TY - JOUR A1 - Endrullat, Christoph A1 - Glökler, Jörn A1 - Franke, Philipp A1 - Frohme, Marcus T1 - Standardization and quality management in next-generation sequencing JF - Applied & Translational Genomics N2 - DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data. KW - next-generation sequencing KW - quality management KW - data quality KW - standardization KW - validation KW - guideline Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6637 SN - 2212-0661 VL - 10 SP - 2 EP - 9 ER - TY - JOUR A1 - Tillich, Ulrich M. A1 - Wolter, Nick A1 - Franke, Philipp A1 - Dühring, Ulf A1 - Frohme, Marcus T1 - Screening and genetic characterization of thermo-tolerant Synechocystis sp. PCC6803 strains created by adaptive evolution JF - BMC Biotechnology N2 - Temperature tolerance is an important aspect for commercial scale outdoor cultivation of microalgae and cyanobacteria. While various genes are known to be related to Synechocystis sp. PCC6803's heat shock response, there is very limited published data concerning the specific genes involved in long term thermal tolerance. We have previously used random mutagenesis and adaptive evolution to generate a mixture of strains of Synechocystis sp. PCC6803 with significantly increased thermal tolerance. The genetic modifications leading to the phenotypes of the newly generated strains are the focus of this work. KW - cyanobacteria KW - synechocystis KW - thermal tolerance KW - HTS KW - NGS KW - adaptive evolution Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6014 SN - 1472-6750 VL - 14 IS - 66 ER - TY - GEN A1 - Michel, Stephanie A1 - Jork, Nadine A1 - Rockmann, Christian A1 - Grohme, Markus A1 - Franke, Philipp A1 - Menzel, Detlef A1 - Frohme, Marcus T1 - Charakterisierung des mikrobiellen Symbioms von Blutegeln T2 - Wissenschaftliche Beiträge 2013 N2 - Die medizinischen Blutegel, Hirudo medicinalis und Hirudo verbana, werden wegen ihrer kurativen Wirkung in der Humanmedizin angewandt. Während des Blutsaugens injizieren sie über ihren Speichel eine Vielzahl bioaktiver, derzeit noch unbekannter Moleküle. Eine vollständige Aufklärung aller Inhaltsstoffe mit Wirkmechanismen ist für die Entwicklung von neuen Pharmaka von großem Interesse. Vor diesem Hintergrund wurden verschiedene Organe beider Arten auf ihre Besiedlung durch symbiontische Bakterien untersucht. Dazu wurden die Bakterien zunächst unter geeigneten Bedingungen kultiviert und mittels biochemischer Methoden charakterisiert. Die Identifizierung der Symbionten erfolgte durch Polymerasekettenreaktion (PCR) und Sequenzierung der 16S rDNA. Die biochemischen Tests ergaben, dass die kultivierbaren Bakterien Amylase positiv, Gram negativ und Ornithin Decarboxylase negativ sind. Mit Hilfe von datenbankgestützten Analysen der 16S rDNA-Sequenzen konnte Aeromonas veronii biovar sobria nachgewiesen werden. Hochdurchsatzsequenzierungen der gesamtgenomischen DNA des Bakteriums aus H. medicinalis zeigten deutliche Abweichungen zum Referenzgenom von Aeromonas veronii B565. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-3084 SN - 0949-8214 VL - 17 SP - 8 EP - 12 ER -