PVDF Detectors in Supersonic Molecular Jet Experiments

Im Rahmen dieser Arbeit wurden verschiedene Teilchendetektoren zur Verwendung in einem gepulsten Überschallmolekularstrahlexperiment entworfen und hergestellt. In den hier durchgeführten Experimenten kollidiert ein Molekularstrahl mit einer sensitiven Detektoroberfläche, nämlich einer Polyvinylidenfluorid(PVDF)-Folie. Da PVDF sowohl pyroelektrisch wie auch piezoelektrisch ist, entstehen durch die Kollision der Molekularstrahlteilchen auf der Folie Oberflächenladungen. Vorteile von PVDF-Detektoren sind die hohe Effizient der Detektion, die Detektion von neutralen Atomen und Molekülen (eine Ionisierung der zu detektierenden Teilchen ist nicht notwendig), ein einfaches und leicht anzupassendes Detektordesign und außerdem eine schnelle Antwortzeit (im Mikrosekundenbereich). Da nur Ladungen im Bereich von wenigen Pikocoulomb generiert werden, sind verschiedene Verstärker getestet worden. Zur Analyse und Beschreibung des detektierten Signals wird der piezoelektrische Anteil durch ein Materialmodell in Verbindung mit einem schwingenden System, nämlich der erzwungenen Schwingung einer gedämpften Kreismembran, beschrieben. Der pyroelektrische Anteil wird durch einen Energieaustausch beschrieben. Durch die Ausnutzung des pyroelektrischen sowie des piezoelektrischen Effektes können zusätzliche wichtige Informationen wie zum Beispiel der Restitutionskoeffizient oder der Energieakkommodationkoeffizient experimentell erhalten werden. Zur Demonstration der Anwendungsmöglichkeiten sind Detektoren in verschiedenen Größen zur Messung von unterschiedlichen Strahleigenschaften verwendet worden. Untersucht wurde dabei die Strahlgeschwindigkeit von verschiedenen Edelgasen über einen großen Stagnationsdruck- und Stagnationstemperaturbereich. Außerdem wurden Strahlprofile zur Bestimmung der Strahldichte gemessen und mathematisch beschrieben. Zusätzlich wird eine Methode zur Bestimmung der Strahltemperatur mit Hilfe der Strahldichte und der Strahlgeschwindigkeit vorgestellt.In this study, different particle detectors with a foil of polyvinylidene difluoride have been designed and built for use in a pulsed supersonic molecular jet experiment. Here, the molecular jet collides with the sensitive detector area and generates a charge. This generated charge is caused by the piezo- and the pyroelectric effect. Advantages of polyvinylidene difluoride detectors are a high detection efficiency, the detection of neutral atoms or molecules --- no ionization is required, a simple setup which can be easily incorporated in an existing experiment, an easy adjustment of the detector design because the shape and size can be changed easily, and a fast response-time in the sub-microsecond regime. Because the amount of charges generated is in the order of some picocoulomb, different amplifiers are used. In this analysis of the detected signal, the piezoelectric contribution is defined by the constitutive equations of piezoelectricity, which are used in combination with the concept of a driven damped circular membrane in order to obtain an analytic solution. The pyroelectric contribution is described via the exchanged energy. Because both the piezo- and the pyroelectric effects can be exploited, valuable additional information such as the coefficient of energy accommodation or the coefficient of restitution can be determined experimentally. In order to demonstrate the application possibilities of polyvinylidene difluoride detectors, detectors of different sizes are used as a local jet probe to determine different jet properties. The mean velocities of different rare gases for a wide range of source conditions are determined. Density profiles of various supersonic jets are measured and described mathematically in detail. In addition, both quantities, the velocity and the density, are used to determine the temperature of the supersonic jet

Lust Flour Life

Winner: Best in Show Literary inspiration: Lust for Lifehttps://scholarworks.umass.edu/ediblebookfest_2018/1001/thumbnail.jp

Intestinal organoid cocultures with microbes

This protocol comprises various methods to coculture organoids (particularly human small intestinal and colon organoids) with microbes, including microinjection into the lumen and periphery of 3D organoids and exposure of organoids to microbes in a 2D layer.Adult-stem-cell-derived organoids model human epithelial tissues ex vivo, which enables the study of host-microbe interactions with great experimental control. This protocol comprises methods to coculture organoids with microbes, particularly focusing on human small intestinal and colon organoids exposed to individual bacterial species. Microinjection into the lumen and periphery of 3D organoids is discussed, as well as exposure of organoids to microbes in a 2D layer. We provide detailed protocols for characterizing the coculture with regard to bacterial and organoid cell viability and growth kinetics. Spatial relationships can be studied by fluorescence live microscopy, as well as scanning electron microscopy. Finally, we discuss considerations for assessing the impact of bacteria on gene expression and mutations through RNA and DNA sequencing. This protocol requires equipment for standard mammalian tissue culture, or bacterial or viral culture, as well as a microinjection device

Colon Tumors in Enterotoxigenic Bacteroides fragilis (ETBF)-Colonized Mice Do Not Display a Unique Mutational Signature but Instead Possess Host-Dependent Alterations in the APC Gene

Enterotoxigenic Bacteroides fragilis (ETBF) is consistently found at higher frequency in individuals with sporadic and hereditary colorectal cancer (CRC) and induces tumorigenesis in several mouse models of CRC. However, whether specific mutations induced by ETBF lead to colon tumor formation has not been investigated. To determine if ETBF-induced mutations impact the Apc gene, and other tumor suppressors or proto-oncogenes, we performed whole-exome sequencing and whole-genome sequencing on tumors isolated after ETBF and sham colonization of Apcmin/+ and Apcmin/+Msh2fl/flVC mice, as well as whole-genome sequencing of organoids cocultured with ETBF. Our results indicate that ETBF-induced tumor formation results from loss of heterozygosity (LOH) of Apc, unless the mismatch repair system is disrupted, in which case, tumor formation results from new acquisition of protein-truncating mutations in Apc. In contrast to polyketide synthase-positive Escherichia coli (pks+ E. coli), ETBF does not produce a unique mutational signature; instead, ETBF-induced tumors arise from errors in DNA mismatch repair and homologous recombination DNA damage repair, established pathways of tumor formation in the colon, and the same genetic mechanism accounting for sham tumors in these mouse models. Our analysis informs how this procarcinogenic bacterium may promote tumor formation in individuals with inherited predispositions to CRC, such as Lynch syndrome or familial adenomatous polyposis (FAP). IMPORTANCE Many studies have shown that microbiome composition in both the mucosa and the stool differs in individuals with sporadic and hereditary colorectal cancer (CRC). Both human and mouse models have established a strong association between particular microbes and colon tumor induction. However, the genetic mechanisms underlying putative microbe-induced colon tumor formation are not well established. In this paper, we applied whole-exome sequencing and whole-genome sequencing to investigate the impact of ETBF-induced genetic changes on tumor formation. Additionally, we performed whole-genome sequencing of human colon organoids exposed to ETBF to validate the mutational patterns seen in our mouse models and begin to understand their relevance in human colon epithelial cells. The results of this study highlight the importance of ETBF colonization in the development of sporadic CRC and in individuals with hereditary tumor conditions, such as Lynch syndrome and familial adenomatous polyposis (FAP)

Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer

Co-culture of intestinal organoids with a colibactin-producing pks+ E. coli strain (EcC) revealed mutational signatures also found in colorectal cancer (CRC). E. coli Nissle 1917 (EcN) remains a commonly used probiotic, despite harboring the pks operon and inducing double strand DNA breaks. We determine the mutagenicity of EcN and three CRC-derived pks+ E. coli strains with an analytical framework based on sequence characteristic of colibactin-induced mutations. All strains, including EcN, display varying levels of mutagenic activity. Furthermore, a machine learning approach attributing individual mutations to colibactin reveals that patients with colibactin-induced mutations are diagnosed at a younger age and that colibactin can induce a specific APC mutation. These approaches allow the sensitive detection of colibactin-induced mutations in ~12% of CRC genomes and even in whole exome sequencing data, representing a crucial step toward pinpointing the mutagenic activity of distinct pks+ E. coli strains