7,519 research outputs found
Genetic population structure of the precious coral Corallium japonicum in the Northwest Pacific
Population sizes of the Japanese red coral Corallium japonicum have been severely affected by poaching and overfishing. Although genetic structure and connectivity patterns are considered important parameters for conservation strategies, there are few studies focusing on the population genetics of C. japonicum in the Northwest Pacific. We examined the genetic population structure of C. japonicum, in the Northwest Pacific. We used restriction-site-associated DNA sequencing (RAD-seq), which can be used to identify genome-wide single-nucleotide polymorphism (SNPs), to reveal detailed within-species genetic variations. Using the variable SNP loci identified from this analysis, we successfully evaluated the population-level genetic diversity and patterns of gene flow among multiple populations of C. japonicum around Japan. The results of genetic analysis basically showed that gene flow is widely maintained in the geographic range examined in this study, but the analysis in combination with larval dispersal simulations revealed several populations that were genetically distinct from the other populations, suggesting geographically limited gene flows. The information obtained from this study will be useful for the design of effective management schemes for C. japonicum, which is under threat from overfishing
Anuário científico da Escola Superior de Tecnologia da Saúde de Lisboa - 2021
É com grande prazer que apresentamos a mais recente edição (a 11.ª) do Anuário Científico da Escola Superior de Tecnologia da Saúde de Lisboa. Como instituição de ensino superior, temos o compromisso de promover e incentivar a pesquisa científica em todas as áreas do conhecimento que contemplam a nossa missão. Esta publicação tem como objetivo divulgar toda a produção científica desenvolvida pelos Professores, Investigadores, Estudantes e Pessoal não Docente da ESTeSL durante 2021. Este Anuário é, assim, o reflexo do trabalho árduo e dedicado da nossa comunidade, que se empenhou na produção de conteúdo científico de elevada qualidade e partilhada com a Sociedade na forma de livros, capítulos de livros, artigos publicados em revistas nacionais e internacionais, resumos de comunicações orais e pósteres, bem como resultado dos trabalhos de 1º e 2º ciclo. Com isto, o conteúdo desta publicação abrange uma ampla variedade de tópicos, desde temas mais fundamentais até estudos de aplicação prática em contextos específicos de Saúde, refletindo desta forma a pluralidade e diversidade de áreas que definem, e tornam única, a ESTeSL. Acreditamos que a investigação e pesquisa científica é um eixo fundamental para o desenvolvimento da sociedade e é por isso que incentivamos os nossos estudantes a envolverem-se em atividades de pesquisa e prática baseada na evidência desde o início dos seus estudos na ESTeSL. Esta publicação é um exemplo do sucesso desses esforços, sendo a maior de sempre, o que faz com que estejamos muito orgulhosos em partilhar os resultados e descobertas dos nossos investigadores com a comunidade científica e o público em geral. Esperamos que este Anuário inspire e motive outros estudantes, profissionais de saúde, professores e outros colaboradores a continuarem a explorar novas ideias e contribuir para o avanço da ciência e da tecnologia no corpo de conhecimento próprio das áreas que compõe a ESTeSL. Agradecemos a todos os envolvidos na produção deste anuário e desejamos uma leitura inspiradora e agradável.info:eu-repo/semantics/publishedVersio
Early Neanderthal social and behavioural complexity during the Purfleet Interglacial: handaxes in the latest Lower Palaeolithic.
Only a handful of ‘flagship’ sites from the Purfleet Interglacial (Marine Isotope Stage 9, c. 350-290,000 years ago) have been properly examined, but the archaeological succession at the proposed type-site at Purfleet suggests a period of complexity and transition, with three techno-cultural groups represented in Britain. The first was a simple toolkit lacking handaxes (the Clactonian), and
the last a more sophisticated technology presaging the coming Middle Palaeolithic (simple prepared core or proto-Levallois technology). Sandwiched between were Acheulean groups, whose handaxes comprise the great majority of the extant archaeological record of the period – these are the focus of this study. It has previously been suggested that some features of the Acheulean in the Purfleet Interglacial were chronologically restricted, particularly the co-occurrence of ficrons and cleavers. These distinctive forms may have exceeded pure functionality and were perhaps imbued with a deeper social and cultural meaning. This study supports both the previously suggested preference for narrow, pointed morphologies, and the chronologically restricted pairing of ficrons and cleavers. By drawing on a wide spatial and temporal range of sites these patterns could be identified beyond the handful of ‘flagship’ sites
previously studied. Hypertrophic ‘giants’ have now also been identified as a chronologically restricted form. Greater metrical variability was found than had been anticipated, leading to the creation of two new sub-groups (IA and IB) which are tentatively suggested to represent spatial and
perhaps temporal patterning. The picture in the far west of Britain remains unclear, but the possibility of different Acheulean groups operating in the Solent area, and a late survival of the Acheulean, are both suggested. Handaxes with backing and macroscopic asymmetry may represent prehensile or ergonomic considerations not commonly found on handaxes from earlier interglacial periods. It is argued that these forms anticipate similar developments in the Late Middle Palaeolithic in an example of convergent evolution
Cis-Regulation of Gremlin1 Expression during Mouse Limb Bud Development and its Diversification during Vertebrate Evolution
Embryonic development and organogenesis rely on tightly controlled gene expression, which is achieved by cis-regulatory modules (CRMs) interacting with distinct transcription factors (TFs) that control spatio-temporal and tissue-specific gene expression. During organogenesis, gene regulatory networks (GRNs) with selfregulatory feedback properties coordinately control growth and patterning and provide systemic robustness against genetic and/or environmental perturbations. During limb bud development, various interlinked GRNs control outgrowth and patterning along all three limb axes. A paradigm network is the epithelial-mesenchymal (e-m) SHH/GREM1/AER-FGF feedback signaling system which controls limb bud outgrowth and digit patterning. The BMP antagonist GREMLIN1 (GREM1) is central to this e-m interactions as its antagonism of BMP activity is essential to maintain both AER-Fgf and Shh expression. In turn, SHH signaling upregulates Grem1 expression, which results in establishment of a self-regulatory signaling network. One previous study provided evidence that several CRMs could regulate Grem1 expression during limb bud development. However, the cis-regulatory logics underlying the spatio-temporal regulation of the Grem1 expression dynamics remained obscure. From an evolutionary point of view, diversification of CRMs can result in diversification of gene regulation which can drive the establishment of morphological novelties and adaptions. This was evidenced by the observed differences in Grem1 expression in different species that correlates with the evolutionary plasticity of tetrapod digit patterning. Hence, a better understanding of spatio-temporal regulation of the Grem1 expression dynamics and underlying cis-regulatory logic is of interest from both adevelopmental and an evolutionary perspective.
Recently, multiple candidate CRMs have been identified that might be functionally relevant for Grem1 expression during mouse limb bud development. For my PhD project, I genetically analyzed which of these CRMs are involved in the regulation of the spatial-temporal Grem1 expression dynamics in limb buds. Therefore, we generated various single and compound CRM mutant alleles using CRISPR/Cas9. Our CRMs allelic series revealed a complex Grem1 cis-regulation among a minimum of six CRMs, where a subset of CRMs regulates Grem1 transcript levels in an additive manner. Surprisingly, phenotypic robustness depends not on threshold transcript levels but the spatial integrity of the Grem1 expression domain. In particular, interactions among five CRMs control the characteristic asymmetrical and posteriorly biased Grem1 expression in mouse limb buds. Our results provide an example of how multiple seemingly redundant limb-specific CRMs provide phenotypical robustness by cooperative/synergistic regulation of the spatial Grem1 expression dynamics.
Three CRMs are conserved along the phylogeny of extant vertebrates with paired appendages. Of those, the activities of two CRMs recapitulate the major spatiotemporal aspects of Grem1 expression in mouse limb buds. In order to study their functions in species-specific regulation of Grem1 expression and their functional diversification in tetrapods, I tested the orthologous of both CRMs from representative species using LacZ reporter assays in transgenic mice, in comparison to the endogenous Grem1 expression in limb buds of the species of origin. Surprisingly, the activities of CRM orthologues display high evolutionary plasticity, which correlates better with the Grem1 expression pattern in limb buds of the species of origin than its mouse orthologue. This differential responsiveness to the GRNs in mouse suggests that TF binding site alterations in CRMs could underlie the spatial diversification of Grem1 in limb buds during tetrapod evolution.
While the fish fin and tetrapod limb share some homologies of proximal bones, the autopod is a neomorphic feature of tetrapods. The Grem1 requirement for digit patterning and conserved expression in fin buds prompted us to assess the enhancer activity of fish CRM orthologues in transgenic mice. Surprisingly, all tested fish CRMs are active in the mouse autopod primordia providing strong evidence that Grem1 CRMs are active in fin buds and that they predate the fin-to-limb transition. Our results corroborate increasing evidence that CRMs governing autopodial gene expression have been co-opted during the emergence of tetrapod autopod.
Furthermore, as part of a collaboration with Dr. S. Jhanwar, I contributed to the study of shared and species-specific epigenomic and genomic variations during mouse and chicken limb bud development. In this analysis, Dr. S. Jhanwar identified putative enhancers that show higher chicken-specific sequence turnover rates in comparison to their mouse orthologues, which defines them as so-called chicken accelerated regions (CARs). Here, I analyzed the CAR activities in comparison to their mouse orthologues by transgenic LacZ reporter assays, which was complemented by analysis of the endogenous gene expression in limb buds of both species. This analysis indicates that diversified activity of CARs and their mouse orthologues could be linked to the differential gene expression patterns in limb buds of both species
Investigating PAX6 and SOX2 dynamic interactions at the single molecule level in live cells
The abundance of transcription factor (TF) molecules in the nuclei of
eukaryotic cells are in the range of thousands. However, the functional binding
sites of most TFs lie in the range of hundreds. This suggests that there is a
surplus of the number of molecules for many TFs, relative to their binding sites
at any given time. Nevertheless, precise TF levels are instrumental for normal
development and maintenance, with haploinsufficiency (namely lowering the
dosage of a TF by half) being a hallmark of many TF-related human
developmental disorders. Qualitative methods assessing TF binding such as
chromatin immunoprecipitation, provide static information, from fixed cell
populations and so fail to provide insight into TF dynamic behaviour. Live-cell
imaging methodologies such as Fluorescence Correlation Spectroscopy
(FCS) offer the ability to measure kinetics of binding to chromatin, protein-protein interactions, absolute concentrations of molecules and the underlying
cell-to-cell variability.
SOX2 and PAX6 TFs exhibit haploinsufficiency in humans. Heterozygous point
mutations, deletions or insertions in these genes can lead to a plethora of
abnormal ocular developmental disorders (e.g. coloboma, aniridia,
microphthalmia, anopthalmia). SOX2 encodes a high-mobility group (HMG)
domain-containing TF, essential for maintaining self-renewal of embryonic
stem cells and is expressed in proliferating central nervous system (CNS)
progenitors. PAX6 contains two DNA binding domains; a PAIRED domain (PD)
and a homeodomain (HD). Both DNA binding domains present in PAX6 (PD
and HD) can function either jointly, or separately, to regulate a plethora of
genes implicated in the development and maintenance of the CNS, the eye
and the pancreas. Despite existing genetic and phenotypic evidence, it
remains unclear how PAX6 and SOX2 influence each other at the molecular
level and how sensitive their stoichiometry is during ocular development.
In this thesis I investigated the dynamic interplay between PAX6/SOX2 and
chromatin in live cells, at the molecular level. I compared wild-type protein
function with pathogenic missense variants using advanced fluorescence
microscopy techniques and assessed how these mutations quantitatively and
qualitatively affected molecular behaviour. My results showed that both SOX2
and PAX6 pathogenic missense mutants display differential subnuclear
localisation, as well as altered protein-protein and protein-chromatin
interactions, linking molecular diffusion to pathogenic phenotype in humans.
More importantly, I identified a novel role of SOX2 in stabilising PAX6-
chromatin complexes in live cells, providing further insight into the complex
and dynamic relation of PAX6 and SOX2 in ocular tissue specification,
maintenance and development
Applications of nanopore DNA sequencing for improved genome assembly
An organism\u27s genome is the ultimate determinant of its functional potential. Understanding genomes is therefore essential to understand function, and a foundational knowledge of a genome is required transfer functions to and from microorganisms of interest. Sequencing DNA using nanopores is a recent advance that resolves limitations of previous technologies, enabling an improved understanding of genomes. For this thesis, I improved our understanding of microbial genomes by developing novel approaches to analyze long read sequencing data, setting the foundation for future synthetic biology work.
Long sequencing reads have enabled routine assembly of complete bacterial genomes by directly sequencing DNA extracted from bacterial communities. I showed that visualizing sequencing coverage after filtering read alignments using a 95\% query coverage cutoff (i.e., the entire read aligns to the genome) enabled the detection of mis-assemblies. I also showed it can be applied to detect recoverable alternate haplotypes containing important functional elements. Furthermore, I used this approach to demonstrate that a circular genome for a novel species of Saccharibacteria, enriched from a heavy-metal polluted Northern Albertan tailings pond, contains a recently acquired genomic island. I also determined this genomic island encodes heavy metal-resistance genes, suggesting that horizontal gene transfer may be possible under selective pressure in Saccharibacteria.
Another track of my thesis focused on applying nanopore sequencing on a marine diatom, Phaeodactylum tricornutum, which has significant interest for synthetic biology applications like producing low-cost glycosylated proteins. This species does not have a complete genome assembly, despite a draft sequence being available since 2008. To determine the full structure of the genome, I used ultra-long sequencing reads to build a telomere-to-telomere genome assembly. I also developed a novel, assembly-free approach to determine the number of chromosomes from eukaryotes directly from nanopore sequencing reads as an orthogonal method to validate the assembly, which I term long-read karyocounting.
These studies provide complete genome assemblies for both novel bacterial species and a marine diatom who\u27s genome structure had yet to be resolved. These approaches also demonstrate that there is more information encoded in long read sequencing data than just the sum of assembled sequence
Synthese und Optimierung von Konstruktionsbäumen aus unstrukturierten räumlichen Daten
Sensorsysteme für die dreidimensionale Abtastung von Objektoberflächen sind in vielen Bereichen des täglichen Lebens omnipräsent. Moderne Smartphones und Spielekonsolen im Heimanwenderbereich sowie professionelle Systeme, z.B. eingesetzt zur Qualitätssicherung in Fertigungsprozessen, beinhalten Hard- und Softwarekomponenten zur Ermittlung räumlicher Daten. Aus entsprechenden Quellen stammende Datensätze bestehen meist aus einzelnen dreidimensionalen Punkten, die in unstrukturierter Form und potentiell messfehlerbehaftet vorliegen.
Oft ist die Erzeugung dieser Punktwolke nur der erste Schritt innerhalb eines komplexen Verarbeitungsprozesses, an dessen Ende eine Repräsentation der räumlichen Daten steht, die für den entsprechenden Anwendungsfall als optimal angesehen wird. Ein solcher Anwendungsfall ist z.B. die automatische Erzeugung von Architekturplänen oder das Reverse Engineering (RE), also die Analyse des Aufbaus und der Funktionsweise eines Produkts. In beiden Fällen ist eine Repräsentation von Vorteil, die unnötige Details abstrahiert und dabei weiterführende Information über den Aufbau des Objekts und dessen elementare Bausteine beinhaltet. Eine solche Darstellung ist die sog. Constructive Solid Geometry (CSG)-Repräsentation, die Modelle als Baumstruktur bestehend aus Booleschen Mengenoperatoren in den inneren Knoten und geometrischen Primitiven in den äußeren Knoten beschreibt. Dabei ist die manuelle Erzeugung dieses sog. Konstruktionsbaums (KB) aus einer Punktwolke zeitaufwendig und für komplexe Datensätze kaum zu bewerkstelligen.
Aus diesem Grund werden in dieser Arbeit Methoden vorgestellt, die das Problem der automatischen Synthese von KBs aus fehlerbehafteten Punktwolken robust und effizient lösen. Die vorgestellten Verfahren werden dabei in eine eigens entwickelte Prozess-Pipeline eingebettet und miteinander verknüpft. Den Anfang macht die Einführung eines Systems, das geometrische Primitive, wie Kugeln, Zylinder und allgemeine konvexe Polytope, mittels Maschinellem Lernen (ML) und Evolutionären Algorithmen (EA) in der Eingabepunktwolke detektiert und in diese einpasst. Dieser folgt die Vorstellung einer Methode, die das eigentliche KB-Syntheseproblem für bekannte Primitive löst und dazu auf graphbasierte Partitionierungs- und Vereinfachungsstrategien zur Steigerung von Laufzeiteffizienz und Robustheit zurückgreift. Da die Repräsentation als KB nicht eindeutig ist, lassen sich zusätzliche Metriken, wie z.B. die Baumgröße, bestimmen und existierende KBs entsprechend optimieren. Dieses Problem steht abschließend im Fokus dieser Arbeit, zu dessen vorgestellter Lösung ein Spektrum unterschiedlicher Lösungsstrategien evaluiert und diskutiert wird.Sensor systems for three-dimensional object surface scanning are omnipresent in many areas of daily life.
Modern smartphones and game consoles for home users and professional systems, e.g., used for quality assurance in manufacturing processes, contain hard- and software components for measuring spatial data.
Data sets originating from such sources usually consist of individual three-dimensional points which are unstructured and potentially subject to measurement errors.
Often, the generation of this so-called point cloud is only the first step within a complex processing procedure which results in a spatial data representation that is considered optimal for a specific use case.
Such a use case is, for example, the automatic generation of architectural plans or Reverse Engineering (RE), i.e., the analysis of a product's structure and functionality without any prior knowledge.
In both cases, it is advantageous to obtain a representation that abstracts unnecessary details while providing more information about an object's structure and elementary building blocks.
Such a representation is called Constructive Solid Geometry (CSG), which describes models as a tree structure consisting of Boolean set operators in the inner nodes and geometric primitives in the outer nodes.
However, the manual generation of these so-called Construction Trees (CTs) based on a measured point cloud is time-consuming and hardly feasible for complex data sets.
For this reason, this work presents methods that can robustly and efficiently solve the problem of automatically synthesizing CTs from error-prone point clouds.
The presented methods are thereby embedded and interconnected in a newly developed process pipeline.
At first, a system is introduced that detects and fits geometric primitives such as spheres, cylinders and general convex polytopes in the input point cloud using Machine Learning (ML) and Evolutionary Algorithms (EA).
This is followed by an introduction of a method that solves the automatic CT synthesis problem for known primitives using graph-based partitioning and simplification strategies to increase runtime efficiency and robustness.
Since the representation as CTs is not unique additional metrics such as tree size can be determined, and existing CTs can be optimized accordingly.
This problem is the last this work addresses for which a spectrum of different solution strategies is evaluated and discussed
SUBSUMPTION AS DEVELOPMENT: A WORLD-ECOLOGICAL CRITIQUE OF THE SOUTH KOREAN "MIRACLE"
This work offers a critical reinterpretation of South Korean "economic development" from the perspectives of Marxian form critique and Jason Moore's world-ecology. Against the "production in general" view of economic life that dominates the extant debates, it analyzes the rise, spread, and deepening of capitalism's historically specific social forms in twentieth-century (South) Korea: commodity, wage-labor, value, and capital. Eschewing the binary language of development and underdevelopment, we adopt Marx's non-stagist distinctions regarding the relative degree of labor's (and society's) subsumption under capital: hybrid, formal, and real. Examining the (South) Korean experience across three dialectically interrelated scales – regional, global, and "national" – we outline the historical-geographical contingency surrounding South Koreas emergence by c.1980 as a regime of (industrialized) real subsumption, one of the only non-Western societies ever to do so. Crucial to this was the generalization of commodification and proletarianization that betokened deep structural changes in (South) Korea's class structure, but also a host of often-mentioned issues such as land reform, foreign aid, the developmental state, and a "heaven sent" position within the US-led Cold War order. Despite agreeing on the importance of these latter factors, however, the conclusions we draw from them differ radically from those of the extant analyses. For although regimes of real subsumption are the most materially, socially, and technologically dynamic, they are also the most socio-ecologically unsustainable and alienating due to the dualistic tensions inherent to capital's "fully developed" forms, in particular the temporal grounding of value. US protestations about the generalizability of these relations aside, moreover, these regimes have always been in the extreme minority and, crucially, have depended on less developed societies for their success. Historically, this has been achieved through widening the net of capitalist value relations; however, four decades of neoliberalization has all but eliminated any further large-scale "frontier strategies" of this sort. Due to its relatively dense population vis-a-vis its geographical size, contemporary South Korea faces stark challenges that render it anything but a model of "sustainable development," but rather signal the growing anachronism of value as the basis for regulating the future of nature-society relations in the "developed world" and beyond
- …