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Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge
No full textThe recovery of metagenome-assembled genomes is biased towards the most abundant species in a given community. To improve the identification of species, even if only dominant species are recovered, we investigated the integration of flow cytometry cell sorting with bioinformatics tools to recover metagenome-assembled genomes. We used a cell culture of a wastewater microbial community as our model system. Cells were separated based on fluorescence signals via flow cytometry cell sorting into sub-communities: dominant gates, low abundant gates, and outer gates into subsets of the original community. Metagenome sequencing was performed for all groups. The unsorted community was used as control. We recovered a total of 24 metagenome-assembled genomes (MAGs) representing 11 species-level genome operational taxonomic units (gOTUs). In addition, 57 ribosomal operational taxonomic units (rOTUs) affiliated with 29 taxa at species level were reconstructed from metagenomic libraries. Our approach suggests a two-fold increase in the resolution when comparing sorted and unsorted communities. Our results also indicate that species abundance is one determinant of genome recovery from metagenomes as we can recover taxa in the sorted libraries that are not present in the unsorted community. In conclusion, a combination of cell sorting and metagenomics allows the recovery of MAGs undetected without cell sorting
Einfluss von physischer Aktivität und BMI SDS auf den Knochenstoffwechsel bei Kindern und Jugendlichen
No full textZiel: Kinder mit Adipositas haben bekanntermaßen eine verringerte Knochendichte und ein höheres Risiko für Frakturen. Dies kann durch reduzierte körperliche Aktivität oder ein metabolisches Phänomen verursacht werden. In dieser Studie untersuchten wir die Zusammenhänge zwischen körperlicher Aktivität und dem Knochenstoffwechsel bei Kindern und Jugendlichen mit und ohne Adipositas.
Methoden: Die Ergebnisse von 574 Besuchen von 397 Probanden (191 Mädchen und 206 Jungen im Alter von fünf bis 18 Jahren, Durchschnittsalter: 11,7 ± 2,8 Jahre), darunter 180 Kinder mit Adipositas (mittlerer BMI-SDS 2,5 ± 0,4) und 217 Kinder ohne Adipositas (mittlerer BMI-SDS 0,2 ± 1,0), aus der LIFE-Child-Studie, einer bevölkerungsbasierten Kohorte von Kindern und Jugendlichen mit normalem Gewicht und Adipositas, wurden analysiert. Der Einfluss ihrer täglichen körperlichen Aktivität (MET/Tag, SenseWear-Accelerometer) auf die Serum-SDS-Werte für die Knochenbildung (alkalische Phosphatase, Osteocalcin, Prokollagen Typ I N-Propeptid [P1NP]), den Knochenabbau (Beta-Crosslaps) und die Kalziumhomöostase (Parathormon, OH-25-Vitamin D) wurde mithilfe eines linearen Regressionsmodells untersucht, das geschlechts- und altersbedingte Unterschiede berücksichtigte.
Ergebnisse: Bei männlichen Probanden beeinflusste der BMI-SDS signifikant den Zusammenhang zwischen körperlicher Aktivität und den SDS-Werten für PTH, Vitamin D und Beta-Crosslaps. Eine höhere körperliche Aktivität war mit erhöhten PTH-, aber niedrigeren Vitamin-D-SDS-Werten bei Kindern mit Normalgewicht verbunden. Bei Jungen mit Adipositas blieben alle Werte unverändert. Bei weiblichen Probanden hatte der BMI-SDS einen signifikanten Einfluss auf die Assoziation zwischen körperlicher Aktivität und den SDS-Werten für PTH, Vitamin D, P1NP, Beta-Crosslaps und Osteocalcin. Bei adipösen Mädchen war eine höhere körperliche Aktivität mit höheren SDS-Werten für Vitamin D, P1NP und Beta-Crosslaps verbunden. Im Gegensatz dazu war bei Mädchen mit Normalgewicht nur der PTH-SDS-Wert erhöht.
Schlussfolgerungen: Der Einfluss der täglichen körperlichen Aktivität auf Marker des Knochenstoffwechsels und kalziotrope Hormone hängt wesentlich von Geschlecht und BMI-SDS ab. Höhere körperliche Aktivität war jedoch nur bei adipösen Mädchen mit einer erhöhten Knochenumsatzrate verbunden. Daher könnte es hilfreich sein, insbesondere Mädchen mit Adipositas zu mehr körperlicher Aktivität zu motivieren, um ihre Knochengesundheit zu verbessern.:1. Einführung 1
1.1 Knochen und deren Stoffwechsel 1
1.2 Knochenstoffwechsel und dessen systemischen Regulierung 3
1.3 Knochenstoffwechsel und physische Aktivität 4
1.4 Knochenstoffwechsel und Fettgewebe 5
1.5 Knochenstoffwechsel und Geschlechtshormone 6
1.6 Marker für Knochenstoffwechsel 8
1.7 Ziele der Arbeit 8
2. Publikation 10
3. Zusammenfassung 19
3.1 Probandencharakteristika 19
3.2 Knochenstoffwechsel nach Geschlecht und BMI SDS 20
3.3 Physische Aktivität 22
3.4 Effekt von physischer Aktivität auf den Knochenstoffwechsel 22
3.5 Schlussfolgerung 23
4. Literaturverzeichnis 24
5. Anlagen 28
5.1 Verzeichnis der verwendeten Abkürzungen und Symbole 28
5.2 Erklärung über den wissenschaftlichen Beitrag des Promovenden zur Publikation 29
5.3 Erklärung über die eigenständige Abfassung der Arbeit 30
5.4 Curriculum vitae mit Publikationen und Vorträgen 31
5.5 Danksagung 3
Interactive 3D Visualisations of the Mont Terri Underground Research Laboratory
No full textThis thesis demonstrates how interactive 3D visualisations of underground research laboratories (URL) can support the diverse stakeholders of research on the final disposal of radioactive waste. The work conducted in underground research laboratories plays an invaluable role in the research and development of safe solutions for the final disposal of radioactive waste. The thesis presents three interactive 3D visualisation systems for the Mont Terri URL.
The first project focuses on domain experts, who encounter numerous challenges when attempting to visualise the research data generated in URLs. Three main issues were identified and tackled by developing a tailored interactive visualisation system, called VEIS: Firstly, the data obtained at the test site is often available only to researchers directly involved in the specific experiment. Secondly, the visualisation techniques typically employed by domain scientists often lack the larger spatial context. Thirdly, accessing and exploring the data requires prior technical knowledge. The VEIS digitally replicates the Mont Terri laboratory and integrates highly heterogeneous data (e.g. simulation results and observation data) from several sources. The 4D visualisation approach focuses on three exemplary experiments. It facilitates the visual exploration of research data sets and promotes exchange among research groups.
In the second project, the focus was on intermediates, i.e. stakeholders with less prior knowledge than domain experts. The VEIS was employed as a foundation for the development of a virtual field trip on the subject of radioactive waste management research for the purpose of university education. For this purpose, we enhanced the existing system with additional background information, illustrations, tasks, tests, and an improved user interface. To put the tour's content into context, a conventional introductory presentation on the final disposal of radioactive waste was added. We then evaluated the virtual field trip in a user study with 22 participants. It proved a good perceived usability of the virtual tour and the virtual field trip's ability to transfer knowledge. These results support the findings of previous work that suggest a benefit of employing virtual field trips in geoscientific university courses.
The third project focuses on science communication and combines the concepts of serious games and virtual field trips for this purpose. The design, implementation, and evaluation of VR-EX, an immersive virtual reality application that focuses on the electrical resistivity tomography measurements within the CD-A experiment are described in detail. VR-EX enables users to actively re-enact the measurements from planning to execution to analysis of the results, and in this way implements an active and playful learning approach. VR-EX presents the highly relevant work conducted in underground research laboratories to society in an active and appealing way, which is crucial to increase understanding of scientific processes and boost interest. A user study with 35 participants proves the overall good quality of the application and its high effectiveness in terms of knowledge transfer. The high levels of engagement, joy, and immersion reported by the users indicate the potential benefits of employing immersive virtual reality for engaging and effective science communication
Degradation of Bio-Based and Biodegradable Plastic and Its Contribution to Soil Organic Carbon Stock
No full textExpanding the use of environmentally friendly materials to protect the environment is one of the key factors in maintaining a sustainable ecological balance. Poly(butylene succinate-co-adipate) (PBSA) is considered among the most promising bio-based and biodegradable plastics for the future with a high number of applications in soil and agriculture. Therefore, the decomposition process of PBSA and its consequences for the carbon stored in soil require careful monitoring. For the first time, the stable isotope technique was applied in the current study to partitioning plastic- and soil-originated C in the CO2 released during 80 days of PBSA decomposition in a Haplic Chernozem soil as dependent on nitrogen availability. The decomposition of the plastic was accompanied by the C loss from soil organic matter (SOM) through priming, which in turn was dependent on added N. Nitrogen facilitated PBSA decomposition and reduced the priming effect during the first 6 weeks of the experiment. During the 80 days of plastic decomposition, 30% and 49% of the released CO2 were PBSA-derived, while the amount of SOM-derived CO2 exceeded the corresponding controls by 100.2 and 132.3% in PBSA-amended soil without and with N fertilization, respectively. Finally, only 4.1% and 5.4% of the PBSA added into the soil was mineralized to CO2, in the treatments without and with N amendment, respectively
Commodity production and African migration to Turkey, now and in the premodern past
No full textAfrican Migration in Turkey is an under-researched area despite the long history of migration between West Africa and the Ottoman Empire and the large number of African migrants in Turkey. The connection of this historical and contemporary migration movement with commodity production reveals not only the basic dynamics and patterns but also the global character of this mobility. While the flow of labor and commodities between Africa and Turkey continues, especially with Turkey's new Africa policy after 2002, African migrants are also implementing their own interests and agendas. Thus, an interdisciplinary approach encompassing history, economics, and anthropology reveals intertwined transformations and networks that provide a perspective for historical changes.A migração africana na Turquia é uma área pouco pesquisada, apesar da longa história de migração entre a África Ocidental e o Império Otomano e do grande número de migrantes africanos na Turquia. A conexão entre esse movimento migratório histórico e contemporâneo e a produção de commodities revela não apenas as dinâmicas e padrões básicos, mas também o caráter global dessa mobilidade. Enquanto o fluxo de trabalho e commodities entre a África e a Turquia continua, especialmente com o surgimento de uma nova política africana da Turquia após 2002, os migrantes africanos também estão implementando seus próprios interesses e agendas. Assim, uma abordagem interdisciplinar que abrange história, economia e antropologia revela transformações e redes entrelaçadas que nos fornecem uma perspectiva para as mudanças históricas
Isoglutaminyl cyclase contributes to CCL2-driven neuroinflammation in Alzheimer’s disease
No full textThe brains of Alzheimer’s disease (AD) patients are characterized by deposits of Abeta peptides and by accompanying chronic inflammation. Here, we provide evidence that the enzyme isoglutaminyl cyclase (isoQC) is a novel factor contributing to both aspects of AD pathology. Two putative substrates of isoQC, N-truncated Abeta peptides and the monocyte chemoattractant chemokine CCL2, undergo isoQC-catalyzed pyroglutamate (pGlu) modification. This triggers Abeta aggregation and facilitates the biological activity of CCL2, which collectively results in the formation of high molecular weight Abeta aggregates, glial cell activation, neuroinflammation and neuronal cell death. In mouse brain, we found isoQC to be neuron-specifically expressed in neocortical, hippocampal and subcortical structures, localized to the endoplasmic reticulum and Golgi apparatus as well as co-expressed with its substrate CCL2. In aged APP transgenic Tg2576 mice, both isoQC and CCL2 mRNA levels are up-regulated and isoQC and CCL2 proteins were found to be co-induced in Abeta plaque-associated reactive astrocytes. Also, in mouse primary astrocyte culture, a simultaneous up-regulation of isoQC and CCL2 expression was revealed upon Abeta and pGlu-Abeta stimulation. In brains of AD patients, the expression of isoQC and CCL2 mRNA and protein is up-regulated compared to controls and correlates with pGlu-Abeta load and with the decline in mini-mental state examination. Our observations provide evidence for a dual involvement of isoQC in AD pathogenesis by catalysis of pGlu-Abeta and pGlu-CCL2 formation which mutually stimulate inflammatory events and affect cognition. We conclude that isoQC inhibition may target both major pathological events in the development of AD
TEGDMA-Functionalized Dicalcium Phosphate Dihydrate Resin-Based Composites Prevent Secondary Caries in an In Vitro Biofilm Model
No full textThis study evaluated the efficacy of experimental TEGDMA-functionalized dicalcium
phosphate dihydrate (T-DCPD) filler-based resin-based composites (RBC) in preventing caries lesions
around the restoration margins (secondary caries, SC). Standardized Class-II cavities were made
in sound molars with the cervical margin in dentin. Cavities were filled with a commercial resinmodified
glass-ionomer cement (RMGIC) or experimental RBCs containing a bisGMA-TEGDMA
resin blend and one of the following inorganic fractions: 60 wt.% Ba glass (RBC-0); 40 wt.% Ba glass
and 20 wt.% T-DCPD (RBC-20); or 20 wt.% Ba glass and 40 wt.% T-DCPD (RBC-40). An open-system
bioreactor produced Streptococcus mutans biofilm-driven SC. Specimens were scanned using micro-CT
to evaluate demineralization depths. Scanning electron microscopy and energy-dispersive X-ray
spectroscopy characterized the specimen surfaces, and antimicrobial activity, buffering effect, and ion
uptake by the biofilms were also evaluated. ANOVA and Tukey’s tests were applied at p < 0.05. RBC-0
and RBC-20 showed SC development in dentin, while RBC-40 and RMGIC significantly reduced the
lesion depth at the restoration margin (p < 0.0001). Initial enamel demineralization could be observed
only around the RBC-0 and RBC-20 restorations. Direct antibiofilm activity can explain SC reduction
by RMGIC, whereas a buffering effect on the acidogenicity of biofilm can explain the behavior of
RBC-40. Experimental RBC with CaP-releasing functionalized T-DCPD filler could prevent SC with the same efficacy as F-releasing materials
