Efficient qubit detection using alkali earth metal ions and a double STIRAP process

We present a scheme for robust and efficient projection measurement of a qubit consisting of the two magnetic sublevels in the electronic ground state of alkali earth metal ions. The scheme is based on two stimulated Raman adiabatic passages (STIRAP) involving four partially coherent laser fields. We show how the efficiency depends on experimentally relevant parameters: Rabi frequencies, pulse widths, laser linewidths, one- and two-photon detunings, residual laser power, laser polarization and ion motion.Comment: 14 pages, 15 figure

Optimizing RNA structures by sequence extensions using RNAcop

A key aspect of RNA secondary structure prediction is the identification of novel functional elements. This is a challenging task because these elements typically are embedded in longer transcripts where the borders between the element and flanking regions have to be defined. The flanking sequences impact the folding of the functional elements both at the level of computational analyses and when the element is extracted as a transcript for experimental analysis. Here, we analyze how different flanking region lengths impact folding into a constrained structure by computing probabilities of folding for different sizes of flanking regions. Our method, RNAcop (RNA context optimization by probability), is tested on known and de novo predicted structures. In vitro experiments support the computational analysis and suggest that for a number of structures, choosing proper lengths of flanking regions is critical. RNAcop is available as web server and stand-alone software via http://rth.dk/resources/rnacop

Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture

Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each Cα effectively described by conformational angles resulting in Ramachandran plots. These, however, do not describe the conformations around hydrogen bonds, which can be non-local along the backbone and are of major importance for protein structure. Here, we introduce the spatial rotation between hydrogen bonded peptide planes as a new descriptor for protein structure locally around a hydrogen bond. Strikingly, this rotational descriptor sampled over high-quality structures from the protein data base (PDB) concentrates into 30 localized clusters, some of which correlate to the common secondary structures and others to more special motifs, yet generally providing a unifying systematic classification of local structure around protein hydrogen bonds. It further provides a uniform vocabulary for comparison of protein structure near hydrogen bonds even between bonds in different proteins without alignment

Probing the crossover in CO desorption from single crystal to nanoparticulate Ru model catalysts

cited By 10International audienceUsing model catalysts, we demonstrate that CO desorption from Ru surfaces can be switched from that typical of single crystal surfaces to one more characteristic of supported nanoparticles. First, the CO desorption behaviour from Ru nanoparticles supported on highly oriented pyrolytic graphite was studied. Both mass-selected and thermally evaporated nanoparticles were deposited. TPD spectra from the mass-selected nanoparticles exhibit a desorption peak located around 410 K with a broad shoulder extending from around 480 K to 600 K, while spectra obtained from thermally evaporated nanoparticles exhibit a single broad feature from ∼350 K to ∼450 K. A room temperature deposited 50 Å thick Ru film displays a characteristic nanoparticle-like spectrum with a broad desorption feature at ∼420 K and a shoulder extending from ∼450 K to ∼600 K. Subsequent annealing of this film at 900 K produced a polycrystalline morphology of flat Ru(001) terraces separated by monatomic steps. The CO desorption spectrum from this surface resembles that obtained on single crystal Ru(001) with two large desorption features located at 390 K and 450 K due to molecular desorption from terrace sites, and a much smaller peak at ∼530 K due to desorption of dissociatively adsorbed CO at step sites. In a second experiment, ion sputtering was used to create surface defects on a Ru(0 1 54) single crystal surface. A gradual shift away from the desorption spectrum typical of a Ru(001) surface towards one resembling desorption from supported Ru nanoparticles was observed with increasing sputter time. © 2011 the Owner Societies

A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples

The human gut microbiome (GM) plays an important role in human health and diseases. However, while substantial progress has been made in understanding the role of bacterial inhabitants of the gut, much less is known regarding the viral component of the GM. Bacteriophages (phages) are viruses attacking specific host bacteria and likely play important roles in shaping the GM. Although metagenomic approaches have led to the discoveries of many new viruses, they remain largely uncultured as their hosts have not been identified, which hampers our understanding of their biological roles. Existing protocols for isolation of viromes generally require relatively high input volumes and are generally more focused on extracting nucleic acids of good quality and purity for down-stream analysis, and less on purifying viruses with infective capacity. In this study, we report the development of an efficient protocol requiring low sample input yielding purified viromes containing phages that are still infective, which also are of sufficient purity for genome sequencing. We validated the method through spiking known phages followed by plaque assays, qPCR, and metagenomic sequencing. The protocol should facilitate the process of culturing novel viruses from the gut as well as large scale studies on gut viromes

Armenia: What drives first movers and how can their efforts be scaled up?

The paper examines ways to expand the contribution of the Armenian diaspora to Armenia’s long-term development agenda. It identifies factors that could explain the involvement and dynamics of a small group of entrepreneurs from the diaspora who have been active in and with Armenia. Based on these findings, it develops recommendations, consistent with the diaspora’s institutional capabilities, for increasing the number of such business activists and transforming diaspora efforts from humanitarian relief campaigns to business initiatives and development projects. The findings are based on detailed interviews with a group of prominent diaspora activists

Uropathogenic Escherichia coli Metabolite-Dependent Quiescence and Persistence May Explain Antibiotic Tolerance during Urinary Tract Infection

In the present study, it is shown that although Escherichia coli CFT073, a human uropathogenic (UPEC) strain, grows in liquid glucose M9 minimal medium, it fails to grow on glucose M9 minimal medium agar plates seeded with ≤106 CFU. The cells on glucose plates appear to be in a “quiescent” state that can be prevented by various combinations of lysine, methionine, and tyrosine. Moreover, the quiescent state is characteristic of ~80% of E. coli phylogenetic group B2 multilocus sequence type 73 strains, as well as 22.5% of randomly selected UPEC strains isolated from community-acquired urinary tract infections in Denmark. In addition, E. coli CFT073 quiescence is not limited to glucose but occurs on agar plates containing a number of other sugars and acetate as sole carbon sources. It is also shown that a number of E. coliCFT073 mini-Tn5 metabolic mutants (gnd, gdhA, pykF, sdhA, and zwf) are nonquiescent on glucose M9 minimal agar plates and that quiescence requires a complete oxidative tricarboxylic acid (TCA) cycle. In addition, evidence is presented that, although E. coli CFT073 quiescence and persistence in the presence of ampicillin are alike in that both require a complete oxidative TCA cycle and each can be prevented by amino acids, E. coli CFT073 quiescence occurs in the presence or absence of a functional rpoS gene, whereas maximal persistence requires a nonfunctional rpoS. Our results suggest that interventions targeting specific central metabolic pathways may mitigate UPEC infections by interfering with quiescence and persistence

Uropathogenic <i>Escherichia coli</i> metabolite-dependent quiescence and persistence may explain antibiotic tolerance during urinary tract infection

ABSTRACT In the present study, it is shown that although Escherichia coli CFT073, a human uropathogenic (UPEC) strain, grows in liquid glucose M9 minimal medium, it fails to grow on glucose M9 minimal medium agar plates seeded with ≤106 CFU. The cells on glucose plates appear to be in a “quiescent” state that can be prevented by various combinations of lysine, methionine, and tyrosine. Moreover, the quiescent state is characteristic of ~80% of E. coli phylogenetic group B2 multilocus sequence type 73 strains, as well as 22.5% of randomly selected UPEC strains isolated from community-acquired urinary tract infections in Denmark. In addition, E. coli CFT073 quiescence is not limited to glucose but occurs on agar plates containing a number of other sugars and acetate as sole carbon sources. It is also shown that a number of E. coli CFT073 mini-Tn5 metabolic mutants (gnd, gdhA, pykF, sdhA, and zwf) are nonquiescent on glucose M9 minimal agar plates and that quiescence requires a complete oxidative tricarboxylic acid (TCA) cycle. In addition, evidence is presented that, although E. coli CFT073 quiescence and persistence in the presence of ampicillin are alike in that both require a complete oxidative TCA cycle and each can be prevented by amino acids, E. coli CFT073 quiescence occurs in the presence or absence of a functional rpoS gene, whereas maximal persistence requires a nonfunctional rpoS. Our results suggest that interventions targeting specific central metabolic pathways may mitigate UPEC infections by interfering with quiescence and persistence. IMPORTANCE Recurrent urinary tract infections (UTIs) affect 10 to 40% of women. In up to 77% of those cases, the recurrent infections are caused by the same uropathogenic E. coli (UPEC) strain that caused the initial infection. Upon infection of urothelial transitional cells in the bladder, UPEC appear to enter a nongrowing quiescent intracellular state that is thought to serve as a reservoir responsible for recurrent UTIs. Here, we report that many UPEC strains enter a quiescent state when ≤106 CFU are seeded on glucose M9 minimal medium agar plates and show that mutations in several genes involved in central carbon metabolism prevent quiescence, as well as persistence, possibly identifying metabolic pathways involved in UPEC quiescence and persistence in vivo

Costs and quality of life for prehabilitation and early rehabilitation after surgery of the lumbar spine

During the recent years improved operation techniques and administrative procedures have been developed for early rehabilitation. At the same time preoperative lifestyle intervention (prehabilitation) has revealed a large potential for additional risk reduction