Detection and quantification of methylation in DNA using solid-state nanopores.

Epigenetic modifications in eukaryotic genomes occur primarily in the form of 5-methylcytosine (5 mC). These modifications are heavily involved in transcriptional repression, gene regulation, development and the progression of diseases including cancer. We report a new single-molecule assay for the detection of DNA methylation using solid-state nanopores. Methylation is detected by selectively labeling methylation sites with MBD1 (MBD-1x) proteins, the complex inducing a 3 fold increase in ionic blockage current relative to unmethylated DNA. Furthermore, the discrimination of methylated and unmethylated DNA is demonstrated in the presence of only a single bound protein, thereby giving a resolution of a single methylated CpG dinucleotide. The extent of methylation of a target molecule could also be coarsely quantified using this novel approach. This nanopore-based methylation sensitive assay circumvents the need for bisulfite conversion, fluorescent labeling, and PCR and could therefore prove very useful in studying the role of epigenetics in human disease

Prognostic value of discs large homolog 7 transcript levels in prostate cancer.

Hypoxia has been associated with malignant progression, metastasis and resistance to therapy. Hence, we studied expression of hypoxia-regulated genes in 100 prostate cancer (CaP) bulk tissues and 71 adjacent benign tissues. We found 24 transcripts significantly overexpressed (p ≤ 0.02). Importantly, higher transcript levels of disc large (drosophila) homolog-associated protein 5 (DLGAP5)/discs large homolog 7 (DLG7)/hepatoma up-regulated protein (HURP), hyaluronan-mediated motility receptor (HMMR) and cyclin B1 (CCNB1) were associated with higher Gleason score and more advanced systemic progression. Since the products of HMMR and CCNB1 have been identified recently as molecular markers of CaP progression, we postulated that DLG7 has prognostic value too. To test this hypothesis, we measured transcript levels for DLG7 in a 150-pair case-control cohort. The cases (progression to systemic disease within six years of surgery) and controls (no progression within eight years) were matched for clinical and pathologic prognostic variables, including grade, stage, and preoperative serum levels of PSA. The overall prognostic ability of DLG7, as tested in receiver operating characteristic analysis was of 0.74 (95% CI, 0.68 to 0.8). Overall, our data indicate that expression of DLG7, a hypoxia-controlled gene, holds prognostic potential in high-risk CaP; this also demonstrates that variation of oxygen tension may constitute a tool for identification of novel biomarkers for CaP

Three hypoxia-controlled genes associated with Gleason score and prognosis.

<p>Among the hypoxia-regulated genes significantly overexpressed in CaP, cyclin B1 (CCNB1), DLGAP5 and hyaluronan-mediated motility receptor (HMMR) were associated with Gleason score and disease outcome.</p

Transcript levels for CCNB1, DLG7, and HMMR measured in CaP and noncancerous prostate tissue.

<p>Panels on the left compare transcript levels in CaP bulk tissue (full symbols) with the levels measured in benign prostate tissue (open symbols) from men free of CaP (BP) and in benign prostate tissue (BPC) adjacent to CaP of combined Gleason score 6 (gs6). Panels on the right display transcript levels measured in non-neoplastic prostate epithelial cells isolated by laser capture microdissection (LCM) in benign tissues (open symbols): BP, benign prostatic hyperplasia (BPH) and BPC adjacent to CaP of the indicated Gleason score (gs). Full symbols in panels on the right denote transcript levels measured in LCM-isolated CaP cells: high-grade prostatic intraepithelial neoplasia (HGPIN), the cells isolated from areas of combined Gleason scores 6 through 8 and cells isolated from lymph node metastases (met). CCNB1, cyclin B1; DLG7, discs large homolog 7; HMMR, hyaluronan-mediated motility receptor.</p

Receiver operating characteristic (ROC) analysis for DLG7.

<p>The area under the curve was 0.74 (95% CI, 068–0.80). Inset: Scatter plot of the normalized expression values for cases (red) and controls (green).</p

Tech & Science @ School. Ein fachpraktisches Handbuch für Technik-Lehrkräfte

Kunstgegenstände & Schmuck herzustellen ist ein urmenschliches Bedürfnis. Aus diesem Kernbereich der Schmuckfertigung und des Drechselns sind die vorliegenden Projektideen entstanden. Die in dieser Handreichung vorgestellten Projektideen sind alle von Lehramtsstudierenden im Fach Technik an den Pädagogischen Hochschulen in Schwäbisch Gmünd und Ludwigsburg in offener und selbstgesteuerter Werkstattarbeit seit dem Sommersemester 2021 entstanden. Die Studierenden haben dabei ihre Idee stets fachpraktisch erprobt und fachdidaktisch in den vorliegenden Erklärfilmen und Schritt für Schritt-Anleitungen ausgearbeitet. Der Projektrahmen umfasst das curricular verankerte, handwerklich bedeutsame Arbeiten mit den grundlegenden Werkstoffen Holz, Metall und Kunststoffen sowie den Bereich der Elektrotechnik und des Mikrocontrolling. Die Umsetzung dieser Projektideen soll unterstützend wirken, um individuelle handwerkliche Kompetenzen zu entdecken, erproben und vertiefen sowie technische Interessensbildung und vorberufliche Orientierung in Schulen fördern. Eine Schlüsselrolle für die Anfertigung der Werkstücke nimmt hierbei das Vorführen und Erklären (modellhaftes Vormachen) der notwendigen Fertigungsschritte durch Experten in Form von Erklärfilmen ein. Die zugrundeliegende didaktische Konzeption lehnt sich an die Kognitive Meisterlehre aus der gewerblich-technischen beruflich orientierten Bildung an (Collins et al., 1989). Das Projekt KunstHandWerk wurde durch eine Kooperation zwischen der PH Ludwigsburg und der PH Schwäbisch Gmünd in Zusammenarbeit mit der Gold- und Silberschmiede-Innung Stuttgart-Heilbronn-Reutlingen initiiert und von TRAFO - dem Netzwerk transferorientierter Lehre in Baden-Württemberg gefördert. Die Projektfortsetzung Tech&Science@School mit der Uhland-Realschule Aalen wurde durch die Vector Stiftung gefördert

Associations of autozygosity with a broad range of human phenotypes

Abstract: In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: FROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44–66%] in the odds of having children. Finally, the effects of FROH are confirmed within full-sibling pairs, where the variation in FROH is independent of all environmental confounding

A saturated map of common genetic variants associated with human height

Common single-nucleotide polymorphisms (SNPs) are predicted to collectively explain 40–50% of phenotypic variation in human height, but identifying the specific variants and associated regions requires huge sample sizes1. Here, using data from a genome-wide association study of 5.4 million individuals of diverse ancestries, we show that 12,111 independent SNPs that are significantly associated with height account for nearly all of the common SNP-based heritability. These SNPs are clustered within 7,209 non-overlapping genomic segments with a mean size of around 90 kb, covering about 21% of the genome. The density of independent associations varies across the genome and the regions of increased density are enriched for biologically relevant genes. In out-of-sample estimation and prediction, the 12,111 SNPs (or all SNPs in the HapMap 3 panel2) account for 40% (45%) of phenotypic variance in populations of European ancestry but only around 10–20% (14–24%) in populations of other ancestries. Effect sizes, associated regions and gene prioritization are similar across ancestries, indicating that reduced prediction accuracy is likely to be explained by linkage disequilibrium and differences in allele frequency within associated regions. Finally, we show that the relevant biological pathways are detectable with smaller sample sizes than are needed to implicate causal genes and variants. Overall, this study provides a comprehensive map of specific genomic regions that contain the vast majority of common height-associated variants. Although this map is saturated for populations of European ancestry, further research is needed to achieve equivalent saturation in other ancestries.</p