2,355 research outputs found

    Human norovirus emergence and circulation in humans and animals

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    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    An investigation into mechanisms of regeneration specificity in planarian flatworms.

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    Many animals have the extraordinary ability to replace lost body parts, even so we humans do not. One critical but poorly understood aspect of this phenomenon is how wounds tailor the regeneration response to the particular target structure that needs to be regrown. In my thesis work I have attempted to address this problem in the champions of regeneration, the planarian flatworms. If one of these animals is cut into tiny pieces, each of the pieces will regenerate a head at the anterior end and tail at the posterior end. For over a century investigators have searched for the intrinsic polarity cue underlying this regeneration polarity, but until now its mechanistic basis is not known. The explicit goal of my thesis work was to identify this cue. The general approach that I have taken toward identification of the intrinsic polarity is to systematically compare two different planarian species with subtle variations in the establishment of regeneration polarity, Schmidtea mediterranea and Girardia tigrina. First, I demonstrate through systematic comparison of different amputation paradigms that regeneration polarity is dependent not only on species, but also on piece length, body size and anteroposterior axis position. Second, given that these findings are consistent with a gradient- based intrinsic polarity cue as prevalent hypothesis in the field, I tested whether the recently identified tail-to-head gradient of canonical Wnt (cWnt) signalling could be mechanistic basis of regeneration polarity. As precondition for doing so, I developed new approaches to measure and manipulate cWnt signalling in planaria. The data acquired with these tools suggest that the cWnt gradient may contribute to the observed position-dependence of regeneration polarity but is overall not the (only) intrinsic polarity cue. Third, I present my initial efforts to test whether the longitudinal muscle fibres (LMFs) in which notum is exclusively activated are an intrinsic polarity cue. My results suggest that “bundles” of short, intrinsically polarised LMFs running along the AP axis may express notum when they are cut anterior to their nucleus and moreover that misregulation of such a mechanism may underlie the species-dependence of regeneration polarity. Overall, the work presented in this thesis offers new insight into the cellular and conceptual basis of planarian regeneration polarity and, in doing so, the more general question of how regenerative organisms “sense” precisely what body part is missing and therefore needs to be regrown. Furthermore, it puts forward new hypotheses that through additional experimentation may explain lead to elucidation of the underlying molecular mechanisms

    MUL-Tree Pruning for Consistency and Compatibility

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    A multi-labelled tree (or MUL-tree) is a rooted tree leaf-labelled by a set of labels, where each label may appear more than once in the tree. We consider the MUL-tree Set Pruning for Consistency problem (MULSETPC), which takes as input a set of MUL-trees and asks whether there exists a perfect pruning of each MUL-tree that results in a consistent set of single-labelled trees. MULSETPC was proven to be NP-complete by Gascon et al. when the MUL-trees are binary, each leaf label is used at most three times, and the number of MUL-trees is unbounded. To determine the computational complexity of the problem when the number of MUL-trees is constant was left as an open problem. Here, we resolve this question by proving a much stronger result, namely that MULSETPC is NP-complete even when there are only two MUL-trees, every leaf label is used at most twice, and every MUL-tree is either binary or has constant height. Furthermore, we introduce an extension of MULSETPC that we call MULSETPComp, which replaces the notion of consistency with compatibility, and prove that MULSETPComp is NP-complete even when there are only two MUL-trees, every leaf label is used at most thrice, and every MUL-tree has constant height. Finally, we present a polynomial-time algorithm for instances of MULSETPC with a constant number of binary MUL-trees, in the special case where every leaf label occurs exactly once in at least one MUL-tree

    The largest crossing number of tanglegrams

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    A tanglegram T\cal T consists of two rooted binary trees with the same number of leaves, and a perfect matching between the two leaf sets. In a layout, the tanglegrams is drawn with the leaves on two parallel lines, the trees on either side of the strip created by these lines are drawn as plane trees, and the perfect matching is drawn in straight line segments inside the strip. The tanglegram crossing number cr(T){\rm cr}({\cal T}) of T\cal T is the smallest number of crossings of pairs of matching edges, over all possible layouts of T\cal T. The size of the tanglegram is the number of matching edges, say nn. An earlier paper showed that the maximum of the tanglegram crossing number of size nn tanglegrams is <12(n2)<\frac{1}{2}\binom{n}{2}; but is at least 12(n2)n3/2n2\frac{1}{2}\binom{n}{2}-\frac{n^{3/2}-n}{2} for infinitely many nn. Now we make better bounds: the maximum crossing number of a size nn tanglegram is at most 12(n2)n4 \frac{1}{2}\binom{n}{2}-\frac{n}{4}, but for infinitely many nn, at least 12(n2)nlog2n4\frac{1}{2}\binom{n}{2}-\frac{n\log_2 n}{4}. The problem shows analogy with the Unbalancing Lights Problem of Gale and Berlekamp

    Soil histories continue to structure the bacterial and oomycete communities of Brassicaceae host plants through time on the Canadian prairies

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    Afin d’étudier l’écologie microbienne, il est nécessaire, dans un premier temps, de déterminer quels micro-organismes sont présents dans un milieu et à quel instant. Ces informations sont requises pour pouvoir ensuite développer des outils permettant de prédire l’assemblage des communautés et les fonctions que celles-ci peuvent contenir. Cependant, la multitude des processus entrant en jeu dans la structure et la composition des communautés microbiennes, rendent leur étude complexe. Parmi les nombreux processus à étudier, il est notamment question de l’échelle temporelle à prendre en compte pour comprendre l’assemblage des communautés microbiennes. En effet, les événements historiques conditionnent la composition et la biodiversité des futures communautés microbiennes. Pourtant, dans les sols, peu d’études se sont intéressées à l’impact des événements historiques dans l’assemblage des communautés microbiennes. Par conséquent, l’objectif de cette thèse était de quantifier comment les différentes histoires du sol ont influencé la structure et biodiversité des communautés bactériennes et oomycètes associées aux plantes hôtes des Brassicaceae à travers le temps. Les rotations de cultures de Brassicaceae sont de plus en plus courantes dans le monde et ont démontré des avantages pour les cultures concernées, telles que la rétention de l’humidité du sol ou la suppression de certains agents pathogènes des plantes. En revanche, l’impact des rotations de cultures de Brassicaceae sur la structure et biodiversité des communautés microbiennes résidentes est peu connu. Ainsi, des terrains agricoles des prairies canadiennes ayant des expériences de rotations de cultures en cours ont été utilisés pour modéliser l’impact des histoires de sol précédemment établies sur les futures communautés microbiennes. Les communautés microbiennes des racines, de la rhizosphère, et du sol éloigné des racines des Brassicaceae ont été étudiées grâce aux métabarcodes d’ARNr 16S ou ITS. La PCR quantitative et des méthodes phylogénétiques ont été utilisées pour améliorer l’analyse des communautés microbiennes. Cette thèse illustre comment différentes histories de sol établies par les cultures de l’année précédente ont continué à structurer les communautés microbiennes de la rhizosphère tout au long de la saison de croissance, à différents stades de croissance, jusqu’à un an après leur établissement. Cependant, le phénomène de rétroactions entre plantes et micro-organismes a permis de masquer cet héritage dans la rhizosphere de différentes espèces hôtes de Brassicacea pour lesquelles des communautés bactériennes phylogénétiquement similaires ont été retrouvées malgré diverses histoires du sol. Nos résultats montrent également que les différentes espèces hôtes de Brassicacea n’avaient pas d’impact sur la structure des communautés d’oomycètes et que le stress hydrique limitait également cette structuration pour les communautés bactériennes. Dans ces deux cas, l’effet de l’histoire du sol était donc encore visible sur la structure les communautés microbiennes durant l’année subséquente. Les découvertes selon lesquelles différentes histoires de sol persistent jusqu'à un an, même en présence de nouvelles plantes hôtes, et qu’elles peuvent continuer à façonner les communautés microbiennes ont des implications importantes pour la gestion agricole et les recherches futures sur les composants physiques de l'histoire du sol. Comprendre comment l'histoire du sol est impliquée dans la structure et la biodiversité des communautés microbiennes à travers le temps est une limitation de l'écologie microbienne et est nécessaire pour utiliser les technologies microbiennes à l'avenir pour une agriculture durable et dans toute la société.A fundamental task of microbial ecology is determining which organisms are present, and when, in order to improve the predictive models of community assembly and functions. However, the heterogeneity of community assembly processes that underlie how microbial communities are formed and structured are makes assembly of taxonomic and functional profiles difficult. One reason for this challenge is the compounding effect temporal scales have on microbial communities. For example, historical events have been shown to condition future microbial community composition and biodiversity. Yet, how historical events structure microbial communities in the soil has not been well tested. Therefore, the objective of this thesis was to quantify how different soil histories influenced the structure and biodiversity of bacterial and oomycete communities associated with Brassicaceae host plants through time. Brassicaceae crop rotations are increasingly common globally, and have demonstrated benefits for the crops involved, such as retaining soil moisture, or suppressing certain plant pathogens. In contrast, there is a lack of knowledge surrounding how Brassicaceae crop rotations impact the structure and biodiversity of resident microbial communities. As such, on-going agricultural field experiments with crop rotations on the Canadian prairies were used to model how previously established soil histories impacted future microbial communities. The Brassicaceae microbial communities were inferred from the roots, rhizosphere and bulk soil using 16S rRNA or ITS metabarcodes. Quantitative PCR and phylogenetic methods were used to improve the analysis of the microbial communities. This thesis illustrates how different soil histories established by the previous year’s crops continued to structure the microbial rhizosphere communities throughout the growing season, at various growth stages, and up to a year after being established. However, active plant-soil microbial feedback allowed different Brassicaceae host species to mask the soil history in the rhizosphere and derive phylogenetically similar bacterial communities from these diverse soil histories. Furthermore, host plants were unable to structure the oomycete communities, and lost the ability to structure the bacterial rhizosphere communities under water stress. In both circumstances, the soil history continued to structure the microbial communities. The findings that different soil histories persist for up to a year, even in the presence of new host plants, and can continue to shape microbial communities has important implications for agricultural management and future research on the physical components of soil history. Understanding how soil history is involved in the structure and biodiversity of microbial communities through time is a limitation in microbial ecology and is required for employing microbial technologies in the future for sustainable agriculture and throughout society

    Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem

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    The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal with respect to some objective function and that lies within a constrained version of tree space. The popular species tree estimation method ASTRAL, for example, returns a tree that (1) maximizes the quartet score computed with respect to the input gene trees and that (2) draws its branches (bipartitions) from the input constraint set. This technique has yet to be used for classic parsimony problems where the input are binary characters, sometimes with missing values. Here, we introduce the clade-constrained character parsimony problem and present an algorithm that solves this problem in polynomial time for the Dollo criterion score. Dollo parsimony, which requires traits/mutations to be gained at most once but allows them to be lost any number of times, is widely used for tumor phylogenetics as well as species phylogenetics, for example analyses of low-homoplasy retroelement insertions across the vertebrate tree of life. Thus, we implement our algorithm in a software package, called Dollo-CDP, and evaluate its utility in the context of species phylogenetics using both simulated and real data sets. Our results show that Dollo-CDP can improve upon heuristic search from a single starting tree, often recovering a better scoring tree. Moreover, Dollo-CDP scales to data sets with much larger numbers of taxa than branch-and-bound while still having an optimality guarantee, albeit a more restricted one. Lastly, we show that our algorithm for Dollo parsimony can easily be adapted to Camin-Sokal parsimony but not Fitch parsimony

    Complexity Science in Human Change

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    This reprint encompasses fourteen contributions that offer avenues towards a better understanding of complex systems in human behavior. The phenomena studied here are generally pattern formation processes that originate in social interaction and psychotherapy. Several accounts are also given of the coordination in body movements and in physiological, neuronal and linguistic processes. A common denominator of such pattern formation is that complexity and entropy of the respective systems become reduced spontaneously, which is the hallmark of self-organization. The various methodological approaches of how to model such processes are presented in some detail. Results from the various methods are systematically compared and discussed. Among these approaches are algorithms for the quantification of synchrony by cross-correlational statistics, surrogate control procedures, recurrence mapping and network models.This volume offers an informative and sophisticated resource for scholars of human change, and as well for students at advanced levels, from graduate to post-doctoral. The reprint is multidisciplinary in nature, binding together the fields of medicine, psychology, physics, and neuroscience

    Vitalism and Its Legacy in Twentieth Century Life Sciences and Philosophy

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    This Open Access book combines philosophical and historical analysis of various forms of alternatives to mechanism and mechanistic explanation, focusing on the 19th century to the present. It addresses vitalism, organicism and responses to materialism and its relevance to current biological science. In doing so, it promotes dialogue and discussion about the historical and philosophical importance of vitalism and other non-mechanistic conceptions of life. It points towards the integration of genomic science into the broader history of biology. It details a broad engagement with a variety of nineteenth, twentieth and twenty-first century vitalisms and conceptions of life. In addition, it discusses important threads in the history of concepts in the United States and Europe, including charting new reception histories in eastern and south-eastern Europe. While vitalism, organicism and similar epistemologies are often the concern of specialists in the history and philosophy of biology and of historians of ideas, the range of the contributions as well as the geographical and temporal scope of the volume allows for it to appeal to the historian of science and the historian of biology generally
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