381023 research outputs found
Sort by
Towards the sensing applications of luminescent lanthanide Periodic Mesoporous Organosilicas
No full textUpholding the principle of effective judicial protection by independent and impartial courts established by law in the EU Member States : safeguarding a multi-layered principle based on a multi-layered protection scheme : fact or fiction?
No full textThe principle of effective judicial protection by independent and impartial courts established by law has lately gained significant relevance as a result of the ‘rule of law crisis’ the European Union has been confronted with. The justice system is, however, of cardinal importance as a guarantee for the protection of the effective judicial protection of all rights which individuals derive from European Union law and for safeguarding the values common to the Member States enshrined in Art. 2 TEU. Yet, this principle finds itself on the borderline between EU competences and national sovereignty, given that the organisation and functioning of the justice system remains a competence of the Member States. The main research question of this dissertation, therefore, asks whether and how the European Union is able to uphold the principle of effective judicial protection by independent and impartial courts established by law in case Member States no longer comply with this principle due to the rule of law backsliding occurring in those Member States
From strains to communities : an omics approach to study the diversity and adaptation of Antarctic cyanobacteria
No full textIce-free areas cover less than 0.5 % of the Antarctic, yet they host most of the terrestrial biodiversity of the whole continent. These terrestrial habitats are characterized by truncated and simple food webs consisting almost uniquely of microbial communities. Cyanobacteria are among the main primary producers in these habitats where they are often regarded as ‘ecosystem engineers. Despite the important ecological role cyanobacteria play, our understanding of the factors shaping their diversity and community structure, as well as their adaptions to cope with the extreme abiotic conditions in the Antarctic remains limited.
The main aims of this Ph.D. were to (1) characterize the community structure and distribution of bacteria and micro-eukaryotes in a variety of substrates from different nunataks and valleys of the Sør Rondane Mountains region (East Antarctica); (2) identify keystone taxa in these food-webs and the main abiotic factors structuring these communities (Chapter 2); (3) provide a detailed understanding of the cyanobacterial diversity and community structure in these regions (Chapter 3); (4) identify the main physiological and genetic adaptation mechanisms that a pair of species of Nostoc (cyanobacteria) employ under desiccation – rehydration events which frequently occur the terrestrial environments of the Antarctic (Chapter 4). To achieve these goals, a multidisciplinary approach was applied combining ecophysiological and several omics analyses.
In Chapter 2, the composition of bacterial and micro-eukaryotic communities was examined using high-throughput sequencing of parts of the 16S rRNA and 18S rRNA genes in 105 soil samples across 9 sites within a 100 km radius in the Sør Rondane Mountains (East Antarctica), differing in substrate type and associated physical and chemical conditions. In moraine soils, Actinomycetota and Cercozoa were among the most abundant bacterial and eukaryotic phyla, whereas on gneiss, granite and marble bedrock, Cyanobacteriota and Metazoa were the among the dominant bacterial and eukaryotic phyla. A distinct differentiation was observed within the Cyanobacteriota phylum at a higher taxonomic resolution depending on bedrock type, with granite being dominated by the Nostocaceae family and marble by the Chroococcidiopsaceae family. Surprisingly, metazoans reached a relatively high abundance in the eukaryotic dataset even in samples from the most arid sites, such as moraines in Austkampane and Widerøefjellet. Overall, this study showed that different substrate types support distinct microbial communities in inland Antarctic nunataks and valleys, and that lithological diversity is a major determinant of terrestrial microbiome biodiversity.
In Chapter 3, the cyanobacterial community structures of the same sampled sites as in Chapter 2 were further investigated based on the use of cyanobacterial-specific primers targeting the V3-V4 region of the 16S rRNA gene in a high-throughput sequencing approach. The latest cyanobacterial taxonomic insights used in the recently released CyanoSeq database were applied to these sequences. Ordination analyses revealed that these different substrates harbour distinct cyanobacterial communities. Differences in community structure were significantly related to differences in pH, concentration of TN and N-NO3-, and electrical conductivity. The granitic soils of the Pingvinane nunataks hosted the highest richness followed by those from the granitic Utsteinen ridge. Granitic substrates were characterized by high TN concentrations and a neutral pH and hosted a variety of filamentous Cyanobacteria, such as Leptolyngbyaceae, Gomontiellaceae, Microcoleaceae, Oculatellaceae, Nostocaceae, but also unicellular taxa (Cyanothecaceae). The moraine samples from Austkampane and Widerøefjellet were dominated by Microcoleaceae and Gomontiellaceae, respectively. They were characterized by a high dry weight and low TN, and the diversity and abundance of cyanobacteria was low. The taxonomic richness was also low in soils from the alkaline marble bedrock and the gneiss bedrock from the Perlebandet nunatak, which were both characterized by high TN. Marble bedrock was dominated by Alitarella sp. (Chroococcidiopsaceae), whereas gneiss by Cyanothece sp. (Cyanothecaceae). Overall, our data show that different substrate types host distinct cyanobacterial communities.
Cyanobacteria need to deal frequently with desiccation and rehydration events in Antarctic terrestrial and lacustrine habitats as well as during dispersal between habitats. In Chapter 4, the response to short-term desiccation exposure and rehydration of a terrestrial and freshwater strain belonging to the same Nostoc species was investigated. To achieve this, the pigments and osmolytes (trehalose and sucrose) concentrations as well as the photosynthetic efficiency were measured in combination to a metatranscriptomic (RNA-seq) analysis of the two Nostoc strains after 3h of desiccation, followed by rehydration after 10 min, 24h and up to 72h. Both strains reacted to dehydration by accumulating sucrose, whereas trehalose was present in lower concentrations. Only the freshwater strain showed a recovery in chlorophyll a content after 72h of rehydration. However, the photosynthetic efficiency remained below the original levels measured before desiccation in both strains. Transcriptomics profiles showed that both strains protected their cells during dehydration by inducing stress-related genes, such as those for the production of carotenoids, trehalose synthase and nitrogen fixation-related genes. The terrestrial strain responded with the up-regulation of a higher number of genes compared to the freshwater strain. The photosynthetic metabolism, however, slowly decreased after 24h of rehydration as evidenced by the down-regulation of genes related to phycobilisomes and photosystems, whilst psbA2 gene, encoding the D1 protein synthase necessary for PSII, was found to be significantly up-regulated under desiccation in the terrestrial ULC180, but not in the freshwater ULC008. These results suggest habitat specific adaptions to environmental stress in cyanobacteria, and provide novel insights into the strategies related to survival and adaptation of non-model Antarctic Nostoc strains to desiccation and rehydration events during the first 3 days experienced in extreme environments.
In the final chapter the main findings of this Ph.D. thesis were discussed and a number of future research perspectives are formulated. These include the use of shotgun metagenomics over amplicon sequencing or the use of more specific primers in bacterial and micro-eukaryotic surveys, the characterization of biotic interactions and the integration of non-model organisms in experiments concerning their abiotic tolerance. Overall, the importance of integrating both ecophysiology and ‘omics’ disciplines is highlighted throughout this Ph.D. thesis, with the aim of maximizing our understanding about the ecologic role of microbial communities inhabiting the extreme Antarctic ice-free areas
Disappointed expectations of independence : a postcolonial reading of comics on the Congolese and Zambian Copperbelt (1960-2000)
No full textThe Copperbelt mining region, straddling the border between Zambia and DRCongo, has long been known as a hub for diverse forms of popular art. Among these, comics have remained comparatively under the academic radar. Yet not only were they an integral part of life on the Copperbelt by the 1950s, but they also became a major channel through which to vehiculate “messages” and hold public conversations. While such magazines were often commissioned by institutions – such as Congo’s mining company Gécamines, and Zambia’s Ministry of Education and Franciscan Mission –, they provided aspiring cartoonists with the opportunity to appropriate and transform the medium. Crucially, this artistic reappropriation unfolded amidst rapid economic, political, and social transformations, particularly following the copper price slump of 1974–75. As a result, these magazines constitute a valuable historical source to investigate changing expectations of independence across two regions which, though neighbouring, are attached to two different nation-states. As the article will show, an examination of three decades’ worth of magazines reveals a comparable sequence on both sides of the border: one that starts with institutions working to encourage children to participate in the general project of “modernity” and ends with increasingly vivid discussions about the realities of living in a world marked by rising hardships and the failures of expectations of independence to materialise
Taenia saginata taeniosis and bovine cysticercosis in Ambo and Jimma, Ethiopia : an update on the epidemiology considering the diagnostic challenges
No full textTaenia saginata taeniosis and bovine cysticercosis (BCC) are zoonotic parasitic infections occurring worldwide. The infection both in humans and cattle is endemic in the global south in general and in Ethiopia in particular. This thesis was conducted to increase the knowledge on the occurrence, risk factors, diagnostic challenges, and control of BCC and T. saginata taeniosis in cattle and humans in Ethiopia. The systematic review and meta-analysis summarizes studies on the prevalence, risk factors, and treatment made so far on Taenia saginata infections and bovine cysticercosis in Ethiopia. The average zonal meat inspection-based BCC prevalence ranged from 2% to 24.6%. There was a significant variation in the prevalence of BCC among studies based on the number of predilection sites incised, ranging between 3.4% to 19.4%. Zonal prevalence of human taeniosis based on both questionnaire and stool test varied between 19.0% to 70.0% and 0.6% to 10.7%, respectively
Hyphenated identities on Facebook : a case study of the construction of diasporic communities of Turkish-Germans on Facebook
No full textPinpointing molecular mechanisms of long non-coding RNAs : at the crossroads of biochemistry and genetics
No full textRibonucleic acid (RNA) is one of the major molecular biopolymers in all known forms of life. Although originally known for its crucial roles in directing diverse aspects of translation, today it is know its functions extend to other, if not all, areas of cellular biology. This is demonstrated by the fact that although >80% of the genome is pervasively transcribed, only 2% of the genome accounts for protein-coding genes, putting forward the question on the function, if any, of these non-coding transcripts? Since the sequencing of the human genome, advancements in massively parallel sequencing and RNA extraction methods have revealed a previously unprecedented complexity of the non-coding transcriptome. These ncRNAs comprise a highly diverse group with high structural and functional variation. LncRNAs are of particular interest, as these comprise the bulk of the transcriptome in terms of number of genes. Although some lncRNAs have been extensively studied and characterized, most lncRNAs have long been regarded as transcriptional noise, owing in part by their generally low expression levels. However, for the last three decades, pioneering research has demonstrated that lncRNA transcripts can have important if not essential functions in cellular biology, and it has become clear that the non-coding part of the transcriptome adds several layers of regulation on the central dogma. In addition, dysregulated expression of lncRNAs can contribute to a wide plethora of human diseases. The highly tissue-specific expression profile of many of these lncRNA genes makes the human lncRNome an untapped source of potential targets for precision medicine, and translating these insights to the clinic may lead to new exciting avenues for diagnostic, prognostic, and therapeutic applications.
A big hurdle in lncRNA research remains the elucidation of the molecular mechanism of these transcripts. However, insights in these mechanisms may prove to be very useful for the development of treatment modalities that are synergistic to existing therapy or to predict and counter potential resistance mechanisms. A lncRNA rarely acts as a sole effector molecule, but rather functions by interacting with other biomolecular entities such as DNA or proteins. Although recent technological advances to interrogate an RNA’s interactome have been made, these methods have proven difficult to implement and each has its own benefits and drawbacks. Most methods to characterize an RNA’s interactome rely on RNA pulldown methods using various ways of cross-linking and the use of biotinylated tiling probes complementary to the RNA of interest (e.g. iDRiP-MS, RAP-MS, ChIRP-MS, etc). Although conceptually the same, small technical differences have shown great differences in size and content of the identified interactome. Drawing upon the PPI field, a strong case can be made for the need of orthogonal methods to create high confidence sets of interaction candidates. We combined comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) and RNA-BioID to create a high confidence RBP set of several lncRNAs. To evaluate these methods, they were applied them on HOX Transcript Antisense Intergenic RNA (HOTAIR). HOTAIR is a well-known lncRNA expressed from the HOXC gene cluster and shown to regulate the expression of the HOXD gene cluster in trans during the development limb patterning. Overexpression of HOTAIR has been associated with a metastasis-promoting phenotype in breast and ovarian cancer. Although HOTAIR is known to bind PRC2 and LSD1 protein complexes for its mode of action, an unbiased and comprehensive method to map its interactome has not yet been performed. We overlapped significantly enriched proteins in both methods and identified proteins including the hallmark interactors PRC2 and REST/CoREST chromatin remodeler complexes, but surprisingly also subunits of mitochondrial ribosomes (MRPLs). We elaborated on the MRPL-HOTAIR interaction and show the interaction does not occur in mitochondria.
After optimizing ChIRP-MS on HOTAIR, we applied the method on NESPR, a neuroblastoma-specific lncRNA that we are actively dissecting at a mechanistic level. Neuroblastoma is a childhood cancer derived from the SA lineage that is defined by an adrenergic and mesenchymal cell identity. We screened lncRNAs associated with the adrenergic identity and prioritized NESPR due to its adrenergic-specific expression profile, its association with clinical parameters, and foremost its genomic location. NESPR is abundantly expressed from the PHOX2B super-enhancer, a crucial adrenergic-specific cell identity gene. Knockdown of the NESPR fraction significantly decreases cellular survival and induces an apoptotic program. RNA-sequencing upon NESPR knockdown revealed a significant reduction in the expression of PHOX2B. 4C-sequencing demonstrated that the NESPR and PHOX2B loci form an insulated neighborhood in adrenergic but not mesenchymal cells, demonstrating that NESPR regulates PHOX2B in cis. We show that perturbation of NESPR does not impact the chromatin looping between the PHOX2B and NESPR loci, nor do we find evidence for direct NESPR DNA binding at enhancer elements in the loop. However, RNA-sequencing data from NESPR and PHOX2B knockdown experiments revealed a PHOX2B-independent function for NESPR. After stringent filtering, ChIRP-sequencing revealed one in trans target gene, ESRRG. Consistent with a genetic regulatory role, we show that NESPR interacts with proteins that are involved in genome stability and transcription machinery.Ribonucleïne zuur (RNA) is één van de belangrijkste biopolymeren in het leven zoals we het vandaag kennen. Ondanks dat RNA vooral gekend is voor de diverse functies die het uitoefent in het vertalen van eiwitten, weten we ondertussen dat het ook andere functies omvat. Deze functies beperken zich niet tot het vertalen van eiwitten maar reiken uit naar quasi alle domeinen van de cellulaire biologie. Dit wordt mede ondersteund door het feit dat ondanks dat meer dan 80% van het genoom afgeschreven wordt, slechts 2% van deze RNA transcripten voor een eiwit coderen. Deze vaststelling doet ons de vraag stellen wat de functie, als er een is, van deze niet-coderende RNA transcripten is? Sinds het sequeneren van het menselijk genoom, hebben vooruitgang in hoge-doorvoer sequenerings- en RNA isolatiemethodes ervoor gezorgd dat we vandaag weten dat de complexiteit van het transcriptoom veel hoger ligt dan oorspronkelijk mogelijk geacht. Deze niet-coderende RNAs vormen een zeer diverse en omvangrijke groep die zowel structureel als functioneel zeer verschillend kunnen zijn. Lange niet-coderende RNAs (lncRNAs) zijn specifiek van belang, omdat deze de grootste groep van niet-coderende RNAs vormen. Ondanks dat sommige lncRNAs uitgebreid en zeer grondig onderzocht zijn, zijn de meeste lncRNAs steeds aanzien als transcriptionele ruis. Dit komt ondermeer door hun zeer lage abundantie in de cel. De afgelopen dertig jaar heeft vooruitstrevend onderzoek echter aangetoond dat lncRNAs een zeer belangrijke rol speelt in celbiologie, en in sommige gevallen zelfs een cruciale speler is in onderliggende ceullaire processen. Daarom is het vandaag duidelijk dat het niet-coderende transcriptoom extra dimensies toevoegt aan het centrale dogma van de moleculaire biologie. Sterker nog, het is aangetoond dat misregulatie van verschillende lncRNAs een rol speelt in verschillende ziektebeelden bij de mens. Door de hoge weefsel-specifieke expressie van de meeste lncRNAs, vormen deze aantrekkelijke doelwitten voor toekomstige behandelingen die momenteel nog onbenut blijven. Daarom dat inzichten in lncRNA biologie een veelbelovende weg kunnen vormen voor nieuwe diagnostische, prognostische en therapeutische doeleinden.
Een grote drempel in onderzoek naar lncRNAs blijft het ontrafelen van het moleculaire mechanisme dat onderliggend is aan de functie die zij uitoefenen in de cel. Desondanks kunnen deze inzichten een baanbrekend inzicht geven in de ontwikkeling van behandelingen die synergistisch zijn aan bestaande behandelingen of die mogelijke resistentiemechanismen vermijden. Een lncRNA werkt zelden alleen. Meestal vormt het complexen met andere moleculaire entiteiten in de cel zoals DNA of eiwitten. Desondanks recente technologische doorbraken, blijft het zeer moeilijk om eiwit interacties met een lncRNA te identificeren. De methodes die hiervoor nodig zijn, zijn zeer moeilijk op te zetten en hebben elks hun voor- en nadelen. De meeste van deze methodes steunen op het principe van RNA purificatie met gebiotinyleerde probes die complementair zijn aan het lncRNA. Ondanks dat er meerdere van deze conceptueel dezelfde methodes ontwikkeld zijn, hebben kleine technische verschillen gezorgd voor een groot verschil in de hoeveelheid en de aard van de eiwitten die geïdentificeerd zijn. In het onderzoeksveld van eiwit-eiwit interacties is het ondertussen duidelijk dat orthogonale methodes nodig zijn om eiwit interacties met hoge condifentie te definiëren.
In deze thesis, hebben we ChIRP-MS gecombineerd met RNA-BioID om een set van RNA-bindende eiwitten met hoge betrouwbaarheid te identificeren. Voor het opzetten en evalueren van deze methodes, hebben we deze toegepast op het lncRNA HOTAIR, dat een goed gekende rol speelt in ontwikkeling van de ledematen. Overexpressie van HOTAIR wordt tevens ook geassocieerd met metastases van borst- en eierstokkanker. Ondanks dat het geweten is dat HOTAIR interageert met de PRC2 en LSD1 eiwitcomplexen om zijn functie uit te oefenen, is er nog nooit een hypothese-vrije en comprehensieve methode toegepast om alle eiwit interactors van HOTAIR te identificeren. Hier hebben we de significant aangerijkte eiwitten van beide methodes gecombineerd. Naast PRC2 en LSD1, vinden we ook mitochondriale ribosomen als de voornaamste interactiepartners. We tonen echter aan dat deze interactie niet in de mitochondriën plaatsvindt.
Na de optimalisatie van ChIRP-MS op HOTAIR, hebben we dit ook toegepast op NESPR, een neuroblastoom-specifiek lncRNA dat we mechanistisch aan het onderzoeken zijn. Neuroblastoom is een kinderkanker die afgeleid is van het sympathische zenuwstelsel. Neuroblastoom is een heterogene kanker die bestaat uit een adrenerge en mesenchymale cellulaire identiteit. We hebben specifiek gezocht naar lncRNAs die geassocieerd zijn met de adrenerge identiteit en prioritizeerden NESPR omwille van: zijn adrenerg-specifieke expressie patroon, zijn associatie met klinische parameters, maar vooral omwille van zijn genomische locatie. NESPR wordt zeer sterk tot expressie gebracht van de PHOX2B super-enhancer, een cruciaal adrenerg-specifiek identiteitsgen. Uitschakelen van NESPR toont een significante reductie in PHOX2B expressie, wat aantoont dat NESPR PHOX2B in cis reguleert. 4C-sequenering toont aan dat NESPR en PHOX2B een geïsoleerde genetische zone vormen in adrenerge maar niet in mesenchymale cellen. We tonen aan dat het uitschakelen van NESPR geen invloed heeft op het vormen van deze genetische zone, en daarnaast tonen we ook dat NESPR niet bindt op regulatorische elementen in deze zone. We vinden hiernaast echter ook indirect bewijs dat NESPR wel andere genen zou kunnen binden. Na toepassing van een stringente filterstrategie, tonen we dat NESPR het gene ESRRG in trans kan binden, en aansluitend met een regulatorische rol tonen we aan dat NESPR associeert met eiwitten die een belangrijke rol spelen in het behouden van de integriteit van het genoom en de transcriptionele machinerie
Modelling the future climate and outdoor thermal comfort over Eurasia
No full textUnprecedented widespread and rapid changes in the climate system have been observed over every region across the globe. Moreover, the increase in global near surface temperature is projected to continue until at least 2050, which will lead towards more extreme events. This ongoing global warming will cause more frequent exceedance of human health heat thresholds, leading to reduced well-being, labour productivity and an excess in mortality. Regional climate models (RCMs) are used to downscale the information of global models over particular regions of interest to study the effect of global warming at higher spatial and temporal resolutions. The Coordinated Regional Climate Downscaling Experiment (CORDEX) creates a framework for scientists to perform such regional climate downscaling in a systematic way.
High-resolution climate information over Asia is still scarce and this region deserves attention since it comprises a large range of climatic zones and affects some highly populated regions. To fill this gap, two RCMs, ALARO and REMO, were run over the Central Asia CORDEX (CAS-CORDEX) domain, covering most of the Eurasian continent. The resulting climate data was evaluated to investigate whether these RCMs produce reliable climate information. In general both RCMs reproduced realistic spatial patterns for temperature, but they underestimated the diurnal temperature range. There were also significant biases found in multiple subregions during several seasons, e.g., a warm bias in the north during winter and a wet bias over the Asian monsoon region. The projections of four global-regional climate model combinations of a small multi-model ensemble showed for the 1.5 °C, 2 °C and 3 °C global warming levels geographically unequal warming and precipitation trends over Eurasia, with a faster warming rate and increasing precipitation in northern Eurasia due to the Arctic amplification. Further, a significant decrease in precipitation was found over southeastern China for global warming beyond 2 °C.
Outdoor thermal comfort (OTC) has been quantified using indices that rely on meteorological input to know how the changing climate will affect living conditions and which measures will be needed to keep cities livable. Hourly data of an RCM was used to evaluate and compute the current and future OTC of 58 Eurasian cities. For all cities it was found that higher global warming levels cause larger changes in OTC conditions. The largest OTC changes were found for the high latitude cities with a remarkable reduction in cold stress. The diurnal cycles of OTC were affected differently under
global warming for the different locations, for example only in northeastern European cities we found an OTC increase that is much more pronounced for the night than the day. A serious limitation of the applied approach is that city features are not taken into account. Moreover, the too coarse RCM data makes it impossible to study urban-rural and intra-urban differences in OTC. Measurements of the observational network in the mid-latitude city of Ghent (Belgium) showed there are significant urban-rural and intra-urban OTC differences. It was found that both open rural and urban locations experience the highest fraction of extreme heat stress during heat waves due to the high amount of solar irradiation. Moreover, the rural location was most uncomfortable annually and during heat waves due to fast warming and cooling, leading to both heat stress and cold stress. Further, we found that urban parks will play an important role in urban planning to keep the city livable in the future warmer climate.
This thesis addresses the lack of intercomparable high-resolution climate information over Asia by providing data of two RCMs that were evaluated over the CAS-CORDEX domain. This effort will hopefully lead to the onset of more systematic research and collaboration over this region. Moreover, it is demonstrated that it is possible to compute hourly OTC values with an RCM for main Eurasian cities, which results in the ability to study the impact of climate change on regional differences in the diurnal cycle of OTC. There is a lot more to build on this work. The evaluation study can for instance serve as a basis for investigating a number of parameterisations of the RCMs and a further downscaling with a model that takes urban interactions into account would result in a further refinement of the OTC study
