The mechanism of pRNA-mediated release of RNA polymerase from Bacillus subtilis 6S-1 RNA

Adaptation of the transcriptome to nutrient limitation and resupply is a fundamental process in bacteria, particularly in natural habitats. Bacterial 6S RNA, an ubiquitous and growth phasedependent regulator of transcription, binds to RNA polymerase (RNAP) and inhibits transcription during stationary growth. Upon nutrient resupply, RNAP acts as an RNA-dependent RNA polymerase by transcribing large amounts of short RNAs (pRNAs) from 6S RNA as template, leading to dissociation of 6S RNARNAP complexes. Whereas the majority of bacteria express a single 6S RNA species, Bacillus subtilis encodes two 6S RNAs (6S-1 and 6S-2) of similar secondary structure, but with different expression profiles. In this work, we investigated the two 6S RNAs of B. subtilis, focusing on pRNA synthesis and its role for the function of 6S RNA. Concurrently, we identified pRNA transcription from 6S-1 RNA in vivo using high-troughput sequencing techniques and we developed a novel Northern hybridization protocol for detection of pRNAs in bacterial total cellular extracts. Our results show that the release of RNAP from 6S-1 RNA, the functional homolog of the well investigated E. coli 6S RNA, is regulated by stable pRNA binding. Additionally, we found structural changes of 6S-1 RNA, induced by differences in pRNA length in different growth phases. This specific structural change of 6S RNA seems to be conserved among bacteria. Furthermore, we are able to show that the two processes of RNAP release and 6S-1 RNA degradation are coupled in vivo. Taken together, our results expand the current understanding of 6S RNA function and provide insight into the mechanism of RNAP release from 6S RNA in bacteria. ii

Spin Transport and Polarimetry in the Beam Delivery System of the International Linear Collider

Polarised electron and positron beams are key ingredients to the physics programme of future linear colliders. Due to the chiral nature of weak interactions in the Standard Model - and possibly beyond - the knowledge of the luminosity-weighted average beam polarisation at the $e^+e^-$ interaction point is of similar importance as the knowledge of the luminosity and has to be controlled to permille-level precision in order to fully exploit the physics potential. The current concept to reach this challenging goal combines measurements from Laser-Compton polarimeters before and after the interaction point with measurements at the interaction point. A key element for this enterprise is the understanding of spin-transport effects between the polarimeters and the interaction point as well as collision effects. We show that without collisions, the polarimeters can be cross-calibrated to 0.1 %, and we discuss in detail the impact of collision effects and beam parameters on the polarisation value relevant for the interpretation of the $e^+e^-$ collision data.Comment: 34 pages, 11 figure

Genomewide comparison and novel ncRNAs of Aquificales

Background  The Aquificales are a diverse group of thermophilic bacteria that thrive in terrestrial and marine hydrothermal environments. They can be divided into the families Aquificaceae, Desulfurobacteriaceae and Hydrogenothermaceae. Although eleven fully sequenced and assembled genomes are available, only little is known about this taxonomic order in terms of RNA metabolism.  Results  In this work, we compare the available genomes, extend their protein annotation, identify regulatory sequences, annotate non-coding RNAs (ncRNAs) of known function, predict novel ncRNA candidates, show idiosyncrasies of the genetic decoding machinery, present two different types of transfer-messenger RNAs and variations of the CRISPR systems. Furthermore, we performed a phylogenetic analysis of the Aquificales based on entire genome sequences, and extended this by a classification among all bacteria using 16S rRNA sequences and a set of orthologous proteins.  Combining severalin silicofeatures (e.g. conserved and stable secondary structures, GC-content, comparison based on multiple genome alignments) with an in vivo dRNA-seq transcriptome analysis of Aquifex aeolicus, we predict roughly 100 novel ncRNA candidates in this bacterium.  Conclusions  We have here re-analyzed the Aquificales, a group of bacteria thriving in extreme environments, sharing the feature of a small, compact genome with a reduced number of protein and ncRNA genes. We present several classical ncRNAs and riboswitch candidates. By combining in silico analysis with dRNA-seq data of A. aeolicus we predict nearly 100 novel ncRNA candidates

Tailoring magnetocaloric effect in all-d-metal Ni-Co-Mn-Ti Heusler alloys: a combined experimental and theoretical study

Novel Ni-Co-Mn-Ti all-d-metal Heusler alloys are exciting due to large multicaloric effects combined with enhanced mechanical properties. An optimized heat treatment for a series of these compounds leads to very sharp phase transitions in bulk alloys with isothermal entropy changes of up to 38 J kg$^{-1}$ K$^{-1}$ for a magnetic field change of 2 T. The differences of as-cast and annealed samples are analyzed by investigating microstructure and phase transitions in detail by optical microscopy. We identify different grain structures as well as stoichiometric (in)homogenieties as reasons for differently sharp martensitic transitions after ideal and non-ideal annealing. We develop alloy design rules for tuning the magnetostructural phase transition and evaluate specifically the sensitivity of the transition temperature towards the externally applied magnetic fields ($\frac{dT_t}{\mu_0dH}$) by analyzing the different stoichiometries. We then set up a phase diagram including martensitic transition temperatures and austenite Curie temperatures depending on the e/a ratio for varying Co and Ti content. The evolution of the Curie temperature with changing stoichiometry is compared to other Heusler systems. Density Functional Theory calculations reveal a correlation of T$_C$ with the stoichiometry as well as with the order state of the austenite. This combined approach of experiment and theory allows for an efficient development of new systems towards promising magnetocaloric properties. Direct adiabatic temperature change measurements show here the largest change of -4 K in a magnetic field change of 1.93 T for Ni$_{35}$Co$_{15}$Mn$_{37}$Ti$_{13}$

Organic phase separation opens up new opportunities to interrogate the RNA-binding proteome.

Protein-RNA interactions regulate all aspects of RNA metabolism and are crucial to the function of catalytic ribonucleoproteins. Until recently, the available technologies to capture RNA-bound proteins have been biased toward poly(A) RNA-binding proteins (RBPs) or involve molecular labeling, limiting their application. With the advent of organic-aqueous phase separation-based methods, we now have technologies that efficiently enrich the complete suite of RBPs and enable quantification of RBP dynamics. These flexible approaches to study RBPs and their bound RNA open up new research avenues for systems-level interrogation of protein-RNA interactions

Structural dynamics of first-order phase transition in giant magnetocaloric La(Fe,Si)13: The free energy landscape

Maximizing the performance of magnetic refrigerators and thermomagnetic energy harvesters is imperative for their successful implementation and can be done by maximizing their operation frequency. One of the features delimiting the frequency and efficiency of such devices is the phase transition kinetics of their magnetocaloric/thermomagnetic active material. While previous studies have described the magnetic component governing the kinetics of the magnetovolume phase transition in La(Fe,Si)13 giant magnetocaloric materials, a comprehensive description of its structural component has yet to be explored. In this study, in situ synchrotron X-ray diffraction is employed to describe the structural changes upon magnetic field application/removal. Long magnetic field dependent relaxation times up to a few hundred seconds are observed after the driving field is paused. The phase transition is found to be highly asymmetric upon magnetic field cycling due to the different Gibbs energy landscapes and the absence of an energy barrier upon field removal. An exponential relationship is found between the energy barriers and the relaxation times, suggesting the process is governed by a non-thermal activation over an energy barrier process. Such fundamental knowledge on first-order phase transition kinetics suggests pathways for materials optimization and smarter design of magnetic field cycling in real-life devices

Tailoring Negative Thermal Expansion via Tunable Induced Strain in La–Fe–Si-Based Multifunctional Material

Zero thermal expansion (ZTE) composites are typically designed by combining positive thermal expansion (PTE) with negative thermal expansion (NTE) materials acting as compensators and have many diverse applications, including in high-precision instrumentation and biomedical devices. La(Fe1–x,Six)13-based compounds display several remarkable properties, such as giant magnetocaloric effect and very large NTE at room temperature. Both are linked via strong magnetovolume coupling, which leads to sharp magnetic and volume changes occurring simultaneously across first-order phase transitions; the abrupt nature of these changes makes them unsuitable as thermal expansion compensators. To make these materials more useful practically, the mechanisms controlling the temperature over which this transition occurs and the magnitude of contraction need to be controlled. In this work, ball-milling was used to decrease particles and crystallite sizes and increase the strain in LaFe11.9Mn0.27Si1.29Hx alloys. Such size and strain tuning effectively broadened the temperature over which this transition occurs. The material’s NTE operational temperature window was expanded, and its peak was suppressed by up to 85%. This work demonstrates that induced strain is the key mechanism controlling these materials’ phase transitions. This allows the optimization of their thermal expansion toward room-temperature ZTE applications

Alien pathogens on the horizon: opportunities for predicting their threat to wildlife

According to the Convention on Biological Diversity, by 2020 invasive alien species (IAS) should be identified and their impacts assessed, so that species can be prioritized for implementation of appropriate control strategies and measures put in place to manage invasion pathways. For one quarter of the IAS listed as the “100 of the world's worst” environmental impacts are linked to diseases of wildlife (undomesticated plants and animals). Moreover, IAS are a significant source of “pathogen pollution” defined as the human-mediated introduction of a pathogen to a new host or region. Despite this, little is known about the biology of alien pathogens and their biodiversity impacts after introduction into new regions. We argue that the threats posed by alien pathogens to endangered species, ecosystems, and ecosystem services should receive greater attention through legislation, policy, and management. We identify 10 key areas for research and action, including those relevant to the processes of introduction and establishment of an alien pathogen and to prediction of the spread and associated impact of an alien pathogen on native biota and ecosystems. The development of interdisciplinary capacity, expertise, and coordination to identify and manage threats was seen as critical to address knowledge gaps