2,765 research outputs found

    Middle Pleistocene paleoenvironmental reconstruction through phytolith analysis at the Manyara Beds, northern Tanzania

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    This project is aimed at developing a detailed habitat reconstruction for hominins living at the Manyara Beds of Northern Tanzania during the early Middle Pleistocene using phytolith remains. The dissertation comprises three interlinked, but independent studies. The first study examines the phytolith assemblages from modern surface soils and plants to create a referential baseline for studying phytoliths from the Acacia-Commiphora ecosystem surrounding the Manyara Beds, the same plant regions in which our ancestors reside. Phytoliths from 21 species of plants, including 11 unstudied taxa from this ecosystem, were characterized. Twenty-five composite surface soil samples from five sites were also analyzed. Using Stromberg's 2003 classification and interpretive scheme, this study has demonstrated that the dominant phytoliths for Commiphora are polyhedral epidermal cells, and Acacia is a rare producer of blocky-faceted rectangular plate morphotypes. The second study examines phytolith assemblages from archaeological and non-archaeological sites within the six-meter zone of the uppermost part of the lower Manyara Beds. In general, phytolith assemblage from archaeological and non-archaeological sites confirms the persistence of C4 grasslands. However, varied habitats were available for the Acheulean tool-making hominins at archaeological site MK 4, which featured palms, woody dicots, sedge, and grasslands taxa, including high proportions of warm arid and moist loving C3 and C4 PACMADs and dry adapted C4 chloridoids. There is also a small presence of wet-loving panicoids. The palms, sedges, Commelinaceae, and other aquatic monocots indicate that Manyara Beds were well-watered, at least with the occurrence of freshwater springs or rivers near the Lake shores. Therefore, inferences from phytolith assemblages from the Manyara Beds are consistent with the common predictions of many Plio-Pleistocene sites near the lake shores, pointing to hominin's dependence on water and food resources such as plants and game. The third study presents the analysis of 106 stone tool residue samples from the MK4 site to understand the function of the small flake assemblage found there. Ten tools yielded phytoliths, including two flaked and eight core tools. Phytoliths revealed the exploitation of plant resources, including grasses, palms, sedges, woody dicots, and other unknown taxa

    Computational Analyses of Metagenomic Data

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    Metagenomics studies the collective microbial genomes extracted from a particular environment without requiring the culturing or isolation of individual genomes, addressing questions revolving around the composition, functionality, and dynamics of microbial communities. The intrinsic complexity of metagenomic data and the diversity of applications call for efficient and accurate computational methods in data handling. In this thesis, I present three primary projects that collectively focus on the computational analysis of metagenomic data, each addressing a distinct topic. In the first project, I designed and implemented an algorithm named Mapbin for reference-free genomic binning of metagenomic assemblies. Binning aims to group a mixture of genomic fragments based on their genome origin. Mapbin enhances binning results by building a multilayer network that combines the initial binning, assembly graph, and read-pairing information from paired-end sequencing data. The network is further partitioned by the community-detection algorithm, Infomap, to yield a new binning result. Mapbin was tested on multiple simulated and real datasets. The results indicated an overall improvement in the common binning quality metrics. The second and third projects are both derived from ImMiGeNe, a collaborative and multidisciplinary study investigating the interplay between gut microbiota, host genetics, and immunity in stem-cell transplantation (SCT) patients. In the second project, I conducted microbiome analyses for the metagenomic data. The workflow included the removal of contaminant reads and multiple taxonomic and functional profiling. The results revealed that the SCT recipients' samples yielded significantly fewer reads with heavy contamination of the host DNA, and their microbiomes displayed evident signs of dysbiosis. Finally, I discussed several inherent challenges posed by extremely low levels of target DNA and high levels of contamination in the recipient samples, which cannot be rectified solely through bioinformatics approaches. The primary goal of the third project is to design a set of primers that can be used to cover bacterial flagellin genes present in the human gut microbiota. Considering the notable diversity of flagellins, I incorporated a method to select representative bacterial flagellin gene sequences, a heuristic approach based on established primer design methods to generate a degenerate primer set, and a selection method to filter genes unlikely to occur in the human gut microbiome. As a result, I successfully curated a reduced yet representative set of primers that would be practical for experimental implementation

    Human norovirus emergence and circulation in humans and animals

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    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

    Reachability Analysis for Lexicase Selection via Community Assembly Graphs

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    Fitness landscapes have historically been a powerful tool for analyzing the search space explored by evolutionary algorithms. In particular, they facilitate understanding how easily reachable an optimal solution is from a given starting point. However, simple fitness landscapes are inappropriate for analyzing the search space seen by selection schemes like lexicase selection in which the outcome of selection depends heavily on the current contents of the population (i.e. selection schemes with complex ecological dynamics). Here, we propose borrowing a tool from ecology to solve this problem: community assembly graphs. We demonstrate a simple proof-of-concept for this approach on an NK Landscape where we have perfect information. We then demonstrate that this approach can be successfully applied to a complex genetic programming problem. While further research is necessary to understand how to best use this tool, we believe it will be a valuable addition to our toolkit and facilitate analyses that were previously impossible
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