Finding approximate gene clusters with GECKO 3

Winter S, Jahn K, Wehner S, et al. Finding approximate gene clusters with GECKO 3. Nucleic Acids Research. 2016;44(20):9600-9610.Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding gene clusters in hundreds of genomes. Existing tools are often restricted to few (in many cases, only two) genomes, and often make restrictive assumptions such as short perfect conservation, conserved gene order or monophyletic gene clusters. We present Gecko 3, an open-source software for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphical user interface. The underlying gene cluster model is intuitive, can cope with low degrees of conservation as well as misannotations and is complemented by a sound statistical evaluation. To evaluate the biological benefit of Gecko 3 and to exemplify our method, we search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a reference. We confirm detected gene clusters reviewing the literature and comparing them to a database of operons; we detect two novel clusters, which were confirmed by publicly available experimental RNA-Seq data. The computational analysis is carried out on a laptop computer in <40 min

Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings

Dörr D, Stoye J, Böcker S, Jahn K. Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings. BMC Genomics. 2014;15(Suppl. 6: Proc. of RECOMB-CG 2014): S2.Background: Comparative analyses of chromosomal gene orders are successfully used to predict gene clusters in bacterial and fungal genomes. Present models for detecting sets of co-localized genes in chromosomal sequences require prior knowledge of gene family assignments of genes in the dataset of interest. These families are often computationally predicted on the basis of sequence similarity or higher order features of gene products. Errors introduced in this process amplify in subsequent gene order analyses and thus may deteriorate gene cluster prediction. Results: In this work, we present a new dynamic model and efficient computational approaches for gene cluster prediction suitable in scenarios ranging from traditional gene family-based gene cluster prediction, via multiple conflicting gene family annotations, to gene family-free analysis, in which gene clusters are predicted solely on the basis of a pairwise similarity measure of the genes of different genomes. We evaluate our gene family-free model against a gene family-based model on a dataset of 93 bacterial genomes. Conclusions: Our model is able to detect gene clusters that would be also detected with well-established gene family-based approaches. Moreover, we show that it is able to detect conserved regions which are missed by gene family-based methods due to wrong or deficient gene family assignments

Between-Subject and Within-Subject Variation of Muscle Atrophy and Bone Loss in Response to Experimental Bed Rest

To improve quantification of individual responses to bed rest interventions, we analyzed peripheral quantitative computer tomography (pQCT) datasets of the lower leg of 76 participants, who took part in eight different bed rest studies. A newly developed statistical approach differentiated measurement uncertainty UMeas from betweensubject-variation (BSV) and within-subject variation (WSV). The results showed that UMeas decreased 59.3–80% over the two decades of bed rest studies (p < 0.01), and that it was higher for muscles than for bones. The reduction of UMeas could be explained by improved measurement procedures as well as a higher standardization. The vast majority (89.6%) of the individual responses pci exceeded the 95% confidence interval defined by UMeas, indicating significant and substantial BSV, which was greater for bones than for muscles, especially at the epiphyseal measurement sites. Non-significant to small positive inter-site correlations between bone sites, but very large positive inter-site correlation between muscle sites suggests that substantial WSV exists in the tibia bone, but much less so in the calf musculature. Furthermore, endocortical circumference, an indicator of the individual’s bone geometry could partly explain WSV and BSV. These results demonstrate the existence of substantial BSV bone, and that it is partly driven by WSV, and likely also by physical activity and dietary habits prior to bed rest. In addition, genetic and epigenetic variation could potentially explain BSV, but not WSV. As to the latter, differences of bone characteristics and the bone resorption process could offer an explanation for its existence. The study has also demonstrated the importance of duplicate baseline measurements. Finally, we provide here a rationale for worst case scenarios with partly effective countermeasures in long-term space missions

Swiftly Computing Center Strings

Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S. Swiftly Computing Center Strings. BMC Bioinformatics. 2011;12(1): 106

The role of biospectroscopy and chemometrics as enabling technologies for upcycling of raw materials from the food industry

It is important to utilize the entire animal in meat and fish production to ensure sustainability. Rest raw materials, such as bones, heads, trimmings, and skin, contain essential nutrients that can be transformed into high-value products. Enzymatic protein hydrolysis (EPH) is a bioprocess that can upcycle these materials to create valuable proteins and fats. This paper focuses on the role of spectroscopy and chemometrics in characterizing the quality of the resulting protein product and understanding how raw material quality and processing affect it. The article presents recent developments in chemical characterisation and process modelling, with a focus on rest raw materials from poultry and salmon production. Even if some of the technology is relatively mature and implemented in many laboratories and industries, there are still open challenges and research questions. The main challenges are related to the transition of technology and insights from laboratory to industrial scale, and the link between peptide composition and critical product quality attributes.publishedVersio

Reversible gene knockdown in mice using a tight, inducible shRNA expression system

RNA interference through expression of short hairpin (sh)RNAs provides an efficient approach for gene function analysis in mouse genetics. Techniques allowing to control time and degree of gene silencing in vivo, however, are still lacking. Here we provide a generally applicable system for the temporal control of ubiquitous shRNA expression in mice. Depending on the dose of the inductor doxycycline, the knockdown efficiency reaches up to 90%. To demonstrate the feasibility of our tool, a mouse model of reversible insulin resistance was generated by expression of an insulin receptor (Insr)-specific shRNA. Upon induction, mice develop severe hyperglycemia within seven days. The onset and progression of the disease correlates with the concentration of doxycycline, and the phenotype returns to baseline shortly after withdrawal of the inductor. On a broad basis, this approach will enable new insights into gene function and molecular disease mechanisms

Die Customer Journey - Chance für mehr Kundennähe

Die Vielzahl der Möglichkeiten, um mit Kunden in den Dialog zu treten, ist erheblich gestiegen. Unternehmen sind deshalb gefordert, die verschiedenen Kontaktkanäle mit ihren Kunden systematisch zu managen. Im Mittelpunkt steht dabei der Informations- und Entscheidungsprozess des Kunden, der als Customer Journey bezeichnet wird. Diese Journey ist definiert als Prozess zwischen dem ersten Kaufimpuls und der Kaufentscheidung. Dieser Prozess ist charakterisiert von der Nutzung verschiedener Medien bzw. Kontaktkanäle. Kunden nutzen die Kontaktkanäle, die ihnen in der aktuellen Situation als sehr einfach bzw. bequem erscheinen und zu ihren spezifischen Anliegen (Fragen zum Produkt, Bestellung etc.) passen. Erfahrungen zeigen, dass sich zwar Grundmuster identifizieren lassen, ansonsten die Wege der Kunden jedoch sehr individuell sein können

Marketing für Leistungssysteme

In kaum einem anderen Geschäft ist das Risiko für die Anbieter- und Nachfragerseite so hoch wie im Systemgeschäft. Deshalb müssen Systemanbieter die Charakteristika des Systemgeschäfts kennen und dessen Erfolgsfaktoren beherrschen