Lactobacillus ruminis strains cluster according to their mammalian gut source

peer-reviewedBackground Lactobacillus ruminis is a motile Lactobacillus that is autochthonous to the human gut, and which may also be isolated from other mammals. Detailed characterization of L. ruminis has previously been restricted to strains of human and bovine origin. We therefore sought to expand our bio-bank of strains to identify and characterise isolates of porcine and equine origin by comparative genomics. Results We isolated five strains from the faeces of horses and two strains from pigs, and compared their motility, biochemistry and genetic relatedness to six human isolates and three bovine isolates including the type strain 27780T. Multilocus sequence typing analysis based on concatenated sequence data for six individual loci separated the 16 L. ruminis strains into three clades concordant with human, bovine or porcine, and equine sources. Sequencing the genomes of four additional strains of human, bovine, equine and porcine origin revealed a high level of genome synteny, independent of the source animal. Analysis of carbohydrate utilization, stress survival and technological robustness in a combined panel of sixteen L. ruminis isolates identified strains with optimal survival characteristics suitable for future investigation as candidate probiotics. Under laboratory conditions, six human isolates of L. ruminis tested were aflagellate and non-motile, whereas all 10 strains of bovine, equine and porcine origin were motile. Interestingly the equine and porcine strains were hyper-flagellated compared to bovine isolates, and this hyper-flagellate phenotype correlated with the ability to swarm on solid medium containing up to 1.8% agar. Analysis by RNA sequencing and qRT-PCR identified genes for the biosynthesis of flagella, genes for carbohydrate metabolism and genes of unknown function that were differentially expressed in swarming cells of an equine isolate of L. ruminis. Conclusions We suggest that Lactobacillus ruminis isolates have potential to be used in the functional food industry. We have also identified a MLST scheme able to distinguish between strains of L. ruminis of different origin. Genes for non-digestible oligosaccharide metabolism were identified with a putative role in swarming behaviour.This work was supported by a Principal Investigator Award (07/IN.1/B1780) from Science Foundation Ireland to P.W. O’Toole

The Processing of Verb-Argument Constructions is Sensitive to Form, Function, Frequency, Contingency, and Prototypicality.

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/139741/1/CognitiveLinguisticsUMichOffprint.pd

Crystalfield symmetries of luminescent Eu3+ centers in GaN : the importance of the 5D0 to 7F1 transition

Eu-doped GaN is a promising material with potential application not only in optoelectronics but also in magneto-optical and quantum optical devices ‘beyond the light emitting diode’. Its interesting spectroscopy is unfortunately complicated by spectral overlaps due to ‘site multiplicity’, the existence in a given sample of multiple composite centers in which Eu ions associate with intrinsic or extrinsic defects. We show here that elementary crystalfield analysis of the 5D0 to 7F1 transition can critically distinguish such sites. Hence, we find that the center involved in the hysteretic photochromic switching (HPS) observed in GaN(Mg):Eu, proposed as the basis of a new solid state qubit material, is not in fact Eu1, as previously reported, but a related defect, Eu1(Mg). Furthermore, the decomposition of the crystalfield distortions of Eu0, Eu1(Mg) and Eu1 into axial and non-axial components strongly suggests reasonable microscopic models for the defects themselves

The effects of room design on computer-supported collaborative learning in a multi-touch classroom.

While research indicates that technology can be useful for supporting learning and collaboration, there is still relatively little uptake or widespread implementation of these technologies in classrooms. In this paper, we explore one aspect of the development of a multi-touch classroom, looking at two different designs of the classroom environment to explore how classroom layout may influence group interaction and learning. Three classes of students working in groups of four were taught in the traditional forward-facing room condition, while three classes worked in a centered room condition. Our results indicate that while the outcomes on tasks were similar across conditions, groups engaged in more talk (but not more off-task talk) in a centered room layout, than in a traditional forward-facing room. These results suggest that the use of technology in the classroom may be influenced by the location of the technology, both in terms of the learning outcomes and the interaction behaviors of students. The findings highlight the importance of considering the learning environment when designing technology to support learning, and ensuring that integration of technology into formal learning environments is done with attention to how the technology may disrupt, or contribute to, the classroom interaction practices

New Dependencies of Hierarchies in Polynomial Optimization

We compare four key hierarchies for solving Constrained Polynomial Optimization Problems (CPOP): Sum of Squares (SOS), Sum of Diagonally Dominant Polynomials (SDSOS), Sum of Nonnegative Circuits (SONC), and the Sherali Adams (SA) hierarchies. We prove a collection of dependencies among these hierarchies both for general CPOPs and for optimization problems on the Boolean hypercube. Key results include for the general case that the SONC and SOS hierarchy are polynomially incomparable, while SDSOS is contained in SONC. A direct consequence is the non-existence of a Putinar-like Positivstellensatz for SDSOS. On the Boolean hypercube, we show as a main result that Schm\"udgen-like versions of the hierarchies SDSOS*, SONC*, and SA* are polynomially equivalent. Moreover, we show that SA* is contained in any Schm\"udgen-like hierarchy that provides a O(n) degree bound.Comment: 26 pages, 4 figure

Examination of the Resonance Contributions to Dileptonic Rare B-Decays

We analyse the long-distance contribution to $B\to X_s\ell^+\ell^-$ differential decay rate when the momentum dependence of $\psi$ and $\psi'$-$\gamma$ conversion strength is taken into account. The results indicate that the resonance to nonresonance interference in the dilepton invariant mass distribution is substantially reduced.Comment: 10 pages, Latex, one figure (included