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See detailIntegrated multi-omics for identifying discriminant features in the human microbiome
Wilmes, Paul UL

Scientific Conference (2017, June)

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See detailAnalyse critique de sources numériques: l’Histoire du Luxembourg sur YouTube
Scagliola, Stefania UL

Learning material (2017)

this training was meant to offer civic education lecturers some information on useful approaches to teach pupils to critically assess digital content online

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See detailCatching Speech in Arezzo: A Clarin workshop for developing a transcription-chain for Oral History
Scagliola, Stefania UL

in Scagliola, Stefania (Ed.) Catching Speech in Arezzo: A Clarin workshop for developing a transcription-chain for Oral History (2017)

This blog describes the results of a workshop in Arezzo in which a roadmap is set out to develop an automatic speech transcription and audio-text alignment chain for scholars who work with interview data

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See detailEpigenetics in Parkinson's Disease
Pavlou, Maria Angeliki UL; Outeiro, Tiago

in Neuroepigenomics in Aging and Disease (2017)

Parkinson's disease (PD) is a highly complex neurodegenerative disorder with a multifactorial origin. Although several cellular mechanisms and genes have been implicated in the onset and progression of ... [more ▼]

Parkinson's disease (PD) is a highly complex neurodegenerative disorder with a multifactorial origin. Although several cellular mechanisms and genes have been implicated in the onset and progression of the disease, the precise molecular underpinnings of the disease remain unclear. In this context, epigenetic modulation of gene expression by environmental factors is emerging as an important mechanism in PD and in other neurodegenerative disorders. Thus, epigenetic mechanisms, such as DNA methylation, histone modifications and altered microRNA expression, have been under intense investigation due to their possible involvement in PD. Epigenetic modulation is responsible for inducing differential gene expression, a phenomenon which is essential throughout life in order to regulate multiple cellular responses such as development, cellular fate commitment and adaptation to the environment. Disturbances of a balanced gene expression can, therefore, have detrimental effects. Environmental factors can challenge the establishment and maintenance of epigenetic modifications and could thereby fill the gap in our further understanding of origin and/or progression of neurodegenerative diseases. In this chapter, we focus on the role of epigenetics in PD. [less ▲]

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See detailUntangling the microbial ecology of anaerobic digestion through integrated multi-omics
Wilmes, Paul UL

Scientific Conference (2017, May)

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See detailSystems Ecology of Microbiomes: A New Frontier of Discovery in Microbiology
Wilmes, Paul UL

Scientific Conference (2017, May)

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See detailNit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione
Peracchi, Alessio; Veiga-da-Cunha, Maria; Kuhara, Tomiko et al

in Proceedings of the National Academy of Sciences of the United States of America (2017), 1613736114

The mammalian gene Nit1 (nitrilase-like protein 1) encodes a protein that is highly conserved in eukaryotes and is thought to act as a tumor suppressor. Despite being ∼35% sequence identical to ω-amidase ... [more ▼]

The mammalian gene Nit1 (nitrilase-like protein 1) encodes a protein that is highly conserved in eukaryotes and is thought to act as a tumor suppressor. Despite being ∼35% sequence identical to ω-amidase (Nit2), the Nit1 protein does not hydrolyze efficiently α-ketoglutaramate (a known physiological substrate of Nit2), and its actual enzymatic function has so far remained a puzzle. In the present study, we demonstrate that both the mammalian Nit1 and its yeast ortholog are amidases highly active toward deaminated glutathione (dGSH; i.e., a form of glutathione in which the free amino group has been replaced by a carbonyl group). We further show that Nit1-KO mutants of both human and yeast cells accumulate dGSH and the same compound is excreted in large amounts in the urine of Nit1-KO mice. Finally, we show that several mammalian aminotransferases (transaminases), both cytosolic and mitochondrial, can form dGSH via a common (if slow) side-reaction and provide indirect evidence that transaminases are mainly responsible for dGSH formation in cultured mammalian cells. Altogether, these findings delineate a typical instance of metabolite repair, whereby the promiscuous activity of some abundant enzymes of primary metabolism leads to the formation of a useless and potentially harmful compound, which needs a suitable “repair enzyme” to be destroyed or reconverted into a useful metabolite. The need for a dGSH repair reaction does not appear to be limited to eukaryotes: We demonstrate that Nit1 homologs acting as excellent dGSH amidases also occur in Escherichia coli and other glutathione-producing bacteria. [less ▲]

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See detailDéi fräi Gewerkschaften - en Archiv-Fond an eng Geschichtk
Sauer, Arnaud UL; Scuto, Denis UL

Diverse speeches and writings (2017)

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See detailTowards systems ecology of the human gut microbiome
Wilmes, Paul UL

Presentation (2017, March)

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See detailSystems Ecology of Microbiomes: A New Frontier of Discovery in Microbiology
Wilmes, Paul UL

Scientific Conference (2017, March)

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See detailPaul Eyschen, le recordman oublié de la politique luxembourgeoise
Scuto, Denis UL

Conference given outside the academic context (2017)

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See detailFrom meta-genomics to causality: Understanding the role of colon cancer-associated bacteria in colorectal cancer
Ternes, Dominik UL; Wilmes, Paul UL; Letellier, Elisabeth UL et al

Poster (2017, February 05)

The human gastrointestinal tract is home for trillions of bacteria that influence homeostasis and health in a complex biological system: the gut microbiome. Accumulating evidence suggests that a state of ... [more ▼]

The human gastrointestinal tract is home for trillions of bacteria that influence homeostasis and health in a complex biological system: the gut microbiome. Accumulating evidence suggests that a state of pathological imbalance in the microbiome (dysbiosis) is present in patients suffering from colorectal cancer (CRC). To date, microbiome studies identified specific bacteria being associated with dysbiosis in CRC. Some of these bacteria (e.g. Fusobacteria) directly or indirectly interact with cancer and immune cells of their host. However, current studies only focused on certain microbes in detail, hence, their role in the etiology of the disease remains elusive. Accordingly, my project investigates the role of CRC-associated bacteria in tumor initiation and progression while addressing the question: which and what kind of microbes interact with, favor, or can cause CRC? In a first step, we identified CRC-associated bacteria, enriched at the tumor site of Luxembourgish CRC patients. By using Fusobacterium nucleatum as our study model, we predicted and optimized bacterial growth (media) in silico by using a genome-scale metabolic reconstruction model for a constraint-based modelling approach. Next, we assessed bacterial growth and metabolism in the optimized growth medium by using flow cytometry and mass spectrometry. Finally, we co-cultured the bacteria together with primary patient-derived cultures in the recently developed, microfluidics-based, human-microbial cross-talk model (HuMiX) [1]. As part of our ongoing validations, we infected patient-derived, healthy and cancerous 3D colonic organoids with our bacterial candidate. This workflow enables us to analyze pro-tumorigenic capacities of CRC-associated bacteria on healthy and cancerous colonocytes. It will serve as a promising tool for future analysis of host-microbial interaction mechanisms of various CRC-associated bacteria on a transcriptomic, proteomic, and metabolomic level. [1] Shah P, Fritz JV, Glaab E, Desai MS, Greenhalgh K et al. (2016) A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nature communications 7: 11535. [less ▲]

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See detailFrom gut to sludge: how to sustainably manage microbial communities in future
Wilmes, Paul UL

Scientific Conference (2017, February)

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See detailMulti-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilum(T).
Christel, Stephan; Herold, Malte UL; Bellenberg, Soren et al

in Applied and environmental microbiology (2017)

Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as ... [more ▼]

Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum(T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum(T) DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as substrate and bioleaching cultures containing chalcopyrite (CuFeS2). Leptospirillum ferriphilum(T) adaptations to growth on chalcopyrite included a possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, expression and translation of genes responsible for chemotaxis and motility were enhanced.IMPORTANCELeptospirillum ferriphilum is one of the most important iron-oxidizers in the context of acidic and metal rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilum(T) coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on Leptospirillum ferriphilum(T) adaptation strategies to growth on the copper mineral chalcopyrite. This data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction. [less ▲]

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See detailTimothy Clark, Ecocriticism on the Edge. The Anthropocene as a Threshold Concept
Thiltges, Sébastian UL

in Local Environment (2017), 22(7), 906-908

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