Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies

Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotgun metagenomics on wide scale projects is the high cost associated with the approach. We set out to determine if it is possible to use shallow shotgun metagenomics to characterize complex biological matrices while reducing costs. We used a staggered mock community to estimate the optimal threshold for species detection. We measured the variation of several summary statistics simulating a decrease in sequencing depth by randomly subsampling a number of reads. The main statistics that were compared are diversity estimates, species abundance, and ability of reconstructing de novo the metagenome in terms of length and completeness. Our results show that diversity indices of complex prokaryotic, eukaryotic and viral communities can be accurately estimated with 500,000 reads or less, although particularly complex samples may require 1,000,000 reads. On the contrary, any task involving the reconstruction of the metagenome performed poorly, even with the largest simulated subsample (1,000,000 reads). The length of the reconstructed assembly was smaller than the length obtained with the full dataset, and the proportion of conserved genes that were identified in the meta-genome was drastically reduced compared to the full sample. Shallow shotgun metagenomics can be a useful tool to describe the structure of complex matrices, but it is not adequate to reconstruct-even partially-the metagenome

Distribution of Trace Elements in Plant Parts of Red Clover (\u3cem\u3eTrifolium pratense\u3c/em\u3e L.)

There is little information on the distribution of minerals in plant parts although factors affecting mineral content in forages have been well investigated (Fleming, 1973; Whitehead et al., 1985). The aim of this investigation was to determine the trace mineral content in plant parts of different cultivars of red clover (foreign and domestic) and to assess differences between cultivars. The existence of significant differences between cultivars would indicate the possibility of selecting cultivars to satisfy particular animal requirements for minerals

Charge density waves enhance the electronic noise of manganites

The transport and noise properties of Pr_{0.7}Ca_{0.3}MnO_{3} epitaxial thin films in the temperature range from room temperature to 160 K are reported. It is shown that both the broadband 1/f noise properties and the dependence of resistance on electric field are consistent with the idea of a collective electrical transport, as in the classical model of sliding charge density waves. On the other hand, the observations cannot be reconciled with standard models of charge ordering and charge melting. Methodologically, it is proposed to consider noise-spectra analysis as a unique tool for the identification of the transport mechanism in such highly correlated systems. On the basis of the results, the electrical transport is envisaged as one of the most effective ways to understand the nature of the insulating, charge-modulated ground states in manganites.Comment: 6 two-column pages, 5 figure

Photocatalytic degradation of metoprolol tartrate in suspensions of two TiO2-based photocatalysts with different surface area. Identification of intermediates and proposal of degradation pathways.

This study investigates the efficiency of the photocatalytic degradation of metoprolol tartrate (MET), a widely used β 1-blocker, in TiO 2 suspensions of Wackherr's " Oxyde de titane standard" and Degussa P25. The study encompasses transformation kinetics and efficiency, identification of intermediates and reaction pathways. In the investigated range of initial concentrations (0.01-0.1mM), the photocatalytic degradation of MET in the first stage of the reaction followed approximately a pseudo-first order kinetics. The TiO 2 Wackherr induced a significantly faster MET degradation compared to TiO 2 Degussa P25 when relatively high substrate concentrations were used. By examining the effect of ethanol as a scavenger of hydroxyl radicals (OH), it was shown that the reaction with OH played the main role in the photocatalytic degradation of MET. After 240min of irradiation the reaction intermediates were almost completely mineralized to CO 2 and H 2O, while the nitrogen was predominantly present as NH4+. Reaction intermediates were studied in detail and a number of them were identified using LC-MS/MS (ESI+), which allowed the proposal of a tentative pathway for the photocatalytic transformation of MET as a function of the TiO 2 specimen

Atomically precise lateral modulation of a two-dimensional electron liquid in anatase TiO2 thin films

Engineering the electronic band structure of two-dimensional electron liquids (2DELs) confined at the surface or interface of transition metal oxides is key to unlocking their full potential. Here we describe a new approach to tailoring the electronic structure of an oxide surface 2DEL demonstrating the lateral modulation of electronic states with atomic scale precision on an unprecedented length scale comparable to the Fermi wavelength. To this end, we use pulsed laser deposition to grow anatase TiO2 films terminated by a (1 x 4) in-plane surface reconstruction. Employing photo-stimulated chemical surface doping we induce 2DELs with tunable carrier densities that are confined within a few TiO2 layers below the surface. Subsequent in-situ angle resolved photoemission experiments demonstrate that the (1 x 4) surface reconstruction provides a periodic lateral perturbation of the electron liquid. This causes strong backfolding of the electronic bands, opening of unidirectional gaps and a saddle point singularity in the density of states near the chemical potential

Cryptoferromagnetic state in superconductor-ferromagnet multilayers

We study a possibility of a non-homogeneous magnetic order (cryptoferromagnetic state) in heterostructures consisting of a bulk superconductor and a ferromagnetic thin layer that can be due to the influence of the superconductor. The exchange field in the ferromagnet may be strong and exceed the inverse mean free time. A new approach based on solving the Eilenberger equations in the ferromagnet and the Usadel equations in the superconductor is developed. We derive a phase diagram between the cryptoferromagnetic and ferromagnetic states and discuss the possibility of an experimental observation of the CF state in different materials.Comment: 4 pages, 1 figur

Bulk electronic structure of superconducting LaRu2P2 single crystals measured by soft x-ray angle-resolved photoemission spectroscopy

We present a soft X-ray angle-resolved photoemission spectroscopy (SX-ARPES) study of the stoichiometric pnictide superconductor LaRu2P2. The observed electronic structure is in good agreement with density functional theory (DFT) calculations. However, it is significantly different from its counterpart in high-temperature superconducting Fe-pnictides. In particular the bandwidth renormalization present in the Fe-pnictides (~2 - 3) is negligible in LaRu2P2 even though the mass enhancement is similar in both systems. Our results suggest that the superconductivity in LaRu2P2 has a different origin with respect to the iron pnictides. Finally we demonstrate that the increased probing depth of SX-ARPES, compared to the widely used ultraviolet ARPES, is essential in determining the bulk electronic structure in the experiment.Comment: 4 pages, 4 figures, 1 supplemental material. Accepted for publication in Physical Review Letter

Exotic Kondo crossover in a wide temperature region in the topological Kondo insulator SmB6 revealed by high-resolution ARPES

Temperature dependence of the electronic structure of SmB6 is studied by high-resolution ARPES down to 1 K. We demonstrate that there is no essential difference for the dispersions of the surface states below and above the resistivity saturating anomaly (~ 3.5 K). Quantitative analyses of the surface states indicate that the quasi-particle scattering rate increases linearly as a function of temperature and binding energy, which differs from Fermi-Liquid behavior. Most intriguingly, we observe that the hybridization between the d and f states builds gradually over a wide temperature region (30 K < T < 110 K). The surface states appear when the hybridization starts to develop. Our detailed temperature-dependence results give a complete interpretation of the exotic resistivity result of SmB6, as well as the discrepancies among experimental results concerning the temperature regions in which the topological surface states emerge and the Kondo gap opens, and give new insights into the exotic Kondo crossover and its relationship with the topological surface states in the topological Kondo insulator SmB6.Comment: 8 pages, 5 figure