mating opportunity and familiarity to a (simulated) intruder: (1) the sire of the nestlings with whom the female was familiar and, therefore, potentially less risky in terms of infanticide; (2) a male which was unrelated and unfamiliar to the female and thus posed a higher risk to the offspring; or (3) as a control, cage bedding, which posed neither risk of infanticide nor a mating opportunity. We show that females flexibly allocated pup protection and mating interest based on their familiarity with the male, indicating that the unfamiliar males pose a threat to offspring, which is perceived by the females. Females further adjusted their behaviour to the size and/or age of their current litter, investing more time in male scents when offspring were older, thus balancing future and current investments into reproduction.
Off-grid
(2018)
1. Advances in LED technology combined with solar, storable energy bring light to places remote from electricity grids. Worldwide more than 1.3 billion of people are living off-grid, often in developing regions of high insect biodiversity. In developed countries, dark refuges for wildlife are threatened by ornamental garden lights. Solar powered LEDs (SPLEDs) are cheaply available, dim, and often used to illuminate foot paths, but little is known on their effects on ground living (epigeal) arthropods.
2. We used off-the-shelf garden lamps with a single ‘white’ LED (colour temperature 7250 K) to experimentally investigate effects on attraction and nocturnal activity of ground beetles (Carabidae).
3. We found two disparate and species-specific effects of SPLEDs. (i) Some nocturnal, phototactic species were not reducing activity under illumination and were strongly attracted to lamps (>20-fold increase in captures compared to dark controls). Such species aggregate in lit areas and SPLEDs may become ecological traps, while the species is drawn from nearby, unlit assemblages. (ii) Other nocturnal species were reducing mobility and activity under illumination without being attracted to light, which may cause fitness reduction in lit areas.
4. Both reactions offer mechanistic explanations on how outdoor illumination can change population densities of specific predatory arthropods, which may have cascading effects on epigeal arthropod assemblages. The technology may thus increase the area of artificial light at night (ALAN) impacting insect biodiversity.
5. Measures are needed to mitigate effects, such as adjustment of light colour temperature and automated switch-offs.
It is well-known that prey species often face trade-offs between defense against predation and competitiveness, enabling predator-mediated coexistence. However, we lack an understanding of how the large variety of different defense traits with different competition costs affects coexistence and population dynamics. Our study focusses on two general defense mechanisms, that is, pre-attack (e.g., camouflage)and post-attack defenses (e.g., weaponry) that act at different phases of the predator—prey interaction. We consider a food web model with one predator, two prey types and one resource. One prey type is undefended, while the other one is pre-or post-attack defended paying costs either by a higher half-saturation constant for resource uptake or a lower maximum growth rate. We show that post-attack defenses promote prey coexistence and stabilize the population dynamics more strongly than pre-attack defenses by interfering with the predator’s functional response: Because the predator spends time handling “noncrackable” prey, the undefended prey is indirectly
facilitated. A high half-saturation constant as defense costs promotes coexistence more and stabilizes the dynamics less than a low maximum growth rate. The former imposes high costs at low resource concentrations but allows for temporally high growth rates at predator-induced resource peaks preventing the extinction of
the defended prey. We evaluate the effects of the different defense mechanisms and costs on coexistence under different enrichment levels in order to vary the importance of bottom-up and top-down control of the prey community.
It is well-known that prey species often face trade-offs between defense against predation and competitiveness, enabling predator-mediated coexistence. However, we lack an understanding of how the large variety of different defense traits with different competition costs affects coexistence and population dynamics. Our study focusses on two general defense mechanisms, that is, pre-attack (e.g., camouflage) and post-attack defenses (e.g., weaponry) that act at different phases of the predator—prey interaction. We consider a food web model with one predator, two prey types and one resource. One prey type is undefended, while the other one is pre-or post-attack defended paying costs either by a higher half-saturation constant for resource uptake or a lower maximum growth rate. We show that post-attack defenses promote prey coexistence and stabilize the population dynamics more strongly than pre-attack defenses by interfering with the predator’s functional response: Because the predator spends time handling “noncrackable” prey, the undefended prey is indirectly
facilitated. A high half-saturation constant as defense costs promotes coexistence more and stabilizes the dynamics less than a low maximum growth rate. The former imposes high costs at low resource concentrations but allows for temporally high growth rates at predator-induced resource peaks preventing the extinction of the defended prey. We evaluate the effects of the different defense mechanisms and costs on coexistence under different enrichment levels in order to vary the importance of bottom-up and top-down control of the prey community.
Immunochemical analytical methods are very successful in clinical diagnostics and are nowadays also emerging in the control of food as well as monitoring of environmental issues. Among the different immunoassays, luminescence based formats are characterized by their outstanding sensitivity making this format especially attractive for future applications. The need for multiparameter detection capabilities calls for a tool box of dye labels in order to transduce the biochemical reaction into an optically detectable signal. Here, in a multiparameter approach each analyte may be detected by a different dye with a unique emission color (covering the blue to red spectral range) or a unique luminescence decay kinetics. In the case of a competitive immunoassay format for each of the different dye labels an individual antibody would be needed. In the present paper a slightly modified approach is presented using a 7-aminocoumarin unit as the basic antigen against which highly specific antibodies were generated. Leaving the epitope region in the dyes unchanged but introducing a side group in positon 3 of the coumarin system allowed us to tune the optical properties of the coumarin dyes without the necessity of new antibody generation. Upon modification of the parent coumarin unit the full spectral range from blue to deep red was accessed. In the manuscript the photophysical characterization of the coumarin derivatives and their corresponding immunocomplexes with two highly specific antibodies is presented. The coumarin dyes and their immunocomplexes were characterized by steady-state and time-resolved absorption as well as emission spectroscopy. Moreover, fluorescence depolarization measurements were carried out to complement the data stressing the different binding modes of the two antibodies. The binding modes were evaluated using the photophysics of 7-aminocoumarins and how it was affected in the respective immunocomplexes, namely, the formation of the intramolecular charge transfer (ICT) as well as the twisted intramolecular charge transfer (TICT). In contrast to other antibody-dye pairs reported a distinct fluorescence enhancement upon formation of the antibody-dye complex up to a factor of SO was found. Because of the easy emission color tuning by tailoring the coumarin substitution for the antigen binding in nonrelevant position 3 of the parent molecule, a dye tool box is on hand which can be used in the construction of competitive multiparameter fluorescence enhancement immunoassays (FenIA).
Caffeine protects against anticonvulsant-induced impaired neurogenesis in the developing rat brain
(2018)
In preterm infants, phenobarbital is the first-line antiepileptic drug for neonatal seizures while caffeine is used for the treatment of apnea. Data from experimental animals suggest that phenobarbital and other anticonvulsants are toxic for the developing brain, while neuroprotective effects have been reported for caffeine both in newborn rodents and preterm human infants. To characterize the interaction of phenobarbital and caffeine in the hippocampus of the developing rodent brain, we examined the effects of both drugs given separately or together on postnatal neurogenesis after administration to neonatal rats throughout postnatal day (P) 4 to P6. Phenobarbital treatment (50 mg/kg) resulted in a significant decrease of proliferative capacity in the dentate gyrus. Phenobarbital also reduced expression of neuronal markers (doublecortin (DCX), calretinin, NeuN), neuronal transcription factors (Pax6, Sox2, Tbr1/2, Prox1), and neurotrophins (NGF, BDNF, NT-3) up to 24 h after the last administration. The phenobarbital-mediated impairment of neurogenesis was largely ameliorated by preconditioning with caffeine (10 mg/kg). In contrast, caffeine alone reduced proliferative capacity and expression of the neuronal markers DCX and NeuN at 6 h, but increased expression of neurotrophins and neuronal transcription factors at 6 and 12 h. These results indicate that administration of phenobarbital during the vulnerable phase of brain development negatively interferes with neuronal development, which can be prevented in part by co-administration of caffeine.
Changes in species' distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species' range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.
Changes in species’ distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species’ range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.
Microbial processing of organic matter (OM) in the freshwater biosphere is a key component of global biogeochemical cycles. Freshwaters receive and process valuable amounts of leaf OM from their terrestrial landscape. These terrestrial subsidies provide an essential source of energy and nutrients to the aquatic environment as a function of heterotrophic processing by fungi and bacteria. Particularly in freshwaters with low in-situ primary production from algae (microalgae, cyanobacteria), microbial turnover of leaf OM significantly contributes to the productivity and functioning of freshwater ecosystems and not least their contribution to global carbon cycling.
Based on differences in their chemical composition, it is believed that leaf OM is less bioavailable to microbial heterotrophs than OM photosynthetically produced by algae. Especially particulate leaf OM, consisting predominantly of structurally complex and aromatic polymers, is assumed highly resistant to enzymatic breakdown by microbial heterotrophs. However, recent research has demonstrated that OM produced by algae promotes the heterotrophic breakdown of leaf OM in aquatic ecosystems, with profound consequences for the metabolism of leaf carbon (C) within microbial food webs. In my thesis, I aimed at investigating the underlying mechanisms of this so called priming effect of algal OM on the use of leaf C in natural microbial communities, focusing on fungi and bacteria.
The works of my thesis underline that algal OM provides highly bioavailable compounds to the microbial community that are quickly assimilated by bacteria (Paper II). The substrate composition of OM pools determines the proportion of fungi and bacteria within the microbial community (Paper I). Thereby, the fraction of algae OM in the aquatic OM pool stimulates the activity and hence contribution of bacterial communities to leaf C turnover by providing an essential energy and nutrient source for the assimilation of the structural complex leaf OM substrate. On the contrary, the assimilation of algal OM remains limited for fungal communities as a function of nutrient competition between fungi and bacteria (Paper I, II). In addition, results provide evidence that environmental conditions determine the strength of interactions between microalgae and heterotrophic bacteria during leaf OM decomposition (Paper I, III). However, the stimulatory effect of algal photoautotrophic activities on leaf C turnover remained significant even under highly dynamic environmental conditions, highlighting their functional role for ecosystem processes (Paper III).
The results of my thesis provide insights into the mechanisms by which algae affect the microbial turnover of leaf C in freshwaters. This in turn contributes to a better understanding of the function of algae in freshwater biogeochemical cycles, especially with regard to their interaction with the heterotrophic community.
Humanoid robots, prosthetic limbs and exoskeletons require soft actuators to perform their primary function, which is controlled movement. In this wont we explored whether crosslinked poly[ethylene-co-(vinyl acetate)] (cPEVA) fibers, with different vinyl acetate (VA) content can serve as torsional fiber actuators. exhibiting temperature controlled reversible rotational changes. Broad melting transitions ranging from 50 to 90 degrees C for cPEVA18-165 or from 40 to 80 degrees C for cPEVA28-165 fibers in combination with complete crystallization at temperatures around 10 degrees C make them suitable actuating materials with adjustable actuation temperature ranges between 10 and 70 degrees C during repetitive cooling and heating. The obtained fibers exhibited a circular cross section with diameters around 0.4 +/- 0.1 mm, while a length of 4 cm was employed for the investigation of reversible rotational actuation after programming by twist insertion using 30 complete rotations at a temperature above melting transition. Repetitive heating and cooling between 10 to 60 degrees C or 70 degrees C of one-end-tethered programmed fibers revealed reversible rotations and torsional force. During cooling 3 +/- 1 complete rotations (Delta theta(r) = + 1080 +/- 360 degrees) in twisting direction were observed, while 4 +/- 1 turns in the opposite direction (Delta theta(r) = - 1440 +/- 1360 degrees) were found during heating. Such torsional fiber actuators, which are capable of approximately one rotation per cm fiber length, can serve as miniaturized rotary motors to provide rotational actuation in futuristic humanoid robots.
East Africa is a natural laboratory: Studying its unique geological and biological history can help us better inform our theories and models. Studying its present and future can help us protect its globally important biodiversity and ecosystem services. East African vegetation plays a central role in all these aspects, and this dissertation aims to quantify its dynamics through computer simulations.
Computer models help us recreate past settings, forecast into the future or conduct simulation experiments that we cannot otherwise perform in the field. But before all that, one needs to test their performance. The outputs that the model produced using the present day-inputs, agreed well with present-day observations of East African vegetation. Next, I simulated past vegetation for which we have fossil pollen data to compare. With computer models, we can fill the gaps of knowledge between sites where we have fossil pollen data from, and create a more complete picture of the past. Good level of agreement between model and pollen data where they overlapped in space further validated our model performance.
Once the model was tested and validated for the region, it became possible to probe one of the long standing questions regarding East African vegetation: How did East Africa lose its tropical forests? The present-day vegetation in the tropics is mainly characterized by continuous forests worldwide except in tropical East Africa, where forests only occur as patches. In a series of simulation experiments, I was able to show under which conditions these forest patches could have been connected and fragmented in the past. This study showed the sensitivity of East African vegetation to climate change and variability such as those expected under future climate change.
El Niño Southern Oscillation (ENSO) events that result from the fluctuations in temperature between the ocean and atmosphere, bring further variability to East African climate and are predicted to increase in intensity in the future. But climate models are still not good at capturing the pattens of these events. In a study where I quantified the influence of ENSO events on East African vegetation, I showed how different the future vegetation could be from what we currently predict with these climate models that lack accurate ENSO contribution. Consideration of these discrepancies is important for our future global carbon budget calculations and management decisions.
Numerical knowledge, including number concepts and arithmetic procedures, seems to be a clear-cut case for abstract symbol manipulation. Yet, evidence from perceptual and motor behaviour reveals that natural number knowledge and simple arithmetic also remain closely associated with modal experiences. Following a review of behavioural, animal and neuroscience studies of number processing, we propose a revised understanding of psychological number concepts as grounded in physical constraints, embodied in experience and situated through task-specific intentions. The idea that number concepts occupy a range of positions on the continuum between abstract and modal conceptual knowledge also accounts for systematic heuristics and biases in mental arithmetic, thus inviting psycho-logical approaches to the study of the mathematical mind.
Leptospirosis is a worldwide emerging infectious disease caused by zoonotic bacteria of the genus Leptospira. Numerous mammals, including domestic and companion animals, can be infected by Leptospira spp., but rodents and other small mammals are considered the main reservoir. The annual number of recorded human leptospirosis cases in Germany (2001-2016) was 25-166. Field fever outbreaks in strawberry pickers, due to infection with Leptospira kirschneri serovar Grippotyphosa, were reported in 2007 and 2014. To identify the most commonly occurring Leptospira genomospecies, sequence types (STs), and their small mammal host specificity, a monitoring study was performed during 2010-2014 in four federal states of Germany. Initial screening of kidney tissues of 3,950 animals by PCR targeting the lipl32 gene revealed 435 rodents of 6 species and 89 shrews of three species positive for leptospiral DNA. PCR-based analyses resulted in the identification of the genomospecies L. kirschneri (62.7%), Leptospira interrogans (28.3%), and Leptospira borgpetersenii (9.0%), which are represented by four, one, and two STs, respectively. The average Leptospira prevalence was highest (approximate to 30%) in common voles (Microtus arvalis) and field voles (Microtus agrestis). Both species were exclusively infected with L. kirschneri. In contrast, in bank voles (Myodes glareolus) and yellow-necked mice (Apodemus flavicollis), DNA of all three genomospecies was detected, and in common shrews (Sorex araneus) DNA of L. kirschneri and L. borgpetersenii was identified. The association between individual infection status and demographic factors varied between species; infection status was always positively correlated to body weight. In conclusion, the study confirmed a broad geographical distribution of Leptospira in small mammals and suggested an important public health relevance of common and field voles as reservoirs of L. kirschneri. Furthermore, the investigations identified seasonal, habitat-related, as well as individual influences on Leptospira prevalence in small mammals that might impact public health.
Since the beginning of the 21st century, spotted fever rickettsioses are known as emerging diseases worldwide. Rickettsiae are obligately intracellular bacteria transmitted by arthropod vectors. The ecology of Rickettsia species has not been investigated in detail, but small mammals are considered to play a role as reservoirs. Aim of this study was to monitor rickettsiae in wild small mammals over a period of five years in four federal states of Germany. Initial screening of ear pinna tissues of 3939 animals by Pan-Rick real-time PCR targeting the citrate synthase (gltA) gene revealed 296 rodents of seven species and 19 shrews of two species positive for rickettsial DNA. Outer membrane protein gene (ompB, ompAIV) PCRs based typing resulted in the identification of three species: Rickettsia helvetica (90.9%) was found as the dominantly occurring species in the four investigated federal states, but Rickettsia felis (7.8%) and Rickettsia raoultii (1.3%) were also detected. The prevalence of Rickettsia spp. in rodents of the genus Apodemus was found to be higher (approximately 14%) than in all other rodent and shrew species at all investigated sites. General linear mixed model analyses indicated that heavier (older) individuals of yellow-necked mice and male common voles seem to contain more often rickettsial DNA than younger ones. Furthermore, rodents generally collected in forests in summer and autumn more often carried rickettsial DNA. In conclusion, this study indicated a high prevalence of R. helvetica in small mammal populations and suggests an age-dependent increase of the DNA prevalence in some of the species and in animals originating from forest habitats. The finding of R. helvetica and R. felis DNA in multiple small mammal species may indicate frequent trans-species transmission by feeding of vectors on different species. Further investigations should target the reason for the discrepancy between the high rickettsial DNA prevalence in rodents and the so far almost absence of clinical apparent human infections.
Purpose Prolonged bed rest and microgravity in space cause intervertebral disc (IVD) degeneration. However, the underlying molecular mechanisms are not completely understood. Transient receptor potential canonical (TRPC) channels are implicated in mechanosensing of several tissues, but are poorly explored in IVDs. Methods Primary human IVD cells from surgical biopsies composed of both annulus fibrosus and nucleus pulposus (passage 1-2) were exposed to simulated microgravity and to the TRPC channel inhibitor SKF-96365 (SKF) for up to 5days. Proliferative capacity, cell cycle distribution, senescence and TRPC channel expression were analyzed. Results Both simulated microgravity and TRPC channel antagonism reduced the proliferative capacity of IVD cells and induced senescence. While significant changes in cell cycle distributions (reduction in G1 and accumulation in G2/M) were observed upon SKF treatment, the effect was small upon 3days of simulated microgravity. Finally, downregulation of TRPC6 was shown under simulated microgravity. Conclusions Simulated microgravity and TRPC channel inhibition both led to reduced proliferation and increased senescence. Furthermore, simulated microgravity reduced TRPC6 expression. IVD cell senescence and mechanotransduction may hence potentially be regulated by TRPC6 expression. This study thus reveals promising targets for future studies.
For successful growth and development, plants constantly have to gauge their environment. Plants are capable to monitor their current environmental conditions, and they are also able to integrate environmental conditions over time and store the information induced by the cues. In a developmental context, such an environmental memory is used to align developmental transitions with favourable environmental conditions. One temperature-related example of this is the transition to flowering after experiencing winter conditions, that is, vernalization. In the context of adaptation to stress, such an environmental memory is used to improve stress adaptation even when the stress cues are intermittent. A somatic stress memory has now been described for various stresses, including extreme temperatures, drought, and pathogen infection. At the molecular level, such a memory of the environment is often mediated by epigenetic and chromatin modifications. Histone modifications in particular play an important role. In this review, we will discuss and compare different types of temperature memory and the histone modifications, as well as the reader, writer, and eraser proteins involved.
The primary function of leaves is to provide an interface between plants and their environment for gas exchange, light exposure and thermoregulation. Leaves have, therefore a central contribution to plant fitness by allowing an efficient absorption of sunlight energy through photosynthesis to ensure an optimal growth. Their final geometry will result from a balance between the need to maximize energy uptake while minimizing the damage caused by environmental stresses. This intimate relationship between leaf and its surroundings has led to an enormous diversification in leaf forms. Leaf shape varies between species, populations, individuals or even within identical genotypes when those are subjected to different environmental conditions. For instance, the extent of leaf margin dissection has, for long, been found to inversely correlate with the mean annual temperature, such that Paleobotanists have used models based on leaf shape to predict the paleoclimate from fossil flora. Leaf growth is not only dependent on temperature but is also regulated by many other environmental factors such as light quality and intensity or ambient humidity. This raises the question of how the different signals can be integrated at the molecular level and converted into clear developmental decisions. Several recent studies have started to shed the light on the molecular mechanisms that connect the environmental sensing with organ-growth and patterning. In this review, we discuss the current knowledge on the influence of different environmental signals on leaf size and shape, their integration as well as their importance for plant adaptation.
Monoclonal antibodies (mAbs) are an innovative group of drugs with increasing clinical importance in oncology, combining high specificity with generally low toxicity. There are, however, numerous challenges associated with the development of mAbs as therapeutics. Mechanistic understanding of factors that govern the pharmacokinetics (PK) of mAbs is critical for drug development and the optimisation of effective therapies; in particular, adequate dosing strategies can improve patient quality life and lower drug cost. Physiologically-based PK (PBPK) models offer a physiological and mechanistic framework, which is of advantage in the context of animal to human extrapolation. Unlike for small molecule drugs, however, there is no consensus on how to model mAb disposition in a PBPK context. Current PBPK models for mAb PK hugely vary in their representation of physiology and parameterisation. Their complexity poses a challenge for their applications, e.g., translating knowledge from animal species to humans.
In this thesis, we developed and validated a consensus PBPK model for mAb disposition taking into account recent insights into mAb distribution (antibody biodistribution coefficients and interstitial immunoglobulin G (IgG) pharmacokinetics) to predict tissue PK across several pre-clinical species and humans based on plasma data only. The model allows to a priori predict target-independent (unspecific) mAb disposition processes as well as mAb disposition in concentration ranges, for which the unspecific clearance (CL) dominates target-mediated CL processes. This is often the case for mAb therapies at steady state dosing.
The consensus PBPK model was then used and refined to address two important problems:
1) Immunodeficient mice are crucial models to evaluate mAb efficacy in cancer therapy. Protection from elimination by binding to the neonatal Fc receptor is known to be a major pathway influencing the unspecific CL of both, endogenous and therapeutic IgG. The concentration of endogenous IgG, however, is reduced in immunodeficient mouse models, and this effect on unspecific mAb CL is unknown, yet of great importance for the extrapolation to human in the context of mAb cancer therapy.
2) The distribution of mAbs into solid tumours is of great interest. To comprehensively investigate mAb distribution within tumour tissue and its implications for therapeutic efficacy, we extended the consensus PBPK model by a detailed tumour distribution model incorporating a cell-level model for mAb-target interaction. We studied the impact of variations in tumour microenvironment on therapeutic efficacy and explored the plausibility of different mechanisms of action in mAb cancer therapy.
The mathematical findings and observed phenomena shed new light on therapeutic utility and dosing regimens in mAb cancer treatment.
Understanding the molecular basis of morphological change remains a central challenge in evolutionary-developmental biology. The transition from outbreeding to selfing is often associated with a dramatic reduction in reproductive structures and functions, such as the loss of attractive pheromones in hermaphroditic Caenorhabditis elegans and a reduced flower size in plants. Here, we demonstrate that variation in the level of the brassinosteroid-biosynthesis enzyme CYP724A1 contributes to the reduced flower size of selfing Capsella rubella compared with its outbreeding ancestor Capsella grandiflora. The primary transcript of the C. rubella allele is spliced more efficiently than that of C. grandiflora, resulting in higher brassinosteroid levels. These restrict organ growth by limiting cell proliferation. More efficient splicing of the C. rubella allele results from two de novo mutations in the selfing lineage. Thus, our results highlight the potentially widespread importance of differential splicing efficiency and higher-than-optimal hormone levels in generating phenotypic variation.
Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species’ European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.
Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.
Studies on Oberonia 3. Aberrant flowers and other floral modifications in the orchid genus Oberonia
(2018)
Orchid flowers are amongst the most conspicuous attractions that plants have generated over evolutionary epochs. However, organ homology in particular of androecium and gynoecium of orchid flowers have been, and are still, the subject of long-term discussion. Studies of aberrant - teratologic - flowers have traditionally helped to clarify organ identity in orchids. We here present for the first time teratological flowers within the florally smallest and inconspicuous orchid genus Oberonia and illustrate them by light and scanning electron microscopy. Pseudopeloria with half of a lateral petal transformed into a lip was found in O. costeriana J.J.Sm. and O. mucronata (D.Don) Ormerod & Seidenf. A supernumerary lip is known from O. mucronata. Oberonia rufilabris Lindl. is documented with multiple aberrations: triple gynostemium and a total of 10 tepals, twin flowers, and duplicate lips. We interpret these aberrations in light of known floral developmental and organ identity information.
Background
Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available.
Findings
In order to improve genome contiguity, we have developed Cross-Species Scaffolding—a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico.
Conclusions
We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.
Background
Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available.
Findings
In order to improve genome contiguity, we have developed Cross-Species Scaffolding—a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico.
Conclusions
We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.
Pharmaceuticals are found in freshwater ecosystems where even low concentrations in the range of ng L−1 may affect aquatic organisms. In the current study, we investigated the effects of chronic exposure to three pharmaceuticals on two microalgae, a potential modulation of the effects by additional inorganic phosphorus (Pi) limitation, and a potential propagation of the pharmaceuticals’ effect across a trophic interaction. The latter considers that pharmaceuticals are bioaccumulated by algae, potentially metabolized into more (or less) toxic derivates and consequently consumed by zooplankton. We cultured Acutodesmus obliquus and Nannochloropsis limnetica in Pi-replete and Pi-limited medium contaminated with one of three commonly human used pharmaceuticals: fluoxetine, ibuprofen, and propranolol. Secondly, we tested to what extent first level consumers (Daphnia magna) were affected when fed with pharmaceutical-grown algae. Chronic exposure, covering 30 generations, led to (i) decreased cell numbers of A. obliquus in the presence of fluoxetine (under Pi-replete conditions) (ii) increased carotenoid to chlorophyll ratios in N. limnetica (under Pi-limited conditions), and (iii) increased photosynthetic yields in A. obliquus (in both Pi-conditions). In addition, ibuprofen affected both algae and their consumer: Feeding ibuprofen-contaminated algae to Pi-stressed D. magna improved their survival. We demonstrate, that even very low concentrations of pharmaceuticals present in freshwater ecosystems can significantly affect aquatic organisms when chronically exposed. Our study indicates that pharmaceutical effects can cross trophic levels and travel up the food chain.