For the last two centuries, humans have been changing the Earth through their way of life. Our actions are not only causing climate change and leading to prolonged periods of drought, they are also leading to an overaccumulation of nutrients in soil, due to burning of fossil fuels and fertilization of agricultural fields. Both factors are threatening the world beneath our feet: the soils. They may look rather boring and lifeless, but soils are actually home to many organisms—from tiny bacteria to agile millipedes and slimy earthworms—all of which contribute to processes that are indispensable to life on Earth. For example, the activity of these organisms promotes decomposition of plantmaterial, which ensures that the farmlands on which we grow our food remain fertile. As almost all soil organisms are very sensitive to changes in their environments,wewanted to knowwhatwould happen if drought and over-fertilization occurred together

Skeletal muscles drive voluntary movements. Striated muscles allow fish to swim, birds to fly and our heart to beat. Skeletal muscles are built of multiple fascicles, which are bundles containing many muscle fibers. Looking at these structures under a microscope, smaller structures of muscle fibers, so-called myofibrils, become visible. These structures are highly organized and show regular patterns of specific units. These specific periodic subunits are the sarcomeres. Sarcomeres self-assemble as the smallest unit of skeletal muscles. Mature sarcomeres are crystal-like structures with a specific size of 2-3 micrometer. Sarcomeres are bounded by the so-called Z-disc, which contains more than thirty different proteins. Polar actin filaments are cross-linked to the Z-disc. Myosin motor filaments are anchored, facing the center of the sarcomere. The giant protein titin links myosin and actin filaments and stabilizes the sarcomere. Sarcomeres shorten in length during muscle contraction, by relative sliding of myosin through actin filaments. The myosin motor filaments walk through the polar actin filament, under energy conversion. While this sliding mechanism is known, it is unclear how sarcomeres form during the multi-stage developmental process of skeletal muscles. How to build a sarcomere? Despite many years of research, it is poorly understood how sarcomeres self-assemble into regular patterns. In this context, the main questions are: which sarcomere components regularly align first, and how are actin filaments orientated with the correct polarity? To answer these questions, we observe early stages of myofibrillogenesis in the fruit fly Drosophila melanogaster and quantify the regular alignment of selected proteins using a new algorithm. Our result: Data of early stages of myofibrillogenesis display a temporal order during sarcomere assembly. Myosin, titin (Sallimus in fruit fly) and the Z-disc proteins alpha-actinin pattern first, while actin filaments only follow later. With these experimental observations, we postulate a new theoretical framework of sarcomere assembly. We establish a minimal mathematical model, including possible molecular interactions between myosin and Z-disc proteins. In particular, we show that a non-local interaction with the protein titin is sufficient to drive the pattern formation process. With this non-local interaction, we take into account that myosin and titin are extended filaments of a specific size, setting the sarcomere length. With agent-based simulations we demonstrate that the model is robust to stochastic small number fluctuations. In addition, it is known that mechanical tension is induced during myofibrillogenesis. Local tension, produced by myosin motor activity can guide the assembly of sarcomeres, too. Thus, we formulate a second minimal mathematical model accounting for local tension. Specifically, we set the focus on the non-covalent binding of alpha-actinin (catch-bond behavior). In the presence of local tension, the lifetime of alpha-actinin increases. We demonstrate for this second model that such an alternative non-local interaction can give rise to periodic patterns of a specific length under presence of mechanical tension, even though it is less robust. We discuss similarities and differences of both models and propose the possibility that myofibrillogenesis in biological systems is a combination of both models.

The extracellular matrix (ECM) is the highly hydrated, protein- and glycosaminoglycan- (GAG) based cell environment that provides cell-instructive cues like the mechanical stabilization of the cells and transmission of biochemical and physical signals. To biochemically and mechanically mimic the ECM, hydrogels with the highly negatively charged GAG heparin in interplay with a stabilizing polymer network are of high interest in biomaterial engineering. The application as cell-instructive materials allows for controlling transport processes of signaling molecules within the matrices, cell growth and differentiation behavior, and cellular fate decisions. In particular, heparin-based biomaterials enable targeted sequestration of signaling molecules on the one hand, but also sustained delivery of them with a lower necessary amount to be used, in contrast to the discontinuous application of solutes. In addition, heparin-based biomaterials can protect the loaded cargo from enzymatic degradation and conformational changes.[1]–[3] The affinity to signaling molecules as key feature provides the potential for applications in wound healing and tissue regeneration. Synthetic sulfonated polymers (SSPs) as synthetic heparin analogs can address multiple drawbacks of native heparin, such as its heterogeneous chemical structure and the potential risk of viral contamination from the animal isolation source.[4],[5] Due to a large number of molecular design opportunities in particular the degree of sulfation, sulfate volume concentration, sulfate or sulfonate nature, distance of the sulf(on)ate from the backbone, and hydrophobicity of the polymers, biochemical processes may be controlled in a targeted manner. The chemical possibilities for forming a hydrogel network based on SSPs are far more diverse with synthetic, freely designable polymers to achieve a targeted structure and chemical nature of the network. Here, the aim was to introduce a library of SSPs to replace heparin in fully synthetic hydrogels capable of modulating cell-instructive cues such as soluble factor signaling, adhesiveness, and growth behavior of integrated cells. Accordingly, a library of systematically varied SSPs differing in degree of sulfation, sulfate or sulfonate conjugation, hydrophobicity, and sulf(on)ate distance to the backbone have been synthesized from by polymer analog reaction of various sulf(on)ated amines with a polyacrylate (15 kDa, sodium salt) as the polymeric backbone. The polymers have been thoroughly characterized by proton nuclear magnetic resonance (1H-NMR), Fourier-transform infrared spectroscopy (FTIR), asymmetric flow field flow fractionation (AF4) coupled light scattering analysis, and microscale thermophoresis (MST) for their molecular composition, stability in aqueous solution, conformation, and interaction with a chosen signal molecule. The affinity of the very stable coiled polymers under physiological conditions to signaling molecules depends mainly on the degree of sulfation, sulfate or sulfonate nature, and hydrophobicity. The SSPs are crosslinked with 4-arm star-shaped poly(ethylene glycol) (starPEG) either directly to form amide-crosslinked hydrogels or by pre-functionalization via Michael-type addition to prepare cell-instructive hydrogels, each with graded mechanical properties. The affinity of these hydrogels for various signaling molecules can be quantified compared to heparin-based ones and attributed to the influence of the degree of sulfation, sulfate volume concentration, sulfate or sulfonate nature, and hydrophobicity. The potential of SSPs in functional 3D tissue cultures could be confirmed by renal morphogenesis and neural network formation in the corresponding hydrogels by collaborators. Further on, the synthesis procedure of hydrogel precursors has been transferred to fully automated procedures. Because standardized production of cell-instructive hydrogels at low compositional and batch-to-batch variation and material compliance can benefit from high-throughput synthesis and liquid handling robots. An automated multistage workflow was developed to synthesize hydrogel precursors, carry out hydrogel formation, and execute cell culture experiments with cells embedded in the hydrogels. The protocol combines two robotic liquid handling systems and a microscope for automated sample imaging and cell analysis. The customized heparin and SSP maleimidation procedures, including temperature-regulated synthesis, purification, and aliquotation, were implemented on a customized liquid-handling robot. The resulting hydrogel precursors were analyzed for their maleimide conjugation efficiency and purity by 1H-NMR and conductivity measurements and for their hydrogel formation ability. This automated synthesis can ensure the quality and production of good manufacturing practice (GMP)-compliant hydrogel materials. Automated SSP hydrogel preparation, cell culture, and analysis can further promote combinatorial approaches to biomedical applications of cell-instructive materials. References [1] Lohmann, N.; Schirmer, L.; Atallah, P.; Wandel, E.; Ferrer, R. A.; Werner, C et al. Glycosaminoglycan-Based Hydrogels Capture Inflammatory Chemokines and Rescue Defective Wound Healing in Mice. Sci. Transl. Med. 2017, 9 (386), 1–12. [2] Schirmer, L.; Atallah, P.; Werner, C.; Freudenberg, U. StarPEG-Heparin Hydrogels to Protect and Sustainably Deliver IL-4. Adv. Healthc. Mater. 2016, 5 (24), 3157–3164. [3] Liang, Y.; Kiick, K. L. Heparin-Functionalized Polymeric Biomaterials in Tissue Engineering and Drug Delivery Applications. Acta Biomater. 2014, 10 (4), 1588–1600. [4] Blossom, D. B.; Kallen, A. J.; Patel, P. R.; Elward, A.; Robinson, L.; Gao, G. et al. Outbreak of Adverse Reactions Associated with Contaminated Heparin. N. Engl. J. Med. 2008, 359 (25), 2674–2684. [5] Hirsh, J.; Dalen, J. E.; Anderson, D. R.; Poller, L.; Bussey, H.; Ansell, J. et al. Oral Anticoagulants. Chest 1998, 114 (5), 445S-469S.

The silica-based cell walls of diatoms are prime examples of genetically controlled, species-specific mineral architectures. The physical principles underlying morphogenesis of their hierarchically structured silica patterns are not understood, yet such insight could reveal novel routes towards synthesizing functional inorganic materials. Recent advances in imaging nascent diatom silica allow rationalizing possible mechanisms of their pattern formation. Here, we combine theory and experiments on the model diatom Thalassiosira pseudonana to put forward a minimal model for morphogenesis of branched rib patterns – a widespread feature of diatom cell walls. To this end, we developed an automated image analysis algorithm that enabled quantitative assessment of the morphological discrepancy between the experiments and model predictions. The model proposed here quantitatively recapitulates the time-course of rib pattern formation by accounting for silica biochemistry with autocatalytic formation of diffusible silica precursors followed by conversion into solid silica. We propose that silica deposition releases an inhibitor that slows down up-stream precursor conversion, thereby implementing a self-replicating reaction-diffusion system, recapitulated by a non-classical Turing mechanism. The proposed mechanism highlights the role of geometrical cues for guided self-organization, rationalizing the instructive role for the single initial pattern seed known as primary silicification site present in diatoms. The model features a wide spectrum of possible pattern morphologies depending on the model parameters, suggesting that this model may be applicable in other diatom species. Moreover, due to the generic nature of the proposed model for branching morphogenesis, the mechanism identified here may be relevant also in other biological systems known to exhibit.

Epithelial tissues are one of the most abundant tissues in our body. They make up essential organs like the gut, heart and eyes. These organs take up their complex 3D shapes during normal development of the embryo. Our understanding of such large-scale 3D shape changes is limited mainly due to the technical difficulties of imaging and quantifying such developmental events. In this thesis, I study two events in which epithelial monolayers change their 3D shape. In both the projects, I use data from light-sheet microscopic images of developmental events. These data are provided by my collaborators. In this thesis, I further analyzed them using quantitative approaches and interpreted them using computational models. In the first project, I study a case of a developing tissue inside a rigid confinement. A perfect model system for this is the Drosophila embryo which consists of an epithelial monolayer (blastoderm) inside a rigid shell (vitelline membrane). During gastrulation, the blastoderm is under compressional stresses due to tissue proliferation and compression from the germband extension. During this time, an invagination separating the future head and the trunk region appears. This is known as the cephalic furrow (CF). As the CF disappears after some time, its relevance in the normal development of the embryo is unclear. To understand its role, my collaborators image the blastoderm in mutant embryos which lack CF. These mutant embryos have either of the genes even-skipped (eve) or buttonhead (btd) knocked down. In the absence of CF, temporary ectopic folds appear in the blastoderm in locations which vary between embryos. Unlike the CF, ectopic folds appear suddenly and hence look like buckling events. I hypothesize that ectopic folds appear because of the compressive stresses generated in the blastoderm during the germband extension or by the compression of tissues that are adjacent to mitotic domains. Moreover, in normal embryos, CF, which is a controlled invagination, acts as a sink for the compressive stresses and thus suppresses ectopic folds. To test this hypothesis, I modelled the blastoderm as a 2D elastic tissue which is confined inside a rigid boundary acting as the vitelline membrane. In my model, I show that the stresses generated by both the germband extension and the mitotic domains contribute to the formation of ectopic folds. I model the CF as a region with some preferred intrinsic curvature, thus acting as a programmed fold. I show that ectopic folds are inhibited in the presence of a CF. However, the efficiency of the CF depends on the strength of the CF and, interestingly, the timing of the CF. I observe that even a weak CF can inhibit ectopic folds if it appears before the appearance of mitotic domains. I speculate that this could explain why the CF appears before the mitotic domains in the Drosophila embryo. n the second project, I study a case of shape change associated with the development of the Drosophila wing. Here I focus on the wing disc pouch, an epithelial monolayer that forms the adult wing blade. During metamorphosis, the larval wing disc evaginates to form the pupal wing. This process is known as eversion. During late larval stage, the wing disc pouch looks like a spherical cap. I refer to this stage as wL3 (wandering larval stage 3) in this thesis. Four hours after pupariation (4hAPF), the spherical cap deforms to an asymmetric dome such that it has a higher curvature along one cross-section compared to its perpendicular cross-section. Using segmented outlines of the wing in the two cross-sections of multiple images at different developmental stages, I compute the mean shape and quantify the curvature along the arclength of these shapes. To model this shape change, I use a 3D spring lattice whose initial curvature is matched to the curvature of the wL3 stage. Next, using apical cell shape data, provided by my collaborator, I compute a quantity referred to as a “spontaneous deformation tensor”. This tensor quantifies the amount of deformation, at a specific location between two developmental stages, due to cell area changes, cell elongation changes, and neighbour exchanges. I input this deformation pattern in my model which then changes its 3D shape. I find that the deformation due to changes in cell area and elongation increase the size of the tissue globally without affecting its curvature. However, the deformation due to cell rearrangements enhances curvature along one cross-section more than its perpendicular cross-section. Overall, the quantifications and modelling shows how different cellular behaviours deform the tissue locally. Moreover, a spatial pattern of different cellular behaviours can explain essential aspects of the shape change observed during the development of the wing.

The representation of incoming information, goals and the flexible processing of these are required for cognitive control. Efficient mechanisms are needed to decide when it is important that novel information enters working memory (WM) and when these WM ‘gates’ have to be closed. Compared to neural foundations of maintaining information in WM, considerably less is known about what neural mechanisms underlie the representational dynamics during WM gating. Using different EEG analysis methods, we trace the path of mental representations along the human cortex during WM gate opening and closing. We show temporally nested representational dynamics during WM gate opening and closing depending on multiple independent neural activity profiles. These activity profiles are attributable to a ventral stream-prefrontal cortex processing cascade. The representational dynamics start in the ventral stream during WM gate opening and WM gate closing before prefrontal cortical regions are modulated. A regional specific activity profile is shown within the prefrontal cortex depending on whether WM gates are opened or closed, matching overarching concepts of prefrontal cortex functions. The study closes an essential conceptual gap detailing the neural dynamics underlying how mental representations drive the WM gate to open or close to enable WM functions such as updating and maintenance.

Learning and memory of recurring sound patterns play a crucial role for efficient perception of acoustic signals that dynamically unfold in time. Human listeners are remarkably sensitive to patterns, i.e., short sound segments that repeat within continuous auditory input, and can form robust memory representations for distinct patterns through repeated exposure. While there is compelling evidence for an exceptional perceptual learning capacity even for novel and meaningless acoustic patterns, less is known about whether and how the acquisition of memory representations at multiple time scales is modulated by the listening context. The present thesis comprises one behavioural and two EEG studies, which aimed to explore pattern repetition detection in continuous sounds as well as implicit memory formation for specific patterns that recur over a longer time scale (unbeknownst to the participants) under different listening conditions. More specifically, three aspects of the listening context were experimentally manipulated: presentation format of the repeating pattern (Study 1), listeners’ attentional focus, and temporal regularity of pattern repetition within a longer continuous sound sequence (Study 2 & 3). Combined results suggest that learning of acoustic patterns through repetition builds on a flexible mechanism that is robust against varying contextual demands, such as they often occur during naturalistic listening. Despite reliable pattern repetition detection and longer-term memory formation across all listening contexts, certain contextual features enhanced short-term perceptual representations, which in turn improved longer term memory formation. Together, these findings advance the understanding of (shorter- and longer-term) memory acquisition for novel acoustic patterns and suggest that auditory perceptual learning can be facilitated through targeted design of listening contexts.

Leptin and its receptor are essential for regulating food intake, energy expenditure, glucose homeostasis and fertility. Mutations within leptin or the leptin receptor cause early-onset obesity and hyperphagia, as described in human and animal models. The effect of both heterozygous and homozygous variants is much more investigated than compound heterozygous ones. Recently, we discovered a spontaneous compound heterozygous mutation within the leptin receptor, resulting in a considerably more obese phenotype than described for the homozygous leptin receptor deficient mice. Accordingly, we focus on compound heterozygous mutations of the leptin receptor and their effects on health, as well as possible therapy options in human and animal models in this review.

GRB14/COBLL1 locus has been shown to be associated with body fat distribution (FD), but neither the causal gene nor its role in metabolic diseases has been elucidated. We hypothesize that GRB14/COBLL1 may act as the causal genes for FD-related SNPs (rs10195252 and rs6738627), and that they may be regulated by SNP to effect obesity-related metabolic traits. We genotyped rs10195252 and rs6738627 in 2860 subjects with metabolic phenotypes. In a subgroup of 560 subjects, we analyzed GRB14/COBLL1 gene expression in paired visceral and subcutaneous adipose tissue (AT) samples. Mediation analyses were used to determine the causal relationship between SNPs, AT GRB14/COBLL1 mRNA expression, and obesity-related traits. In vitro gene knockdown of Grb14/Cobll1 was used to test their role in adipogenesis. Both gene expressions in AT are correlated with waist circumference. Visceral GRB14 mRNA expression is associated with FPG and HbA1c. Both SNPs are associated with triglycerides, FPG, and leptin levels. Rs10195252 is associated with HbA1c and seems to be mediated by visceral AT GRB14 mRNA expression. Our data support the role of the GRB14/COBLL1 gene expression in body FD and its locus in metabolic sequelae: in particular, lipid metabolism and glucose homeostasis, which is likely mediated by AT GRB14 transcript levels.

Because having a wide variety of species on earth is essential for human health and our economy, conservation areas have been established worldwide. These conservation efforts mostly focus on “beauties,” such as pandas or tigers. Many other species are not as charismatic and thus merely considered “beasts.” Many “beasts” live invisible lives in the soil but are extremely important for mankind. We asked whether current conservation efforts based on saving the “beauties” can help to automatically protect the “beasts.” In other words, is there high biological diversity in the soil at locations with high aboveground biodiversity? We mapped aboveground and belowground biodiversity across the world and found that there are many areaswhere aboveground biodiversity is high and belowground biodiversity is low, or the other way around. Our results suggest that conserving the “beauties” may not be enough to protect the “beasts.” We need to consider life belowground when planning new conservation areas.