16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

peer-reviewedBackground Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. Results The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. Conclusions Microbiota compositional data differed depending on the primers and sequencing platform that were used. The results demonstrate the risks in comparing data generated using different sequencing approaches and highlight the merits of choosing a standardised approach for sequencing in situations where a comparison across multiple sequencing runs is required.This publication has emanated from research supported in part by a research grant from Science Foundation Ireland (SFI) under Grant Numbers SFI/12/RC/2273 and 11/PI/1137 and by FP7 funded CFMATTERS (Cystic Fibrosis Microbiome-determined Antibiotic Therapy Trial in Exacerbations: Results Stratified, Grant Agreement no. 603038)

Wind conditions and ventilation in high-rise long street models

We regarded high-rise cities as obstacles and channels to wind. We first studied wind conditions and ventilations in idealized high-rise long street models experimentally and numerically with a constant street width (W = 30 mm), variable street heights (H = 2 W, 2.5W, 3W, 4W), variable street lengths (L = 47.4W, 79W, 333W, 667W) and a parallel approaching wind. The flow rates penetrating into windward entries are a little larger than the reference flow rate in the far upstream free flow through the same area with windward entries in all models. The stream-wise velocity decreases along the street as some air leaves upwardly across street roofs. Near the leeward entry, there is a downward flow which brings some air into the street and results in an accelerating process. In the neighborhood scale long streets (L = 47.4W and 79W), wind in taller streets is stronger and the ventilation is better than a lower one. For the city scale long streets (L = 333W and 667W), a constant flow region exists where the vertical velocity is zero and the stream-wise velocity remains constant. In such regions, turbulent fluctuations across the street roof are more important to air exchange than vertical mean flows. In a taller street, the process to establish the constant flow conditions is longer and the normalized balanced horizontal flow rate is smaller than those in a lower street. In the city scale long streets, the turbulence exchange rate can be 5-10 times greater than the mean flow rate. Crown Copyright © 2009.postprin

Performance Evaluation of RAKE Receiver for UWB Systems using Measured Channels in Industrial Environments

The industrial environments are an important scenario for ultra wideband (UWB) communication systems. However, due to large number of metallic scatterers in the surroundings, the multipath offered by UWB channels is dense with significant energy. In this paper, the performance of RAKE receivers operating in a non line-of-sight (NLOS) scenario in these environments is evaluated. The channels used for the evaluation are measured in a medium-sized industrial environment. In addition, a standard IEEE 802.15.4a channel model is used for comparison with the results of the measured data. The performance of partial RAKE (PRake) and selective RAKE (SRake) is evaluated in terms of uncoded bit-error-rate (BER) using different number of fingers. The performance of maximal ratio combining (MRC) and equal gain combining (EGC) is compared for the RAKE receiver assuming perfect knowledge of the channel state. Finally, based on the simulation results, conclusions are drawn considering the performance and complexity issues for system design in these environments

Characterization of Pro-Inflammatory Flagellin Proteins Produced by Lactobacillus ruminis and Related Motile Lactobacilli

peer-reviewedLactobacillus ruminis is one of at least twelve motile but poorly characterized species found in the genus Lactobacillus. Of these, only L. ruminis has been isolated from mammals, and this species may be considered as an autochthonous member of the gastrointestinal microbiota of humans, pigs and cows. Nine L. ruminis strains were investigated here to elucidate the biochemistry and genetics of Lactobacillus motility. Six strains isolated from humans were non-motile while three bovine isolates were motile. A complete set of flagellum biogenesis genes was annotated in the sequenced genomes of two strains, ATCC25644 (human isolate) and ATCC27782 (bovine isolate), but only the latter strain produced flagella. Comparison of the L. ruminis and L. mali DSM20444T motility loci showed that their genetic content and gene-order were broadly similar, although the L. mali motility locus was interrupted by an 11.8 Kb region encoding rhamnose utilization genes that is absent from the L. ruminis motility locus. Phylogenetic analysis of 39 motile bacteria indicated that Lactobacillus motility genes were most closely related to those of motile carnobacteria and enterococci. Transcriptome analysis revealed that motility genes were transcribed at a significantly higher level in motile L. ruminis ATCC27782 than in non-motile ATCC25644. Flagellin proteins were isolated from L. ruminis ATCC27782 and from three other Lactobacillus species, while recombinant flagellin of aflagellate L. ruminis ATCC25644 was expressed and purified from E. coli. These native and recombinant Lactobacillus flagellins, and also flagellate L. ruminis cells, triggered interleukin-8 production in cultured human intestinal epithelial cells in a manner suppressed by short interfering RNA directed against Toll-Like Receptor 5. This study provides genetic, transcriptomic, phylogenetic and immunological insights into the trait of flagellum-mediated motility in the lactobacilli.This work was supported by a Principal Investigator Award (07/IN.1/B1780) from Science Foundation Ireland to PWOT. BAN was the recipient of an Embark studentship from the Irish Research Council for Science Engineering and Technology. TD and KN were supported by the Alimentary Pharmabiotic Centre, funded by Science Foundation Ireland

The coherent {\it d}-wave superconducting gap in underdoped La2−x_{2-x}Srx_{x}CuO4_4 as studied by angle-resolved photoemission

We present angle-resolved photoemission spectroscopy (ARPES) data on moderately underdoped La$_{1.855}$Sr$_{0.145}$CuO$_4$ at temperatures below and above the superconducting transition temperature. Unlike previous studies of this material, we observe sharp spectral peaks along the entire underlying Fermi surface in the superconducting state. These peaks trace out an energy gap that follows a simple {\it d}-wave form, with a maximum superconducting gap of 14 meV. Our results are consistent with a single gap picture for the cuprates. Furthermore our data on the even more underdoped sample La$_{1.895}$Sr$_{0.105}$CuO$_4$ also show sharp spectral peaks, even at the antinode, with a maximum superconducting gap of 26 meV.Comment: Accepted by Phys. Rev. Let

Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal

The genus Lactobacillus is a diverse group with a combined species count of over 200. They are the largest group within the lactic acid bacteria and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties. Lactobacillus salivarius, a species commonly isolated from the gastrointestinal tract of humans and animals, has been described as having potential probiotic properties and results of previous studies have revealed considerable functional diversity existing on both the chromosomes and plasmids. Our study consists of comparative genomic analyses of the functional and phylogenomic diversity of 42 genomes of strains of L . salivarius using bioinformatic techniques. The main aim of the study was to describe intra-species diversity and to determine how this diversity is spread across the replicons. We found that multiple phylogenomic and non-phylogenomic methods used for reconstructing trees all converge on similar tree topologies, showing that different metrics largely agree on the evolutionary history of the species. The greatest genomic variation lies on the small plasmids, followed by the repA-type circular megaplasmid, with the chromosome varying least of all. Additionally, the presence of extra linear and circular megaplasmids is noted in several strains, while small plasmids are not always present. Glycosyl hydrolases, bacteriocins and proteases vary considerably on all replicons while two exopolysaccharide clusters and several clustered regularly interspaced short palindromic repeats-associated systems show a lot of variation on the chromosome. Overall, despite its reputation as a mammalian gastrointestinal tract specialist, the intra-specific variation of L. salivarius reveals potential strain-dependant effects on human health

Electronic structure near the 1/8-anomaly in La-based cuprates

We report an angle resolved photoemission study of the electronic structure of the pseudogap state in \NdLSCO ($T_c<7$ K). Two opposite dispersing Fermi arcs are the main result of this study. The several scenarios that can explain this observation are discussed.Comment: A high-resolution version can be found at http://lns.web.psi.ch/lns/download/Pockets/arXiv.pd

Spectroscopic evidence for preformed Cooper pairs in the pseudogap phase of cuprates

Angle-resolved photoemission on underdoped La$_{1.895}$Sr$_{0.105}$CuO$_4$ reveals that in the pseudogap phase, the dispersion has two branches located above and below the Fermi level with a minimum at the Fermi momentum. This is characteristic of the Bogoliubov dispersion in the superconducting state. We also observe that the superconducting and pseudogaps have the same d-wave form with the same amplitude. Our observations provide direct evidence for preformed Cooper pairs, implying that the pseudogap phase is a precursor to superconductivity