The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays

<p>Abstract</p> <p>Background</p> <p>The MAQC project demonstrated that microarrays with comparable content show inter- and intra-platform reproducibility. However, since the content of gene databases still increases, the development of new generations of microarrays covering new content is mandatory. To better understand the potential challenges updated microarray content might pose on clinical and biological projects we developed a methodology consisting of <it>in silico </it>analyses combined with performance analysis using real biological samples.</p> <p>Results</p> <p>Here we clearly demonstrate that not only oligonucleotide design but also database content and annotation strongly influence comparability and performance of subsequent generations of microarrays. Additionally, using human blood samples and purified T lymphocyte subsets as two independent examples, we show that a performance analysis using biological samples is crucial for the assessment of consistency and differences.</p> <p>Conclusion</p> <p>This study provides an important resource assisting investigators in comparing microarrays of updated content especially when working in a clinical or regulatory setting.</p

Punctuated Equilibrium and the Comparative Study of Policy Agendas

Agenda-setting theory has a long tradition within policy studies but took a major leap forward with the work of Baumgartner and Jones and their formulation of punctuated equilibrium theory (PET). Since then, an extensive literature has developed, both evaluating the notion of punctuated equilibria from a comparative perspective and providing ideas for a broader theoretical development on political processes. The original formulation of the theory was based on the US political system, whose institutional elements make it a likely case to observe the type of political processes that PET highlights. Subsequent comparative studies have demonstrated that the theory’s idea is of general relevance in two regards. First, factors, such as issue characteristics, operate similarly across political systems. Second, political institutions shape agenda-setting processes. This paper expands on the political institutional features that are particularly important when applying PET to a West European context. We illustrate the interplay of these institutional characteristics with the political process regarding the German debate on digitalization

Complex basal conditions influence flow at the onset of the Northeast Greenland Ice Stream

The onset and high upstream ice surface velocities of the North East Greenland Ice Stream (NEGIS) are not yet well reproducible in ice sheet models. A major uncertainty remains the understanding of basal sliding and a parameterization of basal conditions. In this study, we assess the slow-flowing part of the NEGIS in a systematic analysis of the basal conditions and investigate the increased ice flow. We analyze the spectral basal roughness in correlation with basal return power from an airborne radar survey with AWIs ultra-wideband radar system in 2018 and compare our results with current ice flow geometry and ice surface flow. We observe a roughness anisotropy where the ice stream widens, indicating a change from a smooth and soft bed to a harder bedrock as well as the evolution of elongated subglacial landforms. In addition, at the upstream part of the NEGIS we find a clear zoning of the bedrock return power, indicating an increased water content at the base of the ice stream. At the downstream part, we observe an increased bedrock return power throughout the entire width of the ice stream and outside its margins, indicating enhanced melting and the distribution of basal water beyond the shear zones

Ice flow and the conditions of the ice-bed interface at the onset of the Northeast Greenland Ice Stream

The Northeast Greenland Ice Stream (NEGIS) is an important dynamic component contributing to the total mass balance of the Greenland ice sheet, as it reaches up to the central divide and drains 12% of the ice sheet. The ice stream geometry and surface velocities in the onset region of the NEGIS are not yet sufficiently well reproduced by ice sheet models. We present an assessment of the basal conditions of the onset region in a systematic analysis of airborne ultra-wideband radar data. Our data yield a new detailed model of ice-thickness distribution and basal topography in the upstream part of the ice stream. We observe a change from a smooth to a rougher bed where the ice stream widens from 10 to 60 km, and a distinct roughness anisotropy, indicating a preferred orientation of subglacial structures. The observation of off-nadir reflections that are symmetrical to the bed reflection in the radargrams suggests that these structures are elongated subglacial landforms, which in turn indicate potential streamlining of the bed. Together with basal water routing pathways, our observations hint to two different zones in this part of the NEGIS: an accelerating and smooth upstream region, which is collecting water, with reduced basal traction, and in the further downstream part, where the ice stream is slowing down and is widening, with a distribution of basal water towards the shear margins. Our findings support the hypothesis that the NEGIS is strongly interconnected to the subglacial water system in its onset region, but also to the subglacial substrate and morphology

Microbial ecosystem assessment and hydrogen oxidation potential of newly discovered vent systems from the Central and South-East Indian Ridge

In order to expand the knowledge of microbial ecosystems from deep-sea hydrothermal vent systems located on the Central and South-East Indian Ridge, we sampled hydrothermal fluids, massive sulfides, ambient water and sediments of six distinct vent fields. Most of these vent sites were only recently discovered in the course of the German exploration program for massive sulfide deposits and no previous studies of the respective microbial communities exist. Apart from typically vent-associated chemosynthetic members of the orders Campylobacterales, Mariprofundales, and Thiomicrospirales, high numbers of uncultured and unspecified Bacteria were identified via 16S rRNA gene analyses in hydrothermal fluid and massive sulfide samples. The sampled sediments however, were characterized by an overall lack of chemosynthetic Bacteria and the presence of high proportions of low abundant bacterial groups. The archaeal communities were generally less diverse and mostly dominated by members of Nitrosopumilales and Woesearchaeales, partly exhibiting high proportions of unassigned Archaea. Correlations with environmental parameters were primarily observed for sediment communities and for microbial species (associated with the nitrogen cycle) in samples from a recently identified vent field, which was geochemically distinct from all other sampled sites. Enrichment cultures of diffuse fluids demonstrated a great potential for hydrogen oxidation coupled to the reduction of various electron-acceptors with high abundances of Hydrogenovibrio and Sulfurimonas species. Overall, given the large number of currently uncultured and unspecified microorganisms identified in the vent communities, their respective metabolic traits, ecosystem functions and mediated biogeochemical processes have still to be resolved for estimating consequences of potential environmental disturbances by future mining activities

Was eine Data Governance für das Forschungsdatenmanagement leisten kann

In dem Fraunhofer-internen Projekt „Krisenmanagement und Resilienz – Corona“ (KResCo) wurden Maßnahmen gegen die Covid-19-Pandemie in verschiedenen Ländern sowie deren Wirksamkeit untersucht. Hierbei wurden viele Daten erzeugt und nachgenutzt, deren Management in einem eigenen Arbeitspaket gesteuert wurde. Hierzu wurde ein Data-Governance-Ansatz angewendet, im Rahmen dessen verschiedene strategische, rechtliche und operative Bausteine entwickelt und während des Projektverlaufs erprobt wurden. Der Artikel beschreibt diese Bausteine und und beurteilt deren Umsetzungsgad im Projekt anhand eines Reifegrad-Modells. Im Ergebnis zeigte sich, dass nicht alle Ziele der Data Governance im Projekt erreicht werden konnten, da keine ausreichende Akzeptanz bei den Forschenden aufgebaut werden konnte, so dass diese die Bausteine nicht im erforderlichen Umfang nutzten

Non-invasive monitoring of Streptococcus pyogenes vaccine efficacy using biophotonic imaging.

Streptococcus pyogenes infection of the nasopharynx represents a key step in the pathogenic cycle of this organism and a major focus for vaccine development, requiring robust models to facilitate the screening of potentially protective antigens. One antigen that may be an important target for vaccination is the chemokine protease, SpyCEP, which is cell surface-associated and plays a role in pathogenesis. Biophotonic imaging (BPI) can non-invasively characterize the spatial location and abundance of bioluminescent bacteria in vivo. We have developed a bioluminescent derivative of a pharyngeal S. pyogenes strain by transformation of an emm75 clinical isolate with the luxABCDE operon. Evaluation of isogenic recombinant strains in vitro and in vivo confirmed that bioluminescence conferred a growth deficit that manifests as a fitness cost during infection. Notwithstanding this, bioluminescence expression permitted non-invasive longitudinal quantitation of S. pyogenes within the murine nasopharynx albeit with a detection limit corresponding to approximately 10(5) bacterial colony forming units (CFU) in this region. Vaccination of mice with heat killed streptococci, or with SpyCEP led to a specific IgG response in the serum. BPI demonstrated that both vaccine candidates reduced S. pyogenes bioluminescence emission over the course of nasopharyngeal infection. The work suggests the potential for BPI to be used in the non-invasive longitudinal evaluation of potential S. pyogenes vaccines