Prognostic DNA methylation markers for sporadic colorectal cancer: a systematic review

Background Biomarkers that can predict the prognosis of colorectal cancer (CRC) patients and that can stratify high-risk early stage patients from low-risk early stage patients are urgently needed for better management of CRC. During the last decades, a large variety of prognostic DNA methylation markers has been published in the literature. However, to date, none of these markers are used in clinical practice. Methods To obtain an overview of the number of published prognostic methylation markers for CRC, the number of markers that was validated independently, and the current level of evidence (LoE), we conducted a systematic review of PubMed, EMBASE, and MEDLINE. In addition, we scored studies based on the REMARK guidelines that were established in order to attain more transparency and complete reporting of prognostic biomarker studies. Eighty-three studies reporting on 123 methylation markers fulfilled the study entry criteria and were scored according to REMARK. Results Sixty-three studies investigated single methylation markers, whereas 20 studies reported combinations of methylation markers. We observed substantial variation regarding the reporting of sample sizes and patient characteristics, statistical analyses, and methodology. The median (range) REMARK score for the studies was 10.7 points (4.5 to 17.5) out of a maximum of 20 possible points. The median REMARK score was lower in studies, which reported a p value below 0.05 versus those, which did not (p = 0.005). A borderline statistically significant association was observed between the reported p value of the survival analysis and the size of the study population (p = 0.051). Only 23 out of 123 markers (17%) were investigated in two or more study series. For 12 markers, and two multimarker panels, consistent results were reported in two or more study series. For four markers, the current LoE is level II, for all other markers, the LoE is lower. Conclusion This systematic review reflects that adequate reporting according to REMARK and validation of prognostic methylation markers is absent in the majority of CRC methylation marker studies. However, this systematic review provides a comprehensive overview of published prognostic methylation markers for CRC and highlights the most promising markers that have been published in the last two decades

Sequencing of \u3ci\u3eAspergillus nidulans\u3c/i\u3e and comparative analysis with \u3ci\u3eA. fumigatus\u3c/i\u3e and \u3ci\u3eA. oryzae\u3c/i\u3e

The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso, and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation. Document includes all supplementary information (820 pages). Supplementary files are also attached below as Related files. THERE IS NO SUPPLEMENTARY FILE #7. PDF file size (with supplementary files included) is 10 Mbytes. An optimized version of the ARTICLE ONLY is attached as a Related File and is 1.9 Mbytes

Sequencing of \u3ci\u3eAspergillus nidulans\u3c/i\u3e and comparative analysis with \u3ci\u3eA. fumigatus\u3c/i\u3e and \u3ci\u3eA. oryzae\u3c/i\u3e

The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso, and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation. Document includes all supplementary information (820 pages). Supplementary files are also attached below as Related files. THERE IS NO SUPPLEMENTARY FILE #7. PDF file size (with supplementary files included) is 10 Mbytes. An optimized version of the ARTICLE ONLY is attached as a Related File and is 1.9 Mbytes

Silencing of Vlaro2 for chorismate synthase revealed that the phytopathogen Verticillium longisporum induces the cross-pathway control in the xylem

The first leaky auxotrophic mutant for aromatic amino acids of the near-diploid fungal plant pathogen Verticillium longisporum (VL) has been generated. VL enters its host Brassica napus through the roots and colonizes the xylem vessels. The xylem contains little nutrients including low concentrations of amino acids. We isolated the gene Vlaro2 encoding chorismate synthase by complementation of the corresponding yeast mutant strain. Chorismate synthase produces the first branch point intermediate of aromatic amino acid biosynthesis. A novel RNA-mediated gene silencing method reduced gene expression of both isogenes by 80% and resulted in a bradytrophic mutant, which is a leaky auxotroph due to impaired expression of chorismate synthase. In contrast to the wild type, silencing resulted in increased expression of the cross-pathway regulatory gene VlcpcA (similar to cpcA/GCN4) during saprotrophic life. The mutant fungus is still able to infect the host plant B. napus and the model Arabidopsis thaliana with reduced efficiency. VlcpcA expression is increased in planta in the mutant and the wild-type fungus. We assume that xylem colonization requires induction of the cross-pathway control, presumably because the fungus has to overcome imbalanced amino acid supply in the xylem

High value manufacturing : capability, appropriation, and governance

Manufacturing competitiveness is on many policy agendas, born out of a concern for firms in high-cost economies finding themselves outcompeted by low-cost rivals. Government policy makers and manufacturing firm strategists have put their faith in what we label as high value manufacturing (HVM). We see HVM as an incipient phenomenon currently in a situation of prescience, as something that is still “in-the-making,” with manufacturing firms trying to find ways to be able to step away from having to compete on price. This paper consults relevant strategy theories with the purpose to pinpoint the issues and problems that need to be accommodated for bringing HVM into being and for creating the effects that are anticipated. We found that HVM must be seen as a distributed activity, thus realizing complex functionality for a system-of-use, while being subjected to path constitution. For HVM to function, the firms involved need to find solutions to the capability problem, the appropriation problem, and the governance problem. We suggest that further research needs to involve itself in problem-solving activity to assist in bringing HVM about while simultaneously further developing strategy theory geared toward firms that are involved in a distributed activity like HVM

CsnA abhängige Entwicklung und Aminosäurebiosynthese im filamentösen Pilz <i>Aspergillus nidulans</i>.

Die Familie der Aspergillen ist eine sehr heterogene Gruppe filamentöser Pilze. Aspergillus nidulans ist ein wichtiger eukaryotischer Modellorganismus für Metabolismus- und Entwicklungsstudien. Aspergillus oryzae ist von großer biotechnologischer Bedeutung in der asiatischen Lebensmittelindustrie, wohingegen der opportunistische humanpathogene Pilz A. fumigatus von wachsender medizinischer Bedeutung ist. Diese Arbeit konzentriert sich auf das COP9 Signalosom, einen essentiellen, eukaryontischen Entwicklungsregulator und die generelle Kontrolle der Aminosäurebiosynthese (gc). Die generelle Kontrolle regelt die zelluläre Antwort auf Aminosäuremangel. Beide Netzwerke sind von der Bäckerhefe bis zum Menschen hoch konserviert.Das COP9 Signalosom ist ein Multiproteinkomplex, dessen wichtigste zugehörige enzymatische Aktivitäten aus Kinase- und De-ubiquitinierungsaktivitäten und einer intrinsischen Deneddylaseaktivität bestehen. Diese Arbeit untersucht die Relevanz der ersten Untereinheit des COP9 Signalosoms CsnA anhand der Expression von verkürzten Proteinvarianten. csnA Deletionsmutanten weisen diverse pleiotrophe Phänotypen auf. Die Expression von verkürzten CsnA Peptiden ermöglichte es, die Funktionen des COP9 Signalosoms von Aktivitäten des CsnA Proteins zu trennen. Der CsnA C-Terminus ist wichtig für die Aufrechterhaltung des Komplexzusammenhalts und der COP9 Aktivitäten. Der CsnA N-Terminus hingegen scheint eine wichtige Rolle in der Regulation der Ausbildung von Lufthyphen zu spielen. Im Zuge der manuellen Annotation der Genome der Pilze A. nidulans, A. fumigatus und A. oryzae wurden grundlegende Gene der generellen Kontrolle der Aminosäurebiosynthese (cpc) im Vergleich zu niederen und höheren Eukaryonten untersucht. Die Resultate der Untersuchung zeigen, daß die grundlegenden Mechanismen der cpc der filamentösen Pilze eher denen der Hefen ähneln und etwas weniger komplex als bei höheren Organismen sind. Die externen und internen Sensoren und die Aufnahmesysteme für Aminosäuren hingegen scheinen eher denen höherer Eukaryonten zu ähneln als denen einzelliger Hefen. Die Ergebnisse weisen darauf hin, daß die Aufnahme- und Sensorsysteme für Aminosäuren einen Einfluß auf das Wachstum und die Entwicklung der Pilze haben könnten, wie man sie aus Säugersystemen kennt.Die Untersuchung des Transports des zentralen Transkriptionsfaktors der cpc CpcA in den Zellkern wurde in S. cerevisiae und A. nidulans untersucht. Für einen effizienten Transport in den Nukleus ist das Kernlokalisierungssignal von CpcA notwendig. In der Bäckerhefe wurden zwei Importine Srp1p und Kap95p identifiziert, die essentiell für den Kerntransport von CpcA sind. Diese wurden auch hoch konserviert in in silico Untersuchungen in den Aspergillengenomen wiedergefunden. Die hypothetischen Aspergillenproteine SrpA und KapA könnten auch in Aspergillus notwendig für den Kerntransport von CpcA sein

Der Einfluss von Pfadintegration und räumlicher visueller Wahrnehmung auf die Aktivität von Ortszellen

Ortszellen ("place cells") sind Nervenzellen im Hippocampus, die eine entscheidende Rolle bei der neuronalen Repräsentation der Lokalisation im Raum, räumlichem Lernen und der Bildung eines räumlichen Gedächtnisses spielen. Dies gelingt durch Verarbeitung unterschiedlicher sensorischer Einflüsse, darunter sowohl externe visuelle als auch interne, idiothetische Informationen und die Mechanismen der Pfadintegration. In dieser Arbeit wurde die Aktivität von Ortszellen untersucht, während Ratten eine Umgebung explorierten, in der diese beiden Informationsquellen in Widerspruch zueinanderstanden. Wir beobachteten, dass Ortszellen in Tieren, die den Versuch zum ersten Mal durchliefen, primär von visuellen Informationen kontrolliert werden. Mit zunehmender Erfahrung jedoch werden idiothetische Informationen in die Ausbildung einer räumlichen neuronalen Repräsentation integriert