A genomic perspective on variations in the molecular toolkit for development and on the evolution of parthenogenesis in Nematoda

The phylum Nematoda is characterised by a huge diversity of species that exploit almost all habitats on earth. Despite their prevalence in a wide range of different ecosystems, nematodes adhere to a strikingly strict Bauplan with only minor variations, even between two large groups that split more than 400 million years ago. The conservation of the final adult body form is quite special and not common in other animal taxa; this exceptional conservatism in the Bauplan, and the very similar patterns of early development observed in the model organisms C. elegans, P. pacificus and Ascaris together, have led scientist to suggest that these mechanisms of early development are archetypical for the phylum. However, analysis pioneered in the Schierenberg laboratory throughout the last 25 years challenged this view by describing considerable variations of early development in several species from different branches of the phylum. These observations together with data from divergent species in Panarthropoda gave rise to the question whether the molecular toolkit for nematode development could be subject to change as well. In the thesis presented here, this question is addressed from a genomic perspective, assembling and analysing large-scale data from species on different taxonomical levels. Based on these data comparisons have been made ranging from species at phylogenetically antipodal positions in the phylum separated by hundreds of millions of years of evolution to genera in one specific clade of the nema- tode tree, and finally the comparison of two closely related genera. In all these taxa Gene Regulatory Networks (GRNs) of early development are analysed and set into perspective with the common model of the nematode developmental toolkit drawn from C. elegans. I used these assays to test whether recently widely discussed theories on the role of GRNs for development deliver valid predictions for the evolution of early development in Nematoda. In fact, I find that the emerging picture supports such hypotheses of GRN evolution: in many pathways intermediate genetic switches appear to be exchanged by processes collectively called “Developmental System Drift (DSD), while upstream and downstream acting genes are more likely to be conserved. Despite this disparity across Nematoda, an analysis of genes retained across all Bilateria shows that this hugely diverse taxon, comprising Nematoda, could be characterized by aprocess of minimal divergence namely the phase in development when the adult body form is constructed. In Nematoda, parthenogenesis evolved in several genera, with a hotspot in clade IV of the phylum. The data sampled to assess the evolution of development in this thesis are used to elucidate the origin and molecular mechanisms underlying parthenogenesis in the genus Panagrolaimus. While the establishment of a re-shuffling mechanisms of GRNs through DSD does not yet allow us to unravel the distinct molecular mechanisms underpinning the establishment and maintenance of parthenogenesis, we have good evidence that parthenogenetic species in the genus Panagrolaimus are polyploid hybrids. This finding supports the hypothesis that hybridisation is a common route to parthenogenesis in Nematoda, as found in many other taxa as well. Parthenogenesis has also been linked to survival in novel and extreme environments, this would be facilitated in the Panagrolaimus species as they are capable of undergoing cryptobiosis (complete desiccation) in contrat to C.elegans and most other nematodes tested. Exploring the trait from a genomic perspective, we found genes known to be acting in this process in Panagrolaimus, but more importantly an intriguing link to Horizontal Gene Transfer (HGT) was found. Genes acquired through HGT appear to lend Panagrolaimus an adaptive advantage in extreme environments by acting in DNA repair mechanisms, which are important during rehydration. This illustrates the previously underestimated importance of HGT in Metazoa. The genomic and transcriptomic data sampled and assembled for this thesis can serve as a basis for future projects analysing the evolution of developmental systems with regards to GRNs and DSD, as well as detailed analyses of anhydrobiosis and the molecular background of parthenogenesis

The Politics of Knowledge in Inclusive Development and Innovation

This book develops an integrated perspective on the practices and politics of making knowledge work in inclusive development and innovation. While debates about development and innovation commonly appeal to the authority of academic researchers, many current approaches emphasise the plurality of actors with relevant expertise for addressing livelihood challenges. Adopting an action-oriented and reflexive approach, this volume explores the variety of ways in which knowledge works, paying particular attention to dilemmas and controversies. The six parts of the book address the complex interplay of knowledge and politics, starting with the need for knowledge integration in the first part and decolonial perspectives on the politics of knowledge integration in the second part. The following three parts focus on the practices of inclusive development and innovation through three major themes of learning for transformative change, evidence, and digitisation. The final part of the book addresses the governance of knowledge and innovation in the light of political struggles about inclusivity. Exploring conceptual and practical themes through case studies from the Global North and South, this book will be of great interest to students, scholars, and practitioners researching and working in development studies, epistemology, innovation studies, science and technology studies, and sustainability studies more broadly

The politics of knowledge in inclusive development and innovation

This book develops an integrated perspective on the practices and politics of making knowledge work in inclusive development and innovation. While debates about development and innovation commonly appeal to the authority of academic researchers, many current approaches emphasize the plurality of actors with relevant expertise for addressing livelihood challenges. Adopting an action-oriented and reflexive approach, this volume explores the variety of ways in which knowledge works, paying particular attention to dilemmas and controversies. The six parts of the book address the complex interplay of knowledge and politics, starting with the need for knowledge integration in the first part and decolonial perspectives on the politics of knowledge integration in the second part. The following three parts focus on the practices of inclusive development and innovation through three major themes of transformative learning, evidence, and digitization. The final part of the book addresses the governance of knowledge and innovation in the light of political struggles about inclusivity. Exploring conceptual and practical themes through case studies from the Global North and South, this book will be of great interest to students, scholars and practitioners researching and working in development studies, epistemology, innovation studies, science and technology studies and sustainability studies more broadly

Semantic discovery and reuse of business process patterns

Patterns currently play an important role in modern information systems (IS) development and their use has mainly been restricted to the design and implementation phases of the development lifecycle. Given the increasing significance of business modelling in IS development, patterns have the potential of providing a viable solution for promoting reusability of recurrent generalized models in the very early stages of development. As a statement of research-in-progress this paper focuses on business process patterns and proposes an initial methodological framework for the discovery and reuse of business process patterns within the IS development lifecycle. The framework borrows ideas from the domain engineering literature and proposes the use of semantics to drive both the discovery of patterns as well as their reuse

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Issues of recognition and participation in changing times: the inclusion of refugees in higher education in the UK

Higher Education has become and an increasingly diverse and globalised system in which the binaries between ‘traditional’ and ‘non-traditional’ students, exclusion and inclusion have less resonance and analytical purchase. Drawing on longitudinal, empirical research with a group of refugees in higher education, this paper will argue that higher education can be marked simultaneously by belonging and recognition, deficit and exclusion. Complex differences and inequalities remain hidden and unspoken, raising new questions and challenges for pedagogy and for equal participation of students

Bioinspired metaheuristic algorithms for global optimization

This paper presents concise comparison study of newly developed bioinspired algorithms for global optimization problems. Three different metaheuristic techniques, namely Accelerated Particle Swarm Optimization (APSO), Firefly Algorithm (FA), and Grey Wolf Optimizer (GWO) are investigated and implemented in Matlab environment. These methods are compared on four unimodal and multimodal nonlinear functions in order to find global optimum values. Computational results indicate that GWO outperforms other intelligent techniques, and that all aforementioned algorithms can be successfully used for optimization of continuous functions

Experimental Evaluation of Growing and Pruning Hyper Basis Function Neural Networks Trained with Extended Information Filter

In this paper we test Extended Information Filter (EIF) for sequential training of Hyper Basis Function Neural Networks with growing and pruning ability (HBF-GP). The HBF neuron allows different scaling of input dimensions to provide better generalization property when dealing with complex nonlinear problems in engineering practice. The main intuition behind HBF is in generalization of Gaussian type of neuron that applies Mahalanobis-like distance as a distance metrics between input training sample and prototype vector. We exploit concept of neuron’s significance and allow growing and pruning of HBF neurons during sequential learning process. From engineer’s perspective, EIF is attractive for training of neural networks because it allows a designer to have scarce initial knowledge of the system/problem. Extensive experimental study shows that HBF neural network trained with EIF achieves same prediction error and compactness of network topology when compared to EKF, but without the need to know initial state uncertainty, which is its main advantage over EKF