50 research outputs found

    Metabolic dysfunction-associated steatotic liver disease:A wide-angled perspective on a multifaceted problem

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    In dit proefschrift is metabole dysfunctie-geassocieerde steatotische leverziekte (MASLD) onderzocht, opgedeeld in drie delen:Deel 1 omvat een MRI-onderzoek naar vetstapeling in de lever en pancreas, en een genoombrede associatiestudie in de Amsterdamse multi-etnische populatie, waarbij een relatie tussen het gen MRC1 en niet-invasieve leverfibrosetesten wordt gevonden. Dit gen vertoont variaties tussen etnische groepen, wat wijst op een rol van MRC1 in de bestaande verschillen in MASLD tussen bevolkingsgroepen van verschillende afkomst.In deel 2 is gericht op nieuwe niet-invasieve levertesten van fibrosevorming in mensen met MASLD. Ten eerste een systematische review van de marker Pro-C3 voor het detecteren van fibrose, en ten tweede een onderzoek naar een nieuw niet-invasief biomarkerpanel, van ontdekking in muisstudies tot bevestiging in humane cohorten.Deel 3 van het proefschrift beschrijft de potentie van het darmmicrobioom om MASLD te beïnvloeden. Een fecestransplantatiestudie toont aan dat het manipuleren van het darmmicrobioom leidt tot veranderingen in circulerende metabolieten en lever-DNA-methylatie. Daarnaast beschrijft een muisonderzoek het effect van de boterzuurproducerende bacterie A. soehngenii op de ernst van MASLD, waarbij toediening ervan de suikerhuishouding verbeterde zonder verbetering van de leverhistologie.Gezamenlijk leveren de studies die in dit proefschrift beschreven zijn waardevolle inzichten in de complexiteit van MASLD en bieden ze verschillende potentiële mogelijkheden om de zorg voor mensen met MASLD te verbeteren door middel van genetische, metabole en microbioom-gerichte benaderingen

    RNA, the Epicenter of Genetic Information

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    The origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information. Key Features Documents the confused early history of DNA, RNA and proteins - a transformative history of molecular biology like no other. Integrates the influences of biochemistry and genetics on the landscape of molecular biology. Chronicles the important discoveries, preconceptions and misconceptions that retarded or misdirected progress. Highlights major pioneers and contributors to molecular biology, with a focus on RNA and noncoding DNA. Summarizes the mounting evidence for the central roles of non-protein-coding RNA in cell and developmental biology. Provides a thought-provoking retrospective and forward-looking perspective for advanced students and professional researchers

    Challenges for engineering students working with authentic complex problems

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    Engineers are important participants in solving societal, environmental and technical problems. However, due to an increasing complexity in relation to these problems new interdisciplinary competences are needed in engineering. Instead of students working with monodisciplinary problems, a situation where students work with authentic complex problems in interdisciplinary teams together with a company may scaffold development of new competences. The question is: What are the challenges for students structuring the work on authentic interdisciplinary problems? This study explores a three-day event where 7 students from Aalborg University (AAU) from four different faculties and one student from University College North Denmark (UCN), (6th-10th semester), worked in two groups at a large Danish company, solving authentic complex problems. The event was structured as a Hackathon where the students for three days worked with problem identification, problem analysis and finalizing with a pitch competition presenting their findings. During the event the students had workshops to support the work and they had the opportunity to use employees from the company as facilitators. It was an extracurricular activity during the summer holiday season. The methodology used for data collection was qualitative both in terms of observations and participants’ reflection reports. The students were observed during the whole event. Findings from this part of a larger study indicated, that students experience inability to transfer and transform project competences from their previous disciplinary experiences to an interdisciplinary setting

    Generating and characterizing primate iPSCs for evolutionary analyses

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    The similarities and differences between us and our closest relatives, the primates, have fascinated researchers for decades and evoked various approaches to better understand the underlying genotype-phenotype relationship. Starting with early comparisons of protein sequences between humans and chimpanzees, substantial technological advances in genomics have led to a deeper understanding of the complexities in this relationship, ranging from cataloging genetic differences to modeling genetic differences in cellular and animal systems. Furthermore, the lack of genetic differences - sequence conservation - is crucial to annotate the human genome and interpret biomedically relevant variants within humans. Charting differences and similarities in molecular and cellular properties can take such a comparative approach to the next phenotypic level. In particular, similar to the information obtained from DNA conservation, expression conservation could help annotating and interpreting human gene expression patterns and thus also provide biomedically relevant information. However, the major limiting factor in this venture is the availability of comparable samples of different primates, mainly due to ethical constraints. Induced pluripotent stem cells (iPSCs) are used in humans to overcome such limitations, as they can be propagated indefinitely and differentiated to many different cell types. Thus, they can provide a valuable and unique resource for functional primate genomics. In this context, I established a method to generate iPSCs from primates. One of the major challenges in generating iPSCs from non-model organisms is the acquisition of the somatic cells for reprogramming. Therefore, I focused on urine as a non-invasive cell source and could show that cells can be isolated from very small amounts of primate urine samples, which were collected in an unsterile manner. These cells can be efficiently reprogrammed into iPSCs using the footprint-free Sendai Virus reprogramming method. Utilizing this approach, we generated four iPSC lines from two orangutans, three iPSC lines from one gorilla and nine lines from five humans. We validated the pluripotecy of these lines using immunocytochemistry, differentiation assays and also classified the cells as pluripotent using bulk RNA-sequencing. We further showed that expression differences among clones are comparable to those among individuals and considerably larger than technical sources of variation, suggesting that these cells are a suitable resource for functional primate genomics. As RNA-sequncing (RNA-seq) is a decisive assay to classify cells and to study gene expression in a comparative context, a robust and affordable method to quantify RNA expression levels is indispensable. I contributed to develop prime-seq, a sensitive bulk RNA-seq protocol that we showed to perform equivalently to standard bulk RNA-seq methods, but at a fourfold higher efficiency due to almost 50-fold cheaper library costs. This is highly useful to e.g. classify generated iPSCs as described above. However, to compare heterogenous cell populations, as they arise for example during the differentiation of iPSCs, RNA-seq with single-cell resolution (scRNA-seq) is crucial. I contributed to develop mcSCRB-seq, a sensitive, powerful and efficient single cell RNA-seq method, that is plate-based and hence, can be used for scRNA-seq on sorted single cells. Finally, I utilized mcSCRB-seq to compare gene expression trajectories during differentiation of our primate iPSCs towards neural precursor cells (NPCs). We sampled single cells of nine different clones from three species at six different time points during early neural differentiation and thus generated a comprehensive dataset to study this process in a comparable manner. We identify genes with a conserved constant up-regulation throughout the trajectory and find that these genes have a higher probability of being mutation intolerant and a higher probability to be associated with neurodevelopmental disorders. This strengthens the hypothesis that identifying conserved expression patterns in primate iPSCs could carry unique functional information to annotate and interpret the human genome.\par In summary, within my thesis I describe the basis for comparative research settings, by providing a non-invasive and footprint-free method to generate iPSCs from various primates. Additionally, I contributed to efficient methods to characterize these cells and showcase in an encompassing study how expression conservation can help to better understand the human genome

    The Increasing Necessity of Skills Diversity in Team Teaching

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    Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

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    This work was supported by the National Institute of General Medical Sciences [GM131919].In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.PostprintPeer reviewe
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