A non-bilaterian perspective on the development and evolution of animal digestive systems

Digestive systems and extracellular digestion are key animal features, but their emergence during early animal evolution is currently poorly understood. As the last common ancestor of non-bilaterian animal groups (sponges, ctenophores, placozoans and cnidarians) dates back to the beginning of animal life, their study and comparison provides important insights into the early evolution of digestive systems and functions. Here, I have compiled an overview of the development and cell biology of digestive tissues in non-bilaterian animals. I will highlight the fundamental differences between extracellular and intracellular digestive processes, and how these are distributed among animals. Cnidarians (e.g. sea anemones, corals, jellyfish), the phylogenetic outgroup of bilaterians (e.g. vertebrates, flies, annelids), occupy a key position to reconstruct the evolution of bilaterian gut evolution. A major focus will therefore lie on the development and cell biology of digestive tissues in cnidarians, especially sea anemones, and how they compare to bilaterian gut tissues. In that context, I will also review how a recent study on the gastrula fate map of the sea anemone Nematostella vectensis challenges our long-standing conceptions on the evolution of cnidarian and bilaterian germ layers and guts.publishedVersio

Comparative molecular and morphogenetic characterisation of larval body regions in the polychaete annelid Platynereis dumerilii

The aim of this thesis was the molecular and morphogenetic characterisation of the larval body regions of the polychaete Platynereis dumerilii for evolutionary comparison with the body regions of other protostome and deuterostome model species. I have described the expression of several conserved homeobox transcription factors that broadly mark the neuroectoderm of the different larval body regions and can therefore be used as regionalisation markers in the trochophore larva of Platynereis dumerilii. A six3 orthologue is a marker gene for the prostomium, the most anterior region of the trochophore larva. The peristomium that harbours the mouth region and the prototroch ciliary band expresses an otx orthologue as regionalisation marker in Platynereis. The subdivision of the metastomium into larval segments has been analysed by Pdu-engrailed expression. It is found to give rise to four larval segments, of which the first one is reduced and bears the first tentacular cirri. It is furthermore characterised as the most anterior gbx-expressing segment and is innervated by axons that connect to the circumoesophageal connectives left and right of the mouth opening. The second larval segment develops into the first chaetiferous segment and is characterised by the anterior-most hox1 expression. The molecular and morphological comparison of the Platynereis anterior CNS with arthropods brains has allowed homologisation of the polychaete prostomial ganglia to the “archicerebrum” (putative most anterior part of the protocerebrum of arthropods), the peristomial ganglia with the “prosocerebrum” (putative posterior part of the protocerebrum), the ganglia of the first larval segment with the deutocerebrum and the second larval segment (first chaetiferous) ganglia with the tritocerebrum. Comparison with enteropneust (basal deuterostomes) larvae suggests homology and evolutionary conservation in Bilateria of the following larval body regions: prostomium/prosoma (six3), peristomium/mesosoma (otx) and metastomium/metasoma (gbx and hox1). This is supported by the origin and localisation of the different mesodermal populations in Platynereis that I have characterised by the expression of six3, fgfr, myoD, twist, mef2 and troponin I. I have found that the Platynereis “brain mesoderm” expresses six3 as does the enteropneust prosoma. The mesodermal sheath around the stomodaeum in Platynereis has morphological similarities to the enteropneust mesosomal coelomic pouches and expresses fgfr and twist in Platynereis. The trunk mesoderm in Platynereis dynamically expresses myoD, twist, and mef2, forms differentiated muscles cells as described by troponin I expression and originates from a similar position as the enteropneust metasomal mesoderm. The molecular comparison of Platynereis neuroectodermal regions with lower vertebrates’ brain regions suggests homology of prostomium/forebrain (six3), peristomium/midbrain (otx) and trunk CNS/hindbrain (gbx and hox1). In vertebrates, the midbrain-hindbrain boundary (positioned at the otx/gbx boundary) is a morphogenetic boundary between the posterior hindbrain/spinal chord region that undergoes convergent extension and the anterior forebrain-/midbrain regions that do not extend. I have found that reminiscent to vertebrate convergent extension in the hindbrain, the gbx-/hox1-expressing neural plate in Platynereis undergoes convergent extension by mediolateral cell intercalation that is possibly controlled by the non-canonical Wnt pathway. Similar to the vertebrate midbrain, the otx-expressing peristomium does not extend. Yet, these movements take place along a slit-like blastopore that develops into both mouth and anus in Platynereis, but occur in front of the blastopore that develops exclusively into the anus in vertebrates. This suggests that convergent extension movements are ancestral in Bilateria and have evolved in early bilaterians to relocate the blastopore-derived mouth and anus to opposite ends of the elongating body axis

Evolutionarily conserved aspects of animal nutrient uptake and transport in sea anemone vitellogenesis

The emergence of systemic nutrient transport was a key challenge during animal evolution, yet it is poorly understood. Circulatory systems distribute nutrients in many bilaterians (e.g., vertebrates and arthropods) but are absent in non-bilaterians (e.g., cnidarians and sponges), where nutrient absorption and transport remain little explored at molecular and cellular levels. Vitellogenesis, the accumulation of egg yolk, necessitates high nutrient influx into oocytes and is present throughout animal phyla and therefore represents a well-suited paradigm to study nutrient transport evolution. With that aim, we investigated dietary nutrient transport to the oocytes in the cnidarian Nematostella vectensis (Anthozoa). Using a combination of fluorescent bead labeling and marker gene expression, we found that phagocytosis, micropinocytosis, and intracellular digestion of food components occur within the gonad epithelium. Pulse-chase experiments further show that labelled fatty acids rapidly translocate from the gonad epithelium through the extracellular matrix (ECM) into oocytes. Expression of conserved lipid transport proteins vitellogenin (vtg) and apolipoprotein-B (apoB) and colocalization of labeled fatty acids with a fluorescently tagged ApoB protein further support the lipid-shuttling role of the gonad epithelium. Complementary oocyte expression of very low-density lipoprotein receptor (vldlr) orthologs, which mediate endocytosis of bilaterian ApoB- and Vtg-lipoproteins, supports that this evolutionarily conserved ligand/receptor pair underlies lipid transport during sea anemone vitellogenesis. In addition, we identified lipid- and ApoB-rich cells with potential lipid transport roles in the ECM. Altogether, our work supports a long-standing hypothesis that an ECM-based lipid transport system predated the cnidarian-bilaterian split and provided a basis for the evolution of bilaterian circulatory systems.publishedVersio

Conducting a Large-scale Field Test of a Smartphone-based Communication Network for Emergency Response

Smartphone-based communication networks form a basis for services in emergency response scenarios, where communication infrastructure is impaired or overloaded. Still, their design and evaluation are largely based on simulations that rely on generic mobility models and weak assumptions regarding user behavior. For a realistic assessment, scenario-specific models are essential. To this end, we conducted a large-scale field test of a set of emergency services that relied solely on ad hoc communication. Over the course of one day, we gathered data from smartphones distributed to 125 participants in a scripted disaster event. In this paper, we present the scenario, measurement methodology, and a first analysis of the data. Our work provides the first trace combining user interaction, mobility, and additional sensor readings of a large-scale emergency response scenario, facilitating future research

NvPrdm14d-expressing neural progenitor cells contribute to non-ectodermal neurogenesis in Nematostella vectensis

Neurogenesis has been studied extensively in the ectoderm, from which most animals generate the majority of their neurons. Neurogenesis from non-ectodermal tissue is, in contrast, poorly understood. Here we use the cnidarian Nematostella vectensis as a model to provide new insights into the molecular regulation of non-ectodermal neurogenesis. We show that the transcription factor NvPrdm14d is expressed in a subpopulation of NvSoxB(2)-expressing endodermal progenitor cells and their NvPOU4-expressing progeny. Using a new transgenic reporter line, we show that NvPrdm14d-expressing cells give rise to neurons in the body wall and in close vicinity of the longitudinal retractor muscles. RNA-sequencing of NvPrdm14d::GFP-expressing cells and gene knockdown experiments provide candidate genes for the development and function of these neurons. Together, the identification of a population of endoderm-specific neural progenitor cells and of previously undescribed putative motoneurons in Nematostella provide new insights into the regulation of non-ectodermal neurogenesis.publishedVersio

Stackelberg Planning: Towards Effective Leader-Follower State Space Search

Inspired by work on Stackelberg security games, we introduce Stackelberg planning, where a leader player in a classical planning task chooses a minimum-cost action sequence aimed at maximizing the plan cost of a follower player in the same task. Such Stackelberg planning can provide useful analyses not only in planning-based security applications like network penetration testing, but also to measure robustness against perturbances in more traditional planning applications (eg with a leader sabotaging road network connections in transportation-type domains). To identify all equilibria–exhibiting the leader's own-cost-vs.-follower-cost tradeoff–we design leader-follower search, a state space search at the leader level which calls in each state an optimal planner at the follower level. We devise simple heuristic guidance, branch-and-bound style pruning, and partial-order reduction techniques for this setting. We run experiments on Stackelberg variants of IPC and pentesting benchmarks. In several domains, Stackelberg planning is quite feasible in practice

Towards Automated Network Mitigation Analysis (extended version)

Penetration testing is a well-established practical concept for the identification of potentially exploitable security weaknesses and an important component of a security audit. Providing a holistic security assessment for networks consisting of several hundreds hosts is hardly feasible though without some sort of mechanization. Mitigation, prioritizing counter-measures subject to a given budget, currently lacks a solid theoretical understanding and is hence more art than science. In this work, we propose the first approach for conducting comprehensive what-if analyses in order to reason about mitigation in a conceptually well-founded manner. To evaluate and compare mitigation strategies, we use simulated penetration testing, i.e., automated attack-finding, based on a network model to which a subset of a given set of mitigation actions, e.g., changes to the network topology, system updates, configuration changes etc. is applied. Using Stackelberg planning, we determine optimal combinations that minimize the maximal attacker success (similar to a Stackelberg game), and thus provide a well-founded basis for a holistic mitigation strategy. We show that these Stackelberg planning models can largely be derived from network scan, public vulnerability databases and manual inspection with various degrees of automation and detail, and we simulate mitigation analysis on networks of different size and vulnerability

Towards Automated Network Mitigation Analysis

Penetration testing is a well-established practical concept for the identification of potentially exploitable security weaknesses and an important component of a security audit. Providing a holistic security assessment for networks consisting of several hundreds hosts is hardly feasible though without some sort of mechanization. Mitigation, prioritizing counter-measures subject to a given budget, currently lacks a solid theoretical understanding and is hence more art than science. In this work, we propose the first approach for conducting comprehensive what-if analyses in order to reason about mitigation in a conceptually well-founded manner. To evaluate and compare mitigation strategies, we use simulated penetration testing, i.e., automated attack-finding, based on a network model to which a subset of a given set of mitigation actions, e.g., changes to the network topology, system updates, configuration changes etc. is applied. Using Stackelberg planning, we determine optimal combinations that minimize the maximal attacker success (similar to a Stackelberg game), and thus provide a well-founded basis for a holistic mitigation strategy. We show that these Stackelberg planning models can largely be derived from network scan, public vulnerability databases and manual inspection with various degrees of automation and detail, and we simulate mitigation analysis on networks of different size and vulnerability

Faster Stackelberg Planning via Symbolic Search and Information Sharing

Stackelberg planning is a recent framework where a leader and a follower each choose a plan in the same planning task, the leader's objective being to maximize plan cost for the follower. This formulation naturally captures security-related (leader=defender, follower=attacker) as well as robustness- related (leader=adversarial event, follower=agent) scenarios. Solving Stackelberg planning tasks requires solving many related planning tasks at the follower level (in the worst case, one for every possible leader plan). Here we introduce new methods to tackle this source of complexity, through sharing information across follower tasks. Our evaluation shows that these methods can significantly reduce both the time needed to solve follower tasks and the number of follower tasks that need to be solved in the first place