Towards Comparing the Robustness of Synchronous and Asynchronous Circuits by Fault Injection

As transient error rates are growing due to smaller feature sizes, designing reliable synchronous circuits becomes increasingly challenging. Asynchronous logic design constitutes a promising alternative with respect to robustness and stability. In particular, delay-insensitive asynchronous circuits provide interesting properties, like an inherent resilience to delay-faults

The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5’ Leader Featuring the sRNA UpsM

Cell division and cell wall synthesis mechanisms are similarly conserved among bacteria. Consequently some bacterial species have comparable sets of genes organized in the dcw (division and cell wall) gene cluster. Dcw genes, their regulation and their relative order within the cluster are outstandingly conserved among rod shaped and gram negative bacteria to ensure an efficient coordination of growth and division. A well studied representative is the dcw gene cluster of E. coli. The first promoter of the gene cluster (mraZ1p) gives rise to polycistronic transcripts containing a 38 nt long 5’ UTR followed by the first gene mraZ. Despite reported conservation we present evidence for a much longer 5’ UTR in the gram negative and rod shaped bacterium Rhodobacter sphaeroides and in the family of Rhodobacteraceae. This extended 268 nt long 5’ UTR comprises a Rho independent terminator, which in case of termination gives rise to a non-coding RNA (UpsM). This sRNA is conditionally cleaved by RNase E under stress conditions in an Hfq- and very likely target mRNA-dependent manner, implying its function in trans. These results raise the question for the regulatory function of this extended 5’ UTR. It might represent the rarely described case of a trans acting sRNA derived from a riboswitch with exclusive presence in the family of Rhodobacteraceae

A genomic view of food-related and probiotic Enterococcus strains

The study of enterococcal genomes has grown considerably in recent years. While special attentionis paid to comparative genomic analysis among clinical relevant isolates, in this study we performedan exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential tobe used as probiotics. Beyond common genetic features, we especially aimed to identify those thatare specific to enterococcal strains isolated from a certain food-related source as well as features presentin a species-specific manner. Thus, the genome sequences of 25 Enterococcus strains, from 7different species, were examined and compared. Their phylogenetic relationship was reconstructedbased on orthologous proteins and whole genomes. Likewise, markers associated with a successfulcolonization (bacteriocin genes and genomic islands) and genome plasticity (phages and clusteredregularly interspaced short palindromic repeats) were investigated for lifestyle specific genetic features.At the same time, a search for antibiotic resistance genes was carried out, since they are of bigconcern in the food industry. Finally, it was possible to locate 1617 FIGfam families as a core proteomeuniversally present among the genera and to determine that most of the accessory genes codefor hypothetical proteins, providing reasonable hints to support their functional characterization.Fil: Bonacina, Julieta. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Suárez, Nadia Elina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Hormigo, Daniel Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Fadda, Silvina G.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Lechner, Marcus. University Marburg; AlemaniaFil: Saavedra, Maria Lucila. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; Argentin

Salts of Picramic Acid – Nearly Forgotten Temperature‐Resistant Energetic Materials

Thermally stable explosives are becoming more and more important nowadays due to their important role in the oil and mining industry. The requirements of these explosives are constantly changing. Picramate‐based compounds are poorly investigated towards their energetic properties as well as sensitivities. In this work, 13 different salts of picramic acid were synthesized as potential energetic materials with high thermal stability in a simple one‐step reaction and compared with commercially used lead picramate. The obtained compounds were extensively characterized by e. g. XRD, IR, EA, DTA, and TGA. In addition, the sensitivities towards impact and friction were determined with the BAM drop hammer and the BAM friction tester. Also, the electrostatic discharge sensitivity was explored. Calculations of the energetic performance of selected compounds were carried out with the current version of EXPLO5 code. Therefore, heats of formation were computed and X‐ray densities were converted to room temperature. Some of the synthesized salts show promising characteristics with high exothermic decomposition temperatures. Especially, the water‐free rubidium, cesium, and barium salts 5 , 6 and 10 with decomposition temperatures of almost 300 °C could be promising candidates for future applications

Structural and mechanistic characterization of 6S RNA from the hyperthermophilic bacterium Aquifex aeolicus

© 2015 Elsevier B.V. and Socie;acuteacute& Franc de Biochimie et Biologie Moleculaire (SFBBM). All rights reserved. Bacterial 6S RNAs competitively inhibit binding of RNA polymerase (RNAP) holoenzymes to DNA promoters, thereby globally regulating transcription. RNAP uses 6S RNA itself as a template to synthesize short transcripts, termed pRNAs (product RNAs). Longer pRNAs (approx. ≥ 10 nt) rearrange the 6S RNA structure and thereby disrupt the 6S RNA:RNAP complex, which enables the enzyme to resume transcription at DNA promoters. We studied 6S RNA of the hyperthermophilic bacterium Aquifex aeolicus, representing the thermodynamically most stable 6S RNA known so far. Applying structure probing and NMR, we show that the RNA adopts the canonical rod-shaped 6S RNA architecture with little structure formation in the central bulge (CB) even at moderate temperatures (≤37°C). 6S RNA:pRNA complex formation triggers an internal structure rearrangement of 6S RNA, i.e. formation of a so-called central bulge collapse (CBC) helix. The persistence of several characteristic NMR imino proton resonances upon pRNA annealing demonstrates that defined helical segments on both sides of the CB are retained in the pRNA-bound state, thus representing a basic framework of the RNA's architecture. RNA-seq analyses revealed pRNA synthesis from 6S RNA in A. aeolicus, identifying 9 to ∼17-mers as the major length species. A. aeolicus 6S RNA can also serve as a template for in vitro pRNA synthesis by RNAP from the mesophile Bacillus subtilis. Binding of a synthetic pRNA to A. aeolicus 6S RNA blocks formation of 6S RNA:RNAP complexes. Our findings indicate that A. aeolicus 6S RNA function in its hyperthermophilic host is mechanistically identical to that of other bacterial 6S RNAs. The use of artificial pRNA variants, designed to disrupt helix P2 from the 3;prime&-CB instead of the 5;prime&-CB but preventing formation of the CBC helix, indicated that the mechanism of pRNA-induced RNAP release has been evolutionarily optimized for transcriptional pRNA initiation in the 5;prime&-CB.DFG (SPP 1258 and IRTG 1384) to RKH, by the DFG (SFB 902 A2) to EDF and the Spanish Ministry of Economy and Competitiveness (BFU2011-23645) to M.S.Peer Reviewe

The effect of size and density on the mean retention time of particles in the reticulorumen of cattle (Bos primigenius f. taurus), muskoxen (Ovibos moschatus) and moose (Alces alces)

Particle passage from the reticulorumen (RR) depends on particle density and size. Forage particle density and size are related and change over time in the RR. Particle density mainly influences sorting in the reticulum, whereas particle size influences particle retention in the fibre mat of stratified rumen contents (‘filter-bed' effect). We investigated these effects independently, by inserting plastic particles of different sizes (1, 10 and 20mm) and densities (1·03, 1·20 and 1·44mg/ml) in the RR of cattle (Bos primigenius f. taurus) as a pilot study, and of muskoxen (Ovibos moschatus; n 4) and moose (Alces alces; n 2) both fed two diets (browse and grass). Faeces were analysed for plastic residues for 13d after dosing to calculate mean retention times (MRT). The results confirmed previous findings of differences in absolute MRT between species. Comparing muskoxen with moose, there was no difference in the effect of particle density on the MRT between species but particle size had a more pronounced effect on the MRT in muskoxen than in moose. This indicated a stronger ‘filter-bed effect' in muskoxen, in accord with the reports of stratified RR contents in this species v. the absence of RR content stratification in moose. Low-density particles were retained longer in both species fed on grass diets, indicating a contribution of forage type to the ‘filter-bed effect'. The results indicate that retention based on particle size may differ between ruminant species, depending on the presence of a fibre mat in the RR, whereas the density-dependent mechanism of sedimentation in the RR is rather constant across specie

Insights into 6S RNA in lactic acid bacteria (LAB)

Background: 6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute a group of microorganisms with strong biotechnological relevance, often exploited as starter cultures for industrial products through fermentation. Some strains are used as probiotics while others represent potential pathogens. Occasional reports of 6S RNA within this group already indicate striking metabolic implications. A conceivable idea is that LAB with 6S RNA defects may metabolize nutrients faster, as inferred from studies of Echerichia coli. This may accelerate fermentation processes with the potential to reduce production costs. Similarly, elevated levels of secondary metabolites might be produced. Evidence for this possibility comes from preliminary findings regarding the production of surfactin in Bacillus subtilis, which has functions similar to those of bacteriocins. The prerequisite for its potential biotechnological utility is a general characterization of 6S RNA in LAB. Results: We provide a genomic annotation of 6S RNA throughout the Lactobacillales order. It laid the foundation for a bioinformatic characterization of common 6S RNA features. This covers secondary structures, synteny, phylogeny, and product RNA start sites. The canonical 6S RNA structure is formed by a central bulge flanked by helical arms and a template site for product RNA synthesis. 6S RNA exhibits strong syntenic conservation. It is usually flanked by the replication-associated recombination protein A and the universal stress protein A. A catabolite responsive element was identified in over a third of all 6S RNA genes. It is known to modulate gene expression based on the available carbon sources. The presence of antisense transcripts could not be verified as a general trait of LAB 6S RNAs. Conclusions: Despite a large number of species and the heterogeneity of LAB, the stress regulator 6S RNA is well-conserved both from a structural as well as a syntenic perspective. This is the first approach to describe 6S RNAs and short 6S RNA-derived transcripts beyond a single species, spanning a large taxonomic group covering multiple families. It yields universal insights into this regulator and complements the findings derived from other bacterial model organisms.Fil: Cataldo, Pablo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Klemm, Paul. Universitat Phillips; AlemaniaFil: Thüring, Marietta. Universitat Phillips; AlemaniaFil: Saavedra, Maria Lucila. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Hebert, Elvira Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Hartmann, Roland K.. Universitat Phillips; AlemaniaFil: Lechner, Marcus. Universitat Phillips; Alemani

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

Covariant actions for N=1, D=6 Supergravity theories with chiral bosons

We show that the recently found covariant formulation for chiral $p$--forms in $2(p+1)$ dimensions with $p$ even, can be naturally extended to supersymmetric theories. We present the general method for writing covariant actions for chiral bosons and construct, in particular, in six dimensions covariant actions for one tensor supermultiplet, for pure supergravity and for supergravity coupled to an arbitrary number of tensor supermultiplets.Comment: LaTeX file, 20 pages, no figure