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

In-situ Investigation of the Early Stage of TiO2 epitaxy on (001) SrTiO3

We report on a systematic study of the growth of epitaxial TiO2 films deposited by pulsed laser deposition on Ti-terminated (001) SrTiO3 single crystals. By using in-situ reflection high energy electron diffraction, low energy electron diffraction, x-ray photoemission spectroscopy and scanning probe microscopy, we show that the stabilization of the anatase (001) phase is preceded by the growth of a pseudomorphic Sr-Ti-O intermediate layer, with a thickness between 2 and 4 nm. The data demonstrate that the formation of this phase is related to the activation of long range Sr migration from the substrate to the film. The role of interface Gibbs energy minimization, as a driving force for Sr diffusion, is discussed. Our results enrich the phase diagram of the Sr-Ti-O system under epitaxial strain opening the roudeficient SrTiO phase.Comment: 8 pages, 7 figure

Time-resolved photoluminescence of n-doped SrTiO_3

Following the recent surge of interest in n-doped strontium titanate as a possible blue light emitter, a time-resolved photoluminescence analysis was performed on nominally pure, Nb-doped and oxygen-deficient single-crystal SrTiO3 samples. The doping-effects on both the electronic states involved in the transition and the decay mechanism are respectively analyzed by comparing the spectral and dynamic features and the yields of the emission. Our time-resolved analysis, besides shedding some light on the basic recombination mechanisms acting in these materials, sets the intrinsic bandwidth limit of the proposed blue light emitting optoelectronic devices made of Ti-based perovskites heterostructures in the GHz range

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

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

Photodoping and in-gap interface states across the metal-insulator transition in LaAlO3/SrTiO3 heterostructures

By using scanning tunneling microscopy/spectroscopy we show that the interface between LaAlO3 and SrTiO3 band insulators is characterized by in-gap interface states. These features were observed in insulating as well as conducting LaAlO3/SrTiO3 bilayers. The data show how the interface density of states evolves across the insulating to metal transition, demonstrating that nanoscale electronic inhomogeneities in the system are induced by spatially localized electrons

Surface Charge-Switching Polymeric Nanoparticles for Bacterial Cell Wall-Targeted Delivery of Antibiotics

Bacteria have shown a remarkable ability to overcome drug therapy if there is a failure to achieve sustained bactericidal concentration or if there is a reduction in activity in situ. The latter can be caused by localized acidity, a phenomenon that can occur as a result of the combined actions of bacterial metabolism and the host immune response. Nanoparticles (NP) have shown promise in treating bacterial infections, but a significant challenge has been to develop antibacterial NPs that may be suitable for systemic administration. Herein we develop drug-encapsulated, pH-responsive, surface charge-switching poly(d,l-lactic-co-glycolic acid)-b-poly(l-histidine)-b-poly(ethylene glycol) (PLGA-PLH-PEG) nanoparticles for treating bacterial infections. These NP drug carriers are designed to shield nontarget interactions at pH 7.4 but bind avidly to bacteria in acidity, delivering drugs and mitigating in part the loss of drug activity with declining pH. The mechanism involves pH-sensitive NP surface charge switching, which is achieved by selective protonation of the imidazole groups of PLH at low pH. NP binding studies demonstrate pH-sensitive NP binding to bacteria with a 3.5 ± 0.2- to 5.8 ± 0.1-fold increase in binding to bacteria at pH 6.0 compared to 7.4. Further, PLGA-PLH-PEG-encapsulated vancomycin demonstrates reduced loss of efficacy at low pH, with an increase in minimum inhibitory concentration of 1.3-fold as compared to 2.0-fold and 2.3-fold for free and PLGA-PEG-encapsulated vancomycin, respectively. The PLGA-PLH-PEG NPs described herein are a first step toward developing systemically administered drug carriers that can target and potentially treat Gram-positive, Gram-negative, or polymicrobial infections associated with acidity.National Institutes of Health (U.S.) (Grant CA151884)National Institutes of Health (U.S.) (Grant EB003647)Prostate Cancer Foundation (Award in Nanotherapeutics)United States. Dept. of Defense (Prostate Cancer Research Program PC 051156)MIT-Portugal ProgramNational Science Foundation (U.S.). Graduate Research FellowshipNational Institutes of Health (U.S.) (Office of the Director Grant DP2OD008435