Lecythophora (Coniochaeta) hoffmannii, a soil- and lignocellulose-inhabiting sordariomycete (Ascomycota) that can also live as a facultative tree pathogen causing soft rot, belongs to the family Coniochaetaceae. The strain CBS 245.38 sequenced here was assembled into 869 contigs, has a size of 30.8 Mb, and comprises 10,596 predicted protein-coding genes.

Bioavailability denotes the ‘degree of interaction of chemicals with living organisms’. High bioavailability is generally needed for efficient biodegradation of environmental contaminants. Therefore, technologies to promote contaminant availability should foster bacterial transport and/or control interactions of chemicals with environmental matrices. Direct current (DC) electric fields and their electrokinetic phenomena (electro-migration, electroosmosis, and electrophoresis) have the potential to promote contaminant bioavailability by both mobilizing bacteria and contaminants. This thesis hence tested electrokinetic factors affecting bacterial transport and deposition and the interactions of contaminants with geo-sorbents, respectively. Studying electrokinetic effects on bacterial transport, we found that DC fields significantly changed bacterial deposition during transport in percolated laboratory columns. By calculating the bacteria collector interaction force FDLVO, the electroosmotic shear force FEOF, the electrophoretic drag force FEP, and the hydraulic shear force FHF, we developed an approach that interlinked the net forces Fnet on a bacterium to observed deposition efficiencies. The driving factor of electrokinetic effects was found to be the relative strength of |FEOF| and |FEP|. If |FEOF| > |FEP|, increased bacterial deposition efficiency and if |FEOF| < |FEP| decreased bacterial deposition efficiency was predicted. Investigating electrokinetic effects on bacterial deposition on planar surfaces using quartz crystal microbalance with dissipation (QCM-D) we confirmed our model by using different bacteria at varying ionic strengths of the electrolyte and of the DC electric applied, respectively. Our model can be used to predict DC field effects on bacterial deposition. Investigating the electrokinetic effects on the sorption/desorption of the model polycyclic aromatic hydrocarbon contaminant phenanthrene (PHE) we found that DC fields changed the rates and extents of PHE sorption and desorption in all geo-sorbents. Matrices of varying sorption strengths were tested. In strongly sorbing carbonaceous sorbents, the electroosmotic flow (EOF) increased the rates of PHE sorption and reduced PHE desorption while in more weakly sorbing matrices, EOF significantly reduced PHE sorption and increased its desorption. By interlinking the Gibbs free energy change of sorption (ΔGº) and the EOF velocity, an approach was developed to estimate electrokinetic effects on the sorption and desorption of PHE. The results of this thesis propose that electrokinetic phenomena have significant impact on both freely dissolved contaminant concentrations and bacterial deposition in porous media. They hence have high effect on contaminant bioavailability. Using conceptual approaches interlinking the electrokinetic forces with ΔGº and bacteria-matrix interactions energies (GDLVO), respectively, we were able to estimate electrokinetic effects on bacterial deposition and contaminant release. Our data thus give rise to future technical applications to control the bioavailability in natural and manmade ecosystems.

Histone methyltransferases are key players in eukaryotic gene regulation. The goal of this thesis was to study the role of the histone methyltransferase Mll2 in developing embryos and adult mice. Targeting of mouse ES cells with a multipurpose allele and blastocyst injection had previously generated a mouse line allowing analysis of Mll2 function by knock-out and conditional mutagenesis using Cre/loxP. The first part of the thesis comprised the analysis of the Mll2-/- phenotype, and included the cloning of a targeting construct to generate an ubiquitous, ligand-regulated Cre line. In the second part, we did conditional mutagenesis using the Rosa26-CreER(T2) line obtained from collaborators, and achieved complete knock-out of Mll2 in most tissues of embryos, neonates and adult mice. Mll2 is essential during embryonic development, as mutant embryos were severely growth retarded, had significant increases in apoptosis, and failed in gestation between E 9.5 and E11. Conditional removal of Mll2 protein at gastrulation (E 6.5) produced a similar phenotype at E 11. In contrast, the absence of Mll2 function after E 11 did not result in obvious defects at E16 and indicates an essential role for Mll2 between E6 and E11. Indeed, we identified a loss of expression of 3 important developmental regulators in mutants of this developmental stage: Hoxb1, Mox1 and Six3 are candidate targets for Mll2 regulation that encode homeobox type transcription factors involved in specifying cellular identity. We observed correct establishment of their developmental expression patterns, which than decay in Mll2-/- mutants at E9.5. These data concord with and extend current thoughts about the fly orthologue of Mll2, Trithorax, which suggest that it acts as an epigenetic lock in chromatin to maintain expression of certain transcription factors key to respective cellular identities, after their expression patterns have been established. After birth, Mll2 is dispensable in most tissues, as conditional knock out in neonates and adult mice did not produce any pathological findings except infertility of mutant males and females. Histological analysis of testis revealed progressive loss of spermatogonia, associated with increases in apoptosis but without overt proliferation, meiotic or differentiation defects or loss of the supporting Sertoli cells. Consequently, in addition to its regulation of homeotic genes during development, Mll2 is required for the maintenance of various mitotic cell populations including ES cells, embryonal cells and germ cells.

Die Phänologie beschäftigt sich mit der Entwicklung von Pflanzen im Jahresverlauf. Das Wort Phänologie stammt aus dem Griechischen und bedeutet wörtlich: Die Lehre von den Erscheinungen. Und genau darum geht es: Phänologen beobachten die regelmäßig wiederkehrenden Wachstums- und Entwicklungserscheinungen von Pflanzen. Dazu gehören z. B. Blühbeginn, Fruchtreife und Laubfall. Die Veränderungen notieren Phänologen in einem speziellen Kalender, der zehn Jahreszeiten aufweist. Dieser phänologische Kalender orientiert sich an den charakteristischen Entwicklungsstadien typischer Zeigerpflanzen ( z. B. Schneeglöckchen, Holunder, Salweide). Redaktionsschluss: 30.10.2019

Der Freistaat Sachsen beteiligt sich an der Entwicklung eines Rahmenplans für die deutschwestpolnische Wolfspopulation, der in nationaler Zuständigkeit und in Abstimmung mit den entsprechenden Stellen der Republik Polen zu erstellen ist und unter anderem Aussagen zur Populationsebene, Populationsentwicklung und Populationszielgröße treffen wird. Der vorliegende Managementplan ist insofern ein vorläufiger Plan, der nach praktischen Erfordernissen bzw. Erkenntnissen oder auf Grund von geänderten Rahmenbedingungen jederzeit fortgeschrieben und ergänzt werden kann. Fachliche Grundlage für den Managementplan ist das im Auftrag des Bundesamtes für Naturschutz erstellte Fachkonzept „Leben mit Wölfen: Leitfaden für den Umgang mit einer konfliktträchtigen Tierart in Deutschland“ (Fachkonzept BfN 2007). Redaktionsschluss: 14.02.2014

Eine Anleitung in leichter Sprache. Worum geht es in diesem Heft? Es geht um Phänologie. Es bedeutet: Wir beobachten, wie sich Pflanzen im Laufe des Jahres verändern. Im Frühling bekommen sie Blätter. Später blühen sie. Dann reifen die Früchte. Im Herbst werden die Blätter bunt und fallen ab. Der Winter beginnt. Es geht vor allem darum: Wann passiert das genau? An welchem Tag blühen die ersten Blüten? Wann genau sind die Früchte reif? Das sollt ihr beobachten und aufschreiben. Eure Ergebnisse schickt ihr an den Deutschen Wetter-Dienst. Dort arbeiten Fach-Leute, die sich mit Wetter und Klima beschäftigen. So könnt ihr mithelfen, unser Klima zu verstehen. Redaktionsschluss: 29.11.2018

Investigating forest soil biodiversity is essential to increase our understanding of ecosystem functions, assess potential consequences of global change, and thus optimize future decision-making processes. This cumulative PhD thesis contributes to this field by elucidating responses of bacterial and fungal forest soil communities, and their associated functions, in relation to tree diversity using a trait-based ecological approach with a focus on microbial living strategies. The three main chapters investigated microbial communities, using PCR-amplicon molecular methods, bioinformatics and novel statistics in the frame of the SoilForEUROPE project funded through the 2015–2016 BiodivERsA COFUND call for research proposals. Links between above-belowground biodiversity are crucial to understand forest functionality. For instance, studies on relationships of tree diversity and tree identity with microbial diversity reveal shifts in litter decomposition, nutrient cycling, primary production and the regulation of greenhouse gas emissions. These kinds of studies commonly compare microbial populations of different tree taxonomical groups. However, the effects of different tree taxa on microorganisms are mediated by tree morphology, physiology, phenology and genetics. Therefore, the use of specific plant traits to study biodiversity has become more frequent, adding a mechanistic understanding of compositional or functional shifts and interactions with soil microbial communities. This generalizable approach provides a common currency to compare similar microbial communities from different regions or environments with few microbial taxa in common. Microbial communities are also filtered by other processes such as global drivers, stochastic events, abiotic and biotic factors in addition to the mentioned tree traits. This environmental filtering process results in a functional microbial community structure, also with their own set of traits to increase their population size through higher performance and as response the capacity to affect their own ecosystem. Furthermore, it is expected that a particular set of microbial traits represents the life history strategies that favored a particular community under specific environmental conditions. This thesis correlates tree traits with bacterial and fungal communities by using a wide-ranged European forest platform with 64 plots of four different latitudinal regions. The SoilForEUROPE design also included multispecies and monospecific forests comprising 13 main tree species and 33 different tree species compositions. All these conditions supplied a diversity of environments to improve our knowledge of microbial soil diversity and above-belowground interactions. The here presented thesis encompasses five individual chapters. Chapter 1 provides the research context, project presentation and the main approach used. The Chapters 2 and 3 were developed in association with colleagues from the University of Freiburg and investigate four major European forest types: boreal forests (Finland), hemi‐boreal forests (Poland), mountainous beech forests (Romania) and thermophilous deciduous forests (Italy). Chapter 4 focuses purely on temperate forest plots and Chapter 5 compiles and concludes the results and presented ecological meanings. In particular, Chapter 2 evaluated the influence of tree species composition and diversity on fungal diversity and community composition, and highlights the relationships of fungal guilds and enzymatic activities with tree traits in detail, while also taking environmental variables into account. We demonstrated, how guilds like fungal saprotrophs mirror the litter quality, while tree root traits are often linked to an increasing number of fungal symbiotrophs. We found that forest types of higher latitudes, which are dominated by fast tree communities, correlated with high carbon‐cycling enzymatic activities. In contrast, Mediterranean forests with slow tree communities showed high enzymatic activities related to nitrogen and phosphorus cycles. In Chapter 3, we investigated links between bacterial communities, their functionality and root trait dispersion. Bacterial diversity revealed no major changes across the root functional dispersion gradient. In contrast, predicted gene profiles linked to plant growth activities suggested an increasing bacterial functionality from monospecific to multispecies forest. We also exposed that in multispecies forests, the bacterial functionality declines with the increasing functional dispersion of the roots. We further revealed important effects of the tree species identity on bacterial community composition, but we did not find significant relationships with root functional dispersion. However, bacterial network analyses indicated that multispecies forest have a higher complexity in their bacterial communities, which points towards more stable forest systems with greater functionality. Chapter 4 aimed to explore microbial communities of different soil depths from 0 to 30 cm across forests covering deciduous, evergreen and mixtures plots. Microbial abundance and diversity were especially affected by soil depth and by the presence of evergreen trees. Results showed higher accuracy to detect niche preference by using taxonomy levels than metabolic pathways or fungal guilds as features of a machine learning model. We found that bacterial communities are primarily shaped by soil depth in contrast to fungal community, which were rather influenced by the forest composition. Results also supported the importance of mixed forest to maintain nutrient cycling and a broad diversity of metabolites compared to monospecific forest and this differences where particular perceived in the upper 10 cm of soil. Chapter 5 concludes the thesis and presents a few remarks highlighting microbial strategies that might be favored under a particular soil forest composition. Overall, this thesis not only revealed the ecological patterns of soil forest microbial communities, but also provides a practical tool with necessary information to support decision-making and enlarge the schemes to conserve soil biodiversity.

Dieser kleine Leitfaden erklärt, was Sie beim Einkauf beachten sollten und welche biozidfreien Alternativen es gibt. Redaktionsschluss: 30.04.2020

After decades of experimental investigation, the dynamics howindividual cellsmove or deform-perfectly orchestrated for the creation and proliferation of tissue - remain partly unknown. In most recent years, the use of computational models, also called in silico experiments, has become a focus of interest. Due to their flexible scaling, compared to classical in vivo and in vitro studies, simulations can give important insights in the dynamics of cellular structures. We investigate Multi-Phasefield models for cellular structures, a versatile approach, capable of capturing complex changes in cell shape. Furthermore, it gives large flexibility in the modeling of cell-cell interactions and subcellular details like the propulsion machinery. The dynamics how these motility mechanisms create complex movement patterns on the tissue scale, will be a particular focus of this thesis. We compare four essentially different ways to introduce activity in Multi-Phasefield models, from movement driven by a random walk or the macroscopic shape of each cell towards a description of the subcellular machinery using either a polar or a nematic approach. For the different propulsion models, we investigate a variety of phenomena. Starting from the observation that the polar model creates collective motion, we observe that the resulting alignments resemble those of passive systems, expressed in Lewis’ and Aboav-Weaire’s law. Furthermore, we study a transition between solid and liquid state of the tissue, known to be important for many developmental processes. Additionally, we analyze the occurring patterns in the cellular alignment and flow, for systems in both confluence and confinement. Afterwards, we investigate the alignment of cell deformations with methods known from nematic structures. This reveals how the different propulsion mechanisms cause contractile or extensile behavior, classified by the movement of topological defects and the distribution of strain in their vicinity. At the end of this thesis, we show two extensions of themodels, capable of including growth and division of cells and generalizations towards curved manifolds as computational domains. Furthermore, we give an outlook on a possible roadmap for the future of Multi-Phasefield models in the description of cellular structures and their potential for a better understanding of the dynamics in the creation of life.

The ability to retrieve DNA from the skeletal remains of ancient humans has yielded many insights into the relationship between humans living today and our nearest evolutionary relatives, the Neandertals and Denisovans. Two important insights emerged from the first high-quality genome sequences of Neandertals and Denisovans: 1) these archaic humans had very low genetic diversity in comparison to most populations of present-day humans, and 2) there was gene flow from archaic humans into the ancestors of present-day people. In my thesis, I explored aspects of both these insights. In my first project, I analysed the consequences of low genetic diversity of archaic humans for immune genes, using genetic diversity in protein-coding genes (‘gene diversity’) as a proxy for functional diversity. I conclude that low gene diversity in archaic humans did not affect immune genes more severely than any other class of protein-coding genes. I then show that the MHC genes, that typical have high genetic diversity and are a component of the adaptive immune system, have substantially higher gene diversity than expected from the genome-wide gene diversity in archaic humans. Moreover, I find no detectable reduction in gene diversity between two Neandertals that lived more than 70,000 years apart. This is first evidence indicating that diversity in late Neandertals did not decrease over the last ~100,000 years of their existence, which would be expected if low gene diversity had played a considerable role in Neandertal extinction, as has been proposed. In my second project I analysed genomic regions depleted of both Neandertal and Denisovan ancestry in the genomes of humans living today (‘shared deserts’). It has been suggested that shared deserts reflect incompatibilities between archaic humans and the ancestors of present-day humans, and were created by negative selection against archaic alleles. By analysing archaic ancestry in almost 2,000 published present-day human genomes, including 155 published genomes from Oceania, I generated a further refined set of genomic regions that are most depleted of archaic ancestry. I discuss candidate variants in these regions that may underlie important phenotypic or functional differences between archaic and modern humans, such as in the brain-expressed genes CADM2 and KCND2, and propose this refined list as a set of candidates for future molecular testing.:Bibliographische Darstellung iii Table of contents iv Summary 8 Zusammenfassung 14 1. Introduction 21 1.1. A strange fossil and its genome 21 1.2. Archaic humans had low genetic diversity 26 1.3. Evidence of gene flow between archaic humans and AMH 29 1.3.1. Identification of archaic sequence and its impact on humans today 32 1.3.1.1. The distribution of archaic sequence in AMH is heterogeneous 34 1.3.1.2. Negative selection against introgressed archaic sequence 37 1.3.1.3. Adaptive introgression: Archaic sequence under positive selection in AMH 39 1.3.1.4. Association of introgressed variants with phenotypes of present-day people 41 1.3.2. Deserts: Gene flow left regions depleted of archaic introgression 43 2. Thesis outline 46 3. Methods 47 3.1. Methods for study of immune gene diversity 47 3.1.1. Data 47 3.1.2. Measure of gene diversity 47 3.1.3. Diversity in innate immune and MHC genes 48 3.1.4. GO enrichment analysis 49 3.2. Methods for study of deserts of archaic ancestry 50 3.2.1. Data sets and processing 50 3.2.2. Identification of introgressed haplotypes 51 3.2.2.1. Hidden Markov Model (HMM) 51 3.2.2.2. Probability cut-off for haplotypes to be archaic 51 3.2.3. Reanalysis of published deserts of archaic ancestry 52 3.2.3.1. Shared deserts 52 3.2.3.2. Sliding windows 52 3.2.3.3. Mean percentage introgression 53 3.2.3.4. Comparison to random regions 53 3.2.3.5. Definition of refined shared desert regions 54 3.2.3.6. Overlap of refined shared deserts with genes 54 3.2.3.7. Enrichment analyses in refined shared desert regions 55 3.2.3.8. Overlap with regions under ancient positive selection on the AMH lineage 55 3.2.3.9. Overlap with (nearly) fixed differences between present-day and archaic humans 56 4. Results 57 4.1. Immune gene diversity in archaic and present-day humans 57 4.1.1. Abstract 58 4.1.2. Introduction 59 4.1.3. Results 61 4.1.3.1. Archaic humans had lower overall gene diversity than present-day humans 61 4.1.3.2. Archaic humans had similarly low gene diversity in innate immune genes compared with non-immune genes 62 4.1.3.3. High MHC gene diversity in archaic humans 64 4.1.3.4. Genes with highest/lowest diversity show similar GO enrichments in archaic and present-day humans 66 4.1.4. Discussion 69 4.1.5. Supplementary results 71 4.1.6. Acknowledgements and author contributions 72 4.2. Refining deserts of archaic ancestry 73 4.2.1. Abstract 73 4.2.2. Introduction 75 4.2.3. Results 78 4.2.3.1. Genome-wide patterns of archaic introgression are consistent with previous maps 78 4.2.3.2. The published shared desert regions are not the most depleted regions in the genome 79 4.2.3.3. Levels of archaic introgression in shared deserts for the IGDP data set are comparable 82 4.2.3.4. Shared deserts unique to either the Vernot or Sankararaman set have lower mean percentage introgression 84 4.2.3.5. Refined shared deserts 84 4.2.3.6. Overlap of refined shared deserts with genes 87 4.2.3.7. Enrichment analyses 88 4.2.3.8. Overlap with regions under ancient positive selection on the AMH lineage 89 4.2.3.9. Overlap of refined shared deserts with (nearly) fixed differences (nFD) 89 4.2.4. Discussion 94 4.2.5. Acknowledgements 98 5. Discussion and outlook 99 5.1. Interpreting immune gene diversity in archaic humans 99 5.2. Implications from refined deserts of archaic ancestry 104 5.2.1. Comments on the origin of desert regions 106 5.2.2. Candidates for functional molecular testing in refined deserts 107 5.2.3. Future directions in the characterisation and definition of shared deserts 110 5.3. Future directions beyond shared deserts 115 6. Outlook: Molecular functional testing of candidate variants 118 7. Conclusions and final remark 122 8. Supplementary information (SI) 124 8.1. SI: Immune gene diversity in archaic and present-day humans 124 8.2. SI: Refining deserts of archaic ancestry 152 Index of figures 216 Index of tables 218 Index of supplementary data files 220 References 221 Abbreviations 240 Acknowledgements/Danksagungen 242 Curriculum vitae 244 Publications 248 Selected talks 249 Poster presentations 249 Selbstständigkeitserklärung 250 Nachweis über Anteile der Co-Autor:innen 251