L7Ae- and LSm-RNA interactomes of Sulfolobus acidocaldarius

The archaeal L7Ae and Sm-like proteins (LSm) are universal RNA-binding proteins. L7Ae stabilizes non-coding RNA species, including ribosomal RNA, by recognizing a structural RNA motif, termed kink-turn (k-turn). Sm family proteins, like bacterial Hfq and eukaryotic Sm/LSm, are involved in multiple RNA-related processes including small RNA (sRNA)-based translational regulation, mRNA decay or splicing. However, the function of the archaeal members is elusive. Using RNA-immunoprecipitation sequencing (RIP-Seq) methodology, this thesis aimed to identify the global RNA interaction partners (RNA interactome) of L7Ae and the three LSm proteins of the thermoacidophilic archaeon Sulfolobus acidocaldarius. Besides many known non-coding RNAs, the SRP RNA was identified as a novel binding partner of the L7Ae protein. Mobility shift assays demonstrated L7Ae binding to a k-turn motif that was found to be conserved among archaeal SRP RNAs. Interestingly, mRNAs, including the l7ae transcript, were enriched in the RIP-Seq analysis and found to comprise putative k-turns that facilitate L7Ae binding. In vivo studies showed that L7Ae autoregulates the translation of its mRNA by binding to a k-turn motif in the 5' untranslated region. A GFP reporter system was established in Escherichia coli that verified the conservation of L7Ae-mediated feedback regulation in archaea and provides a new tool for the modulation of synthetic gene circuits in bacteria. Mobility shift assays confirmed binding of L7Ae to a k-turn in the transcript of nop5-fibrillarin, suggesting that the synthesis of all C/D box sRNP core proteins (L7Ae, Nop5 and fibrillarin) is regulated by L7Ae. These studies revealed the regulation of mRNA translation as a novel function of the archaeal L7Ae protein. The LSm RIP-Seq study found mRNAs and sRNAs as LSm1 and LSm2 interactors, including a recently reported sRNA that regulates biofilm formation in S. acidocaldarius. No RNA-binding capacity was observed for LSm3. A computational analysis of the interaction partners identified the U-rich 3' termination signal of RNAs and a motif composed of UAG triplets as potential LSm binding sites, which was verified by mobility shift assays. Knock-out studies revealed that only the lsm3 gene is dispensable, whereas the genes for lsm1 and lsm2 seem to be essential. Mutant strains producing tagged versions of LSm1 and LSm2 displayed a pleiotropic phenotype. In resemblance to the roles of bacterial Hfq and eukaryotic LSm proteins, this study provides hints that archaeal LSm proteins may be involved in mRNA degradation, C/D box sRNA biogenesis and sRNA-regulated processes, like tRNA maturation and translational regulation of mRNAs

Ägyptische, afghanische und serbische Diasporagemeinden in Deutschland und ihre Beiträge zur Entwicklung ihrer Herkunftsländer

n neueren wissenschaftlichen und politischen Diskussionen ist der Beitrag so genannter Diasporagemeinden zur Entwicklung ihrer Herkunftsländer registriert worden. Es besteht jedoch ein erheblicher Wissensbedarf bezüglich (1.) der Typen und Muster ökonomischer, sozialer und kultureller Transferleistungen zwischen Diaspora und Herkunftsländern, (2.) der sozialen, ökonomischen und politischen Bedingungen für das Zustandekommen oder die Blockierung solcher Leistungen sowie (3.) die Anforderungen an eine Politik, die versucht, solche Leistungen in konstruktiver Weise zu unterstützen und für entwicklungspolitische Zielsetzungen zu nutzen. Vor diesem Hintergrund ist es das Ziel der hier vorgestellten Pilotstudie, am Beispiel der Diasporagemeinden der Ägypter, Afghanen und Serben in Deutschland explorativ einen Forschungsansatz zu entwickeln und zu erproben, der die relevanten Dimensionen bei der Untersuchung des Beitrags von Migration zur Entwicklung erfassen soll. --

Predicting the impact of scientific concepts using full‐text features

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134425/1/asi23612.pd

A horizon scan of emerging technologies for alien species citizen science

Citizen Science (CS) significantly contributes to the study and management of biological invasions. Technological developments such as social media, internet scraping, eDNA, apps, sensors, search engines and predictive analytics can foster projects and increase the reach of CS. The list of tech is long and their potential for alien species CS is unclear. To help research funders and project initiators we performed a horizon scan on the value of emerging technologies for alien species CS. A network of 44 experts from the COST Action Alien-CSI identified and assessed 39 technologies. Assessors rated their usefulness on a 5-point Likert scale with respect to their potential to attract new audiences, improve inclusivity, applicability in daily life, ability to increase engagement, provide feedback, improve data quality and gather new data. The results of the scoring were discussed at a consensus workshop. Consistency among ratings was explored using inter-rater reliability metrics and ordination techniques. Experts were asked to explain and discuss the reasons for inconsistent rating across technologies or criteria, focusing on the evidence used or differences in interpretation of criteria. After this, one new round of individual re-evaluation of technologies followed. The discussions resulted in increased consensus on the potential of the different technologies. Mobile-based data collection platforms and social media (both their use to interact with CS participants as well as their potential for scraping new occurrence records) were the top-ranking technologies for IAS CS, followed by machine learning techniques, the application of AI and collective intelligence. Technologies differed considerably in their potential when different criteria were individually considered. For instance, DNA-based technologies ranked high on acquiring new data, open data technologies scored high on their potential to improve the quality of collected data. Virtual reality and gamification scored high on their potential to increase engagement in IAS CS

Sample preparation for scanning Kelvin probe microscopy studies on cross sections of organic solar cells

We prepared cross sections of P3HT:PCBM bulk heterojunction (BHJ) organic solar cells (OSCs) for the characterization of their potential distribution with scanning Kelvin probe microscopy. We compared results of samples obtained by microtome cutting of OSCs on plastic substrates, cleaving of OSCs on glass substrates, and milling with a focused ion beam. Their potential distributions were in good agreement with each other. Under short circuit conditions, potential gradients were detected in vicinity of the electrode/organics interfaces, with negligible electric fields within the bulk. We contacted the OSCs in a defined manner and studied their potential distribution under operating conditions

DNA Binding Properties of the Small Cascade Subunit Csa5

<div><p>CRISPR-Cas systems provide immunity against viral attacks in archaeal and bacterial cells. Type I systems employ a Cas protein complex termed Cascade, which utilizes small CRISPR RNAs to detect and degrade the exogenic DNA. A small sequence motif, the PAM, marks the foreign substrates. Previously, a recombinant type I-A Cascade complex from the archaeon <i>Thermoproteus tenax</i> was shown to target and degrade DNA <i>in vitro,</i> dependent on a native PAM sequence. Here, we present the biochemical analysis of the small subunit, Csa5, of this Cascade complex. <i>T. tenax</i> Csa5 preferentially bound ssDNA and mutants that showed decreased ssDNA-binding and reduced Cascade-mediated DNA cleavage were identified. Csa5 oligomerization prevented DNA binding. Specific recognition of the PAM sequence was not observed. Phylogenetic analyses identified Csa5 as a universal member of type I-A systems and revealed three distinct groups. A potential role of Csa5 in R-loop stabilization is discussed.</p></div

Numerical Investigation of Chatter Suppression via Parametric Anti-Resonance in a Motorized Spindle unit During Milling

A new concept for increasing process stability during milling processes is presented utilizing a parametric anti-resonance. The beneficial effect is examined by numerical calculations in the time domain for an example spindle which is supported conventionally by ball bearings and is equipped with an additional active magnetic bearing that enables the realization of a deliberate parametric excitation. In the present study the stiffness of this active support bearing is changed periodically with time. The parametric excitation is tuned to a parametric anti-resonance which triggers the transfer of vibration energy between the vibration modes of the underlying system without this additional time-periodicity. It is highlighted how vibration energy is transferred from the first bending mode of the rotor, which is the most critical one by means of regenerative chatter, to a mode with higher damping in order to increase the effective damping of the entire spindle drive unit

Interference assay with reconstituted Cascade complexes.

<p>The Csa5 constructed mutants (Y29A, D33A and D30A/D33A) were assembled into Cascade and tested for dsDNA cleavage. The assembled Cascade complex was loaded with complementary (C) crRNA 5.2 for 20 min at 80°C and the interference reaction was started by the addition of ATP, Mg²⁺, Mn²⁺ and the dsDNA substrate (int_5.2 CCT), which was either labeled on the non-target (forward) or the target strand (reverse) for 10 min at 70°C. The reaction products were separated on 20% denaturing gels. The non-complementary (NC) crRNA 5.13 was used as a control. Cleavage products for both strands are visible for Cascade containing Csa5 WT as reported previously <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105716#pone.0105716-Plagens2" target="_blank">[25]</a>. A decreased cleavage activity can be observed for the Cascade complexes containing the Csa5 mutants. Asterisks indicate the labeled strand.</p