Quantitative characterization of translational riboregulators using an in vitro transcription–translation system

Riboregulators are short RNA sequences that, upon binding to a ligand, change their secondary structure and influence the expression rate of a downstream gene. They constitute an attractive alternative to transcription factors for building synthetic gene regulatory networks because they can be engineered de novo. However, riboregulators are generally designed in silico and tested in vivo, which provides little quantitative information about their performances, thus hindering the improvement of design algorithms. Here we show that a cell-free transcription-translation (TX–TL) system provides valuable information about the performances of in silico designed riboregulators. We first propose a simple model that provides a quantitative definition of the dynamic range of a riboregulator. We further characterize two types of translational riboregulators composed of a cis-repressed (cr) and a trans-activating (ta) strand. At the DNA level we demonstrate that high concentrations of taDNA poisoned the activator until total shut off, in agreement with our model, and that relative dynamic ranges of riboregulators determined in vitro are in agreement with published in vivo data. At the RNA level, we show that this approach provides a fast and simple way to measure dissociation constants of functional riboregulators, in contrast to standard mobility-shift assays. Our method opens the route for using cell-free TX–TL systems for the quantitative characterization of functional riboregulators in order to improve their design in silico

An African Ancestry-Specific Allele of CTLA4 Confers Protection against Rheumatoid Arthritis in African Americans

Cytotoxic T-lymphocyte associated protein 4 (CTLA4) is a negative regulator of T-cell proliferation. Polymorphisms in CTLA4 have been inconsistently associated with susceptibility to rheumatoid arthritis (RA) in populations of European ancestry but have not been examined in African Americans. The prevalence of RA in most populations of European and Asian ancestry is ∼1.0%; RA is purportedly less common in black Africans, with little known about its prevalence in African Americans. We sought to determine if CTLA4 polymorphisms are associated with RA in African Americans. We performed a 2-stage analysis of 12 haplotype tagging single nucleotide polymorphisms (SNPs) across CTLA4 in a total of 505 African American RA patients and 712 African American controls using Illumina and TaqMan platforms. The minor allele (G) of the rs231778 SNP was 0.054 in RA patients, compared to 0.209 in controls (4.462×10−26, Fisher's exact). The presence of the G allele was associated with a substantially reduced odds ratio (OR) of having RA (AG+GG genotypes vs. AA genotype, OR 0.19, 95% CI: 0.13–0.26, p = 2.4×10−28, Fisher's exact), suggesting a protective effect. This SNP is polymorphic in the African population (minor allele frequency [MAF] 0.09 in the Yoruba population), but is very rare in other groups (MAF = 0.002 in 530 Caucasians genotyped for this study). Markers associated with RA in populations of European ancestry (rs3087243 [+60C/T] and rs231775 [+49A/G]) were not replicated in African Americans. We found no confounding of association for rs231778 after stratifying for the HLA-DRB1 shared epitope, presence of anti-cyclic citrullinated peptide antibody, or degree of admixture from the European population. An African ancestry-specific genetic variant of CTLA4 appears to be associated with protection from RA in African Americans. This finding may explain, in part, the relatively low prevalence of RA in black African populations

TET-1 SATELLITE OPERATIONS LESSONS LEARNED: PREPARATION OF MISSION, LEOP AND ROUTINE OPERATIONS OF 11 DIFFERENT EXPERIMENTS

TET-1 is a small experimental satellite with 11 different space experiments on-board. Built by German space industry it’s a satellite dedicated to verification of newly developed space hardware and software. The German Space Operations Center (GSOC) as part of the German Aerospace Center (DLR) is responsible for satellite operations. Development of space and ground segment started back in 2006, with a scheduled launch in the second half of 2011, expected in December. Keeping this in mind we perform a survey of mission preparation activities focusing on first the reuse of existing GSOC mission infrastructure and second the specific adaption’s necessary for TET-1. Lessons learned are compiled with respect to applicability for other missions, especially with respect to flight procedure development and satellite commanding. Operations team training started in 2010 with different training and simulation sessions. Engineering models and the flight model itself have been used; no dedicated software simulator has been available. Advantages and disadvantages of this approach are discussed. After a concise conclusion of preparation of LEOP and commissioning sequences that are commanded from ground control center a short introduction to the activation sequence of the satellite is given. This sequence is a set of predefined commands executed after spacecraft activation at separation. Discussion is extended to our planned routine operations concept for 11 different payloads. We conclude with a collection of space segment design decisions with the biggest (positive as well as negative) impact on ground segment design and subsequent operations

Mission Planning and Operational Constraints and Their Resolution for EO Missions Like EnMAP

Earth observation missions are generally operated by execution of predefined time-tagged commands. However, depending on the type of mission, issues relevant to different types of mission may occur. These issues are drivers for the design of the operations system of EnMAP (Environmental Mapping and Analysis Program). The main challenges are limited transfer of telecommands and limited downlink capabilities; also the cloud coverage in the target area - for optical sensors - plays a huge role. There are certain constraints, concerning this satellite bus in particular. For example a limited time tagged list which allows no more than 120 time tagged commands on board. Further the fact that every dumped house keeping packet has to be requested from the space craft which leads to a delay in the reception of telemetry can be a bottle neck. In addition to these S-band related issues it is a real challenge to coordinate the amount of payload data which will be down-linked via X-band. In this paper the strategy of managing all these difficulties and optimally operating the satellite under these conditions, will be described. For handling of cloud coverage a database with weather statistics will be implemented. These statistics are compared with global forecast models as provided by e.g. the German weather service (DWD). With the calculated forecast values, planning priority of datatakes is increased or decreased

Datenmanagement für Intelligente Verkehrssysteme und Erdbeobachtung: Unterschiedliche Anwendungsbereiche mit gleichen Big Data Herausforderungen?

Die stetige Zunahme von Güter- und Personenverkehr und wachsende Mobilitätsanforderungen im Alltag sind die Haupttreiber für die Entwicklung von Intelligenten Verkehrssystemen (IVS). Ein IVS trägt wesentlich dazu bei, die Vernetzung und Kooperation zwischen Fahrzeug- und Straßensystemen zu verbessern und damit den Straßenverkehr sicherer, effizienter und umweltfreundlicher zu machen. Konkrete Anwendungsgebiete sind unter anderem das hochautomatisierte Fahren, der Datenaustausch zwischen Fahrzeugen und ihrer Umwelt (Verkehrsinfrastruktur und andere Fahrzeuge), intelligente Logistik oder das Parkraumanagement in Ballungsräumen. Um diese vielfältigen Aufgaben bewältigen zu können sind IVS auf große, heterogene Datenmengen aus unterschiedlichsten Quellen angewiesen. Neben Sensoren in Fahrzeugen und der Verkehrsinfrastruktur, kommen hier auch weitere Informationsquellen wie soziale Medien, Daten von Behörden und Ämtern sowie andere Datenquellen zum Tragen. Aufgabe eines IVS ist es nun u.a. auch diese heterogenen Datenquellen zu einem konsistenten Bild der Gesamtlage zusammenzusetzen, um daraus Schlüsse auf die aktuelle Situation zu ziehen, entsprechende Entscheidung zu treffen oder adäquate Entscheidungshilfen anzubieten. Die Anforderungen im Datenmanagement eines IVS gehen allerdings über die reine Datenintegration hinaus. Weiterhin müssen Informationen in nahezu Echtzeit bei den einzelnen Teilnehmern des Systems verfügbar sein. Den meisten Teilnehmern ist es allerdings nicht möglich ein vollständiges Abbild des Gesamtsystems vorzuhalten. Infolgedessen beschränken sich auf die für sie relevanten Daten, die sich meist auf einen bestimmten temporalen bzw. räumlichen Bereich und ggf. einen bestimmten Ausschnitt der Informationen beziehen. Das IVS muss hier also fähig sein jeden Teilnehmer mit dem jeweils benötigten Ausschnitt des gesamten Datenbestands zu versorgen und diesen auch aktuell zu halten. In einem unterliegenden Datenmanagementsystem führt dies zu einer großen Anzahl an heterogenen Anfragen, die nahezu in Echtzeit zu beantworten sind. Weiterhin sind auch Caching Strategien ein adäquates Mittel, um den erforderlichen Datenverkehr zu begrenzen. In dieser Präsentation stellen wir eine Auswahl konkreter Herausforderungen an die Datenverwaltung eines IVS vor und diskutieren inwieweit sich bereits existierende Methoden und Lösungen aus anderen Anwendungsgebieten nutzen bzw. anpassen lassen. Als exemplarisches Anwendungsgebiet ziehen wir hier den Vergleich zur Erdbeobachtung. Wir beleuchten sowohl Gemeinsamkeiten als auch Unterschiede, um so einen gegenseitigen Transfer von Ideen und Lösungen zu fördern