Biologists meet statisticians: A workshop for young scientists to foster interdisciplinary team work

Life science and statistics have necessarily become essential partners. The need to plan complex, structured experiments, involving elaborated designs, and the need to analyse datasets in the era of systems biology and high throughput technologies has to build upon professional statistical expertise. On the other hand, conducting such analyses and also developing improved or new methods, also for novel kinds of data, has to build upon solid biological understanding and practise. However, the meeting of scientists of both fields is often hampered by a variety of communicative hurdles - which are based on field-specific working languages and cultural differences. As a step towards a better mutual understanding, we developed a workshop concept bringing together young experimental biologists and statisticians, to work as pairs and learn to value each others competences and practise interdisciplinary communication in a casual atmosphere. The first implementation of our concept was a cooperation of the German Region of the International Biometrical Society and the Leibnitz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (short: DSMZ), Braunschweig, Germany. We collected feedback in form of three questionnaires, oral comments, and gathered experiences for the improvement of this concept. The long-term challenge for both disciplines is the establishment of systematic schedules and strategic partnerships which use the proposed workshop concept to foster mutual understanding, to seed the necessary interdisciplinary cooperation network, and to start training the indispensable communication skills at the earliest possible phase of education

Physiologische Änderungen durch Gen-Überexpression in pflanzlichen Zellkulturen: Charakterisierung und statistische Signifikanz

Heterotrophic, dedifferentiated suspended cell cultures facilitates the control of stress homogeneity and the characterisation of the cells’ behaviourindependently of plant morphologies. Pathogenesis-related (PR) proteins of group 10 and especially their member PR-10a were reported to show induced gene expression or protein abundance caused by several biotic and abiotic stressors in diverse studies on a variety of plants, organs, tissues and developmental stages. But the mode of action of the PR-10a protein itself as well as the pathways it could interfere with are still less well explored Based on a set of heterotrophic dedifferentiated cell cultures of Solanum tuberosum cv. Désirée (wild-type and transgenic lines homologously overexpressing pr-10a) providing the main biological system to be analysed, this thesis discuss, beside an optimized vector-architecture, cryopreservation as a novel experimental framework for gathering information on GMO, the development of a method for collecting additional physiological data, and last but not least the elaboration of suitable software solutions for convenient data visualization and analysis are investigated. Especially, the concept of respiration measurements is shown to be a meaningful complement for the set of methods when examining phenotypes of heterotrophic dedifferentiated cell cultures. The novel method provides valuable information in situations not more common methods such as growth measurements and the investigated data analyses strategiesform the basis for a forthcoming freely available R package for the analysis of PM data, representative for respiration measurements resulting in longitudinal data sets. The availability of convenient and robust data exploration techniques via freely available software such as R will allow users to conduct in-depth data analyses that go significantly beyond the consideration of mere endpoint measurements and presence/absence calls.Heterotrophe, dedifferentierte Suspensions-Zellkulturen erlauben es Stressoren homogen auf die Zellen wirken zu lassen und eine Charakterisierung unabhängig von morphologischen Strukturen vorzunehmen. Im Zusammenhang mit Pathogenität untersuchte Proteine (Pathogenesis-related (PR) proteins), besonders Vertreter der Untergruppe 10a sind bekannt dafür sowohl unter Einfluss von biotischem als auch abiotischem Stress mit erhöhter Expression zu reagieren. Obwohl dieses Phänomen in verschiedenen Pflanzenarten, -organen, -gewebetypen und Entwicklungsstadien beobachtet werden konnte, ist die eigentliche Funktion des Proteins sowie seine Interaktionspartner weitgehend unerforscht. Basierend auf einem Set von heterotrophen, dedifferenzierten Suspensions-Zellkulturen von Solanum tuberosum cv. Désirée (Wild-typ und pr-10a überexprimierende transgene Linien), wird in dieser Arbeit neben der optimierten Vektor-Architektur, Kryokonservierung als neues Experimentelles Design zur Erhebung von neuartigen physiologischen Informationen erörtert und eine adäquate Software-Lösung zur einfach anzuwendenden Visualisierung und Daten-Analyse vorgestellt. Besonders das Konzept von Respirationsmessungen stellt eine wertvolle Ergänzung des bisher vorhandenen Methodenspektrums zur Untersuchung von Phänotypen in heterotrophen dedifferentierten Zellkulturen dar. Darauf aufbauend steht die Veröffentlichung eines frei erhältliches R-Pakets bevor, um die Auswertung von Respirationskinetiken mit dem hier vorgestellten Methodenspektrum in eine umfassende Software-Lösung zu integrieren. Auf diese Weise wird eine tiefgehende Analyse, die signifikant mehr biologisch relevante Informationen liefert als die Auswertung von Endpunktmessungen oder dichotomen Daten, einem breiten Publikum ermöglicht

MycoBank gearing up for new horizons.

MycoBank, a registration system for fungi established in 2004 to capture all taxonomic novelties, acts as a coordination hub between repositories such as Index Fungorum and Fungal Names. Since January 2013, registration of fungal names is a mandatory requirement for valid publication under the International Code of Nomenclature for algae, fungi and plants (ICN). This review explains the database innovations that have been implemented over the past few years, and discusses new features such as advanced queries, registration of typification events (MBT numbers for lecto, epi- and neotypes), the multi-lingual database interface, the nomenclature discussion forum, annotation system, and web services with links to third parties. MycoBank has also introduced novel identification services, linking DNA sequence data to numerous related databases to enable intelligent search queries. Although MycoBank fills an important void for taxon registration, challenges for the future remain to improve links between taxonomic names and DNA data, and to also introduce a formal system for naming fungi known from DNA sequence data only. To further improve the quality of MycoBank data, remote access will now allow registered mycologists to act as MycoBank curators, using Citrix software

Making sense of big data in health research: Towards an EU action plan.

Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of "big data" for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health and healthcare for all Europeans

Visualization and Curve-Parameter Estimation Strategies for Efficient Exploration of Phenotype Microarray Kinetics

The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed '-omics' techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves.The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats.We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data

MicroRNAs in the host response to viral infections of veterinary importance

The discovery of small regulatory non-coding RNAs has been an exciting advance in the field of genomics. MicroRNAs (miRNAs) are endogenous RNA molecules, approximately 22 nucleotides in length that regulate gene expression, mostly at the post-transcriptional level. MiRNA profiling technologies have made it possible to identify and quantify novel miRNAs and to study their regulation and potential roles in disease pathogenesis. Although miRNAs have been extensively investigated in viral infections of humans, their implications in viral diseases affecting animals of veterinary importance are much less understood. The number of annotated miRNAs in different animal species is growing continuously, and novel roles in regulating host-pathogen interactions are being discovered, for instance miRNA-mediated augmentation of viral transcription and replication. In this review, we present an overview of synthesis and function of miRNAs and an update on the current state of research on host-encoded miRNAs in the genesis of viral infectious diseases in their natural animal host as well as in selected in vivo and in vitro laboratory models

Dining in Blue Light Impairs the Appetite of Some Leaf Epiphytes

Background: The phyllosphere is subjected to fluctuating abiotic conditions. This study examined the phenotypic plasticity (PP) of four selected non-phototrophic phyllosphere bacteria [control strain: Pseudomonas sp. DR 5-09; Pseudomonas agarici, Bacillus thuringiensis serovar israeliensis (Bti), and Streptomyces griseoviridis (SG)] regarding their respiration patterns and surfactant activity as affected by light spectrum and nutrient supply. Methods: The PP of the strains was examined under four light regimes [darkness (control); monochromatic light-emitting diodes (LED) at 460 nm (blue) and 660 nm (red); continuously polychromatic white LEDs], in the presence of 379 substrates and conditions. Results: Light treatment affected the studied bacterial strains regarding substrate utilization (Pseudomonas strains > SG > Bti). Blue LEDs provoked the most pronounced impact on the phenotypic reaction norms of the Pseudomonas strains and Bti. The two Gram-positive strains Bti and SG, respectively, revealed inconsistent biosurfactant formation in all cases. Biosurfactant formation by both Pseudomonas strains was supported by most substrates incubated in darkness, and blue LED exposure altered the surface activity profoundly. Blue and white LEDs enhanced biofilm formation in PA in highly utilized C-sources. Putative blue light receptor proteins were found in both Pseudomonas strains, showing 91% similarity with the sequence from NCBI accession number WP_064119393. Conclusion: Light quality–nutrient interactions affect biosurfactant activity and biofilm formation of some non-phototrophic phyllosphere bacteria and are, thus, crucial for dynamics of the phyllosphere microbiome

Impacts of pr-10a Overexpression at the Molecular and the Phenotypic Level

Biotechnological approaches using genetic modifications such as homologous gene overexpression can be used to decode gene functions under well-defined circumstances. However, only the recording of the resulting phenotypes allows inferences about the impact of the modification on the organisms’ evolutionary, ecological or economic performance. We here compare a potato wild-type cell line with two genetically engineered cell cultures homologously overexpressing Pathogenesis Related Protein 10a (pr-10a). A detailed analysis of the relative gene-expression patterns of pr-10a and its regulators sebf and pti4 over time provides insights into the molecular response of heterotrophic cells to distinct osmotic and salt-stress conditions. Furthermore, this system serves as an exemplar for the tracing of respiration kinetics as a faster and more sensitive alternative to the laborious and time-consuming recording of growth curves. The utility and characteristics of the resulting data type and the requirements for its appropriate analysis are figured out. It is demonstrated how this novel type of phenotypic information together with the gene-expression-data provides valuable insights into the effect of genetic modifications on the behaviour of cells on both the molecular and the macroscopic level

Biologists meet statisticians: A workshop for young scientists to foster interdisciplinary team work

Abstract Life science and statistics have necessarily become essential partners. The need to plan complex, structured experiments, involving elaborated designs, and the need to analyse datasets in the era of systems biology and high throughput technologies has to build upon professional statistical expertise. On the other hand, conducting such analyses and also developing improved or new methods, also for novel kinds of data, has to build upon solid biological understanding and practise. However, the meeting of scientists of both fields is often hampered by a variety of communicative hurdles -which are based on field-specific working languages and cultural differences. As a step towards a better mutual understanding, we developed a workshop concept bringing together young experimental biologists and statisticians, to work as pairs and learn to value each others competences and practise interdisciplinary communication in a casual atmosphere. The first implementation of our concept was a cooperation of the German Region of the International Biometrical Society and the Leibnitz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (short: DSMZ), Braunschweig, Germany. We collected feedback in form of three questionnaires, oral comments, and gathered experiences for the improvement of this concept. The long-term challenge for both disciplines is the establishment of systematic schedules and strategic partnerships which use the proposed workshop concept to foster mutual understanding, to seed the necessary interdisciplinary cooperation network, and to start training the indispensable communication skills at the earliest possible phase of education