Background: Gene flow between species, across ploidal levels, and even between evolutionary lineages is a common phenomenon in the genus Arabidopsis. However, apart from two genetically fully stabilized allotetraploid species that have been investigated in detail, the extent and temporal dynamics of hybridization are not well understood. An introgression zone, with tetraploid A. arenosa introgressing into A. lyrata subsp. petraea in the Eastern Austrian Forealps and subsequent expansion towards pannonical lowlands, was described previously based on morphological observations as well as molecular data using microsatellite and plastid DNA markers. Here we investigate the spatio-temporal context of this suture zone, making use of the potential of next-generation sequencing and whole-genome data. By utilizing a combination of nuclear and plastid genomic data, the extent, direction and temporal dynamics of gene flow are elucidated in detail and Late Pleistocene evolutionary processes are resolved.
Results: Analysis of nuclear genomic data significantly recognizes the clinal structure of the introgression zone, but also reveals that hybridization and introgression is more common and substantial than previously thought. Also tetraploid A. lyrata and A. arenosa subsp. borbasii from outside the previously defined suture zone show genomic signals of past introgression. A. lyrata is shown to serve usually as the maternal parent in these hybridizations, but one exception is identified from plastome-based phylogenetic reconstruction. Using plastid phylogenomics with secondary time calibration, the origin of A. lyrata and A. arenosa lineages is pre-dating the last three glaciation complexes (approx. 550,000 years ago). Hybridization and introgression followed during the last two glacial-interglacial periods (since approx. 300,000 years ago) with later secondary contact at the northern and southern border of the introgression zone during the Holocene.
Conclusions: Footprints of adaptive introgression in the Northeastern Forealps are older than expected and predate the Last Glaciation Maximum. This correlates well with high genetic diversity found within areas that served as refuge area multiple times. Our data also provide some first hints that early introgressed and presumably preadapted populations account for successful and rapid postglacial re-colonization and range expansion.
Abstract The zebrafish (Danio rerio) has proven to be a useful genetic model for studying the circadian timing system. The canonical molecular mechanism underlying circadian rhythms is based upon auto-regulatory transcription-translation feedback loops (TTFLs). It is well established that zebrafish has a TTFLs-dependent light entrainable oscillator (LEO) present in most tissues and even cell lines however, like other vertebrates, they also possess a food entrainable oscillator (FEO). Recent studies have addressed how regular food availability can entrain circadian rhythms of increased locomotor activity that precedes the feeding time (so-called food-anticipatory activity, FAA). Unlike the extensively studied LEO, there is very little known about the molecular components and regulation of the FEO. My PhD programme focuses on the mechanism whereby food regulates the circadian clock in zebrafish. Using behavior recording, we have revealed that FEO exists in adult zebrafish by showing that scheduled, restricted food availability can entrain FAA independently of the timing of the light-dark (LD) cycle. By maintaining fish under a LD cycle and then feeding fish either in the middle of the light period (ML) or in the middle of the dark period (MD), we have performed a circadian metabolome analysis using hydrogen nuclear magnetic resonance (1H NMR) spectroscopy. We have revealed that most circadian metabolites peak in either the FAA or FAA anti-phase periods and thus there is a strong correlation between metabolite phases and mealtime. Furthermore, by comparing the circadian phases of metabolites between ML and MD, we have identified both light and feeding time-regulated rhythmic metabolites. Light-related circadian metabolites include nucleotides and non-essential amino acids while feeding regulated circadian metabolites include essential amino acids. The oxidized form of nicotinamide adenine dinucleotide (NAD+), which operates as a cofactor and occupies a central position connecting most circadian metabolic pathways, is under the control of both LEO and FEO in adult liver. The rhythmic expression of nampta, namptb and sirt1 which encode enzymes in NAD+ salvage pathways are also regulated by both LEO and FEO. Notably, the rhythmic transcripts which constitute elements of TTFLs are not influenced by the feeding time in the fish liver.
In order to explore the cellular metabolism under cell autonomous LEO control, we have performed metabolome measurements in cultured zebrafish primary hepatocytes which were exposed to light-dark (LD) and dark-light (DL) regimes. Unexpectedly, the cycling of nearly all the identified circadian metabolites in primary hepatocyte cultures is independent of the lighting conditions. In comparison, the mRNA expression of metabolism-related genes which oscillate strongly in adult livers are arhythmically expressed in hepatocytes. LEO-independent metabolic oscillations with a 24h period were also observed in zebrafish fibroblast cells (PAC2 and AB9), indicating that a metabolic oscillator could exist widely in zebrafish cells. Our subsequently studies have demonstrated that the phase of the metabolic oscillator is insensitive to serum refresh treatment. Finally, we have revealed that circadian metabolites in cavefish fibroblasts show aberrant rhythmicity with an infradian period of 40h-45h, which matches the extremely long period (~47h) of core circadian clock gene expression.
In conclusion, the zebrafish endogenous timekeeping system can be synchronized by diverse external signals and is under a multi-oscillatory control. The FEO is genetically and functionally independent of the classical core circadian clock TTFL of the LEO in zebrafish liver. Cellular metabolic oscillations could be driven by a non-transcriptional mechanism in both zebrafish and cavefish cell lines. Thus, the study of non-photic oscillators and non-transcriptional dependent circadian periodicity should provide us with a more accurate view of the entire circadian timing system.
The continuous life-long growth of the fish retina is fuelled by neural stem cells located within the ciliary marginal zone (CMZ). These stem cells are characterised by their multipotency and ability to self-renew. Through asymmetric divisions, the neural stem cells give rise to progenitor cells with restricted proliferation potential that ultimately commit to terminally differentiated neurons of the mature retina. In this process, pharmacological manipulation suggests that Wnt signalling acts on both cell proliferation and differentiation, but a refined analysis is missing. Therefore, I present here a detailed analysis of Wnt signalling localisation and function within different cell types and their lineages in the post-embryonic CMZ of medaka. In this thesis, I show that Wnt ligands are expressed by cells of the retinal pigment epithelium, which is located directly adjacent to the CMZ. Wnt/β-catenin signalling activity is restricted to stem cells, whereas β-catenin independent Wnt/LRP6 signalling extends to dividing progenitor cells. To address the role of Wnt signalling in proliferation and differentiation of specific stem and progenitor cells, I created transgenic lines that allow inducible clonal labelling combined with upregulation of Wnt signalling in individual cells. My lineage tracing experiments suggest that Wnt upregulation has diverging effects on stem and progenitor cells. First, stem cells lose stemness characteristics presumably through induction of apoptosis or symmetric division. Second, progenitor cells reacquire the capacity to self-renew, but their pre-existing fate restrictions are irreversible. Finally, committed progenitors shift their fate and/or change their division mode and proliferation characteristics upon Wnt upregulation. Taken together, my results indicate that Wnt signalling functionally divides the CMZ into stem cells, non-committed and committed progenitors, which has far reaching implications for Wnt functions in other stem cell niches.
Forschung fasziniert – neue Technik, neue Heilmethoden, oder einfach das Staunen über fremde Planeten und die Wunder der Tiefsee. Was für Köpfe stecken dahinter? Wie kommen WissenschaftlerInnen mit Rückschlägen und Bürokratie klar?
Campus-Reporter Nils Birschmann trifft Dr. Annika Guse, die ihre Faszination für Forschung zum Beruf gemacht hat.
Der Beitrag erschien in der Sendereihe "Campus-Report" - einer Beitragsreihe, in der über aktuelle Themen aus Forschung und Wissenschaft der Universitäten Heidelberg, Mannheim, Karlsruhe und Freiburg berichtet wird. Zu hören ist "Campus-Report" montags bis freitags jeweils um ca. 19.10h im Programm von Radio Regenbogen (Empfang in Nordbaden: UKW 102,8. In Mittelbaden: 100,4 und in Südbaden: 101,1).
Unsere Immunabwehr ist sehr komplex. Und wie wunderbar wäre es, mehr über Heilungsmöglichkeiten zu wissen. Darum betreibt die Universität Heidelberg Grundlagenforschung in den Lebenswissenschaften. Was man von Korallen und Algen über unser Immunsystem lernen kann, hat Campus-Reporter Nils Birschmann im Gespräch mit Dr. Annika Guse herausgefunden.
Der Beitrag erschien in der Sendereihe "Campus-Report" - einer Beitragsreihe, in der über aktuelle Themen aus Forschung und Wissenschaft der Universitäten Heidelberg, Mannheim, Karlsruhe und Freiburg berichtet wird. Zu hören ist "Campus-Report" montags bis freitags jeweils um ca. 19.10h im Programm von Radio Regenbogen. (Empfang in Nordbaden: UKW 102,8. In Mittelbaden: 100,4 und in Südbaden: 101,1)
Background: Mathematical models are used to gain an integrative understanding of biochemical processes and networks. Commonly the models are based on deterministic ordinary differential equations. When molecular counts are low, stochastic formalisms like Monte Carlo simulations are more appropriate and well established. However, compared to the wealth of computational methods used to fit and analyze deterministic models, there is only little available to quantify the exactness of the fit of stochastic models compared to experimental data or to analyze different aspects of the modeling results. Results: Here, we developed a method to fit stochastic simulations to experimental high-throughput data, meaning data that exhibits distributions. The method uses a comparison of the probability density functions that are computed based on Monte Carlo simulations and the experimental data. Multiple parameter values are iteratively evaluated using optimization routines. The method improves its performance by selecting parameters values after comparing the similitude between the deterministic stability of the system and the modes in the experimental data distribution. As a case study we fitted a model of the IRF7 gene expression circuit to time-course experimental data obtained by flow cytometry. IRF7 shows bimodal dynamics upon IFN stimulation. This dynamics occurs due to the switching between active and basal states of the IRF7 promoter. However, the exact molecular mechanisms responsible for the bimodality of IRF7 is not fully understood. Conclusions: Our results allow us to conclude that the activation of the IRF7 promoter by the combination of IRF7 and ISGF3 is sufficient to explain the observed bimodal dynamics.
Forschung ist aufwändig, jede Antwort wirft neue Fragen auf. Deshalb hat die EU-Kommission den Europäischen Forschungsrat ERC gegründet. Mit einem millionenschweren Fond werden Pionier-Leistungen von Nachwuchsforschern unterstützt. Die Universität Heidelberg ist mit gleich fünf bewilligten Anträgen die erfolgreichste deutsche Universität in der aktuellen Förderrunde. Campus-Reporter Nils Birschmann hat Dr. Annika Buse besucht, die fernab vom Meer Korallen erforscht.
Der Beitrag erschien in der Sendereihe "Campus-Report" - einer Beitragsreihe, in der über aktuelle Themen aus Forschung und Wissenschaft der Universitäten Heidelberg, Mannheim, Karlsruhe und Freiburg berichtet wird. Zu hören ist "Campus-Report" montags bis freitags jeweils um ca. 19.10h im Programm von Radio Regenbogen. (Empfang in Nordbaden: UKW 102,8. In Mittelbaden: 100,4 und in Südbaden: 101,1)
Background: The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. Results: Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. Conclusions: Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.
Background: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now. Description: We present the Nicotiana attenuata Data Hub (NaDH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. The NaDH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. We implemented several visualization tools, including a modified version of the Electronic Fluorescent Pictograph (eFP) browser, co-expression networks and the Interactive Tree Of Life (iTOL) for studying gene expression divergence among duplicated homologous. In addition, the NaDH allows researchers to query phylogenetic trees of 16,305 gene families and provides tools for analyzing their evolutionary history. Furthermore, we also implemented tools to identify co-expressed genes and metabolites, which can be used for predicting the functions of genes. Using the transcription factor NaMYB8 as an example, we illustrate that the tools and data in NaDH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites. Conclusion: The NaDH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes in Nicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. Because N. attenuata shares many genome-wide features with other Nicotiana species including cultivated tobacco, and hence NaDH can be a resource for exploring the function and evolution of genes in Nicotiana species in general. The NaDH can be accessed at: http://nadh.ice.mpg.de/
Mikrotubuli-assoziierte Proteine (MAPs) modulieren die Stabilität und Dynamik von Mikrotubuli. Indem sie das Wachstum der Mikrotubuli regulieren, die den Hauptanteil des axonalen Zytoskeletts ausmachen, spielen MAPs eine entscheidende Rolle für die Elongation und Navigation von Axonen. Eines der fünf klassischen MAPs (MAP1–4 und Tau) ist MAP1B, ein axonales MAP, das als Erstes während der Embryonalentwicklung auftritt. In dieser Arbeit wurde die Rolle von MAP1B bei der Wegfindung von Axonen der retinalen Ganglienzellen (RGZ) in der sich entwickelnden Retina untersucht. Hierzu wurden Retinae von Mausembryonen, die kein MAP1B besitzen (Knockout), in der Phase des maximalen RGZ-Axonwachstums (E14,5) untersucht. Die k.o.-Neuroretina ist im Zentralbereich (um den Sehnervkopf herum) dünner als im Wildtyp. Dies ist jedoch nicht auf eine Reduktion der RGZ-Axone zurückzuführen, sondern auf eine Verminderung der Neuroepithelialzellschicht. RGZ-Axone zeigen auf ihrem Weg zum Sehnerv, auf dem sie sich zunehmend bündeln, in der k.o.-Retina ein abnormales Navigationsverhalten: Einzelne RGZ-Axone und dünne Axonbündel lösen sich häufiger aus ihren Faszikeln, wodurch die Anzahl dünner Faszikel erhöht ist. In vitro Experimente unter genauer definierten Bedingungen und an einzelnen RGZ-Axonen offenbarten, dass zwei Verhaltensweisen im k.o. häufiger auftraten: starke Seitwärtsbewegungen der Axonspitzen und starke Lateralexploration des Wachstumskegels an der Axonspitze. Sowohl in vivo als auch in vitro Befunde weisen also darauf hin, dass bei Fehlen von MAP1B die Feinregulation der Steuerungsbewegungen der Axone reduziert ist, was zu dem beobachteten Abwandern aus den Bündeln führen könnte. Dies bewirkt insbesondere am Sehnervkopf, wo die RGZ-Axone ein Abbiegemanöver durchführen, dramatische Fehlnavigationen im k.o.: Die Axone tauchen zwar in den Sehnervkopf ein, wachsen dann jedoch in die gegenüberliegende Neuroretina. Sie wachsen dabei nicht antiparallel entlang der RGZ-Axone, sondern in einer tieferen Neuroretinaschicht. Die Ergebnisse dieser Arbeit zeigen zum ersten Mal eine wichtige Rolle von MAP1B bei der Moderierung des Wachstumskegelverhaltens sowie der Weg- und Zielfindung navigierender Axone.