PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets

As 16S rRNA gene targeted massively parallel sequencing has become a common tool for microbial diversity investigations, numerous advances have been made to minimize the influence of sequencing and chimeric PCR artifacts through rigorous quality control measures. However, there has been little effort towards understanding the effect of multi-template PCR biases on microbial community structure. In this study, we used three bacterial and three archaeal mock communities consisting of, respectively, 33 bacterial and 24 archaeal 16S rRNA gene sequences combined in different proportions to compare the influences of (1) sequencing depth, (2) sequencing artifacts (sequencing errors and chimeric PCR artifacts), and (3) biases in multi-template PCR, towards the interpretation of community structure in pyrosequencing datasets. We also assessed the influence of each of these three variables on α- and β-diversity metrics that rely on the number of OTUs alone (richness) and those that include both membership and the relative abundance of detected OTUs (diversity). As part of this study, we redesigned bacterial and archaeal primer sets that target the V3–V5 region of the 16S rRNA gene, along with multiplexing barcodes, to permit simultaneous sequencing of PCR products from the two domains. We conclude that the benefits of deeper sequencing efforts extend beyond greater OTU detection and result in higher precision in β-diversity analyses by reducing the variability between replicate libraries, despite the presence of more sequencing artifacts. Additionally, spurious OTUs resulting from sequencing errors have a significant impact on richness or shared-richness based α- and β-diversity metrics, whereas metrics that utilize community structure (including both richness and relative abundance of OTUs) are minimally affected by spurious OTUs. However, the greatest obstacle towards accurately evaluating community structure are the errors in estimated mean relative abundance of each detected OTU due to biases associated with multi-template PCR reactions

New Internal Stress Driven on-Chip Micromachines for Extracting Mechanical Properties of Thin Films

A new concept of micromachines has been developed for measuring the mechanical properties of thin metallic films. The actuator is a beam undergoing large internal stresses built up during the deposition process. Al thin films are deposited partly on the actuator beam and on the substrate. By etching the structure, the actuator contracts and pulls the Al film. Full stress strain curves can be generated by designing a set of micromachines with various actuator lengths. In the present study, the displacements have been measured by scanning electronic microscopy. The stress is derived from simple continuum mechanics relationships. The tensile properties of Al films of various thicknesses have been tested. A marked increase of the strength with decreasing film thickness is observed.Comment: Submitted on behalf of TIMA Editions (http://irevues.inist.fr/tima-editions

Raman-scattering study of the phonon dispersion in twisted bi-layer graphene

Bi-layer graphene with a twist angle \theta\ between the layers generates a superlattice structure known as Moir\'{e} pattern. This superlattice provides a \theta-dependent q wavevector that activates phonons in the interior of the Brillouin zone. Here we show that this superlattice-induced Raman scattering can be used to probe the phonon dispersion in twisted bi-layer graphene (tBLG). The effect reported here is different from the broadly studied double-resonance in graphene-related materials in many aspects, and despite the absence of stacking order in tBLG, layer breathing vibrations (namely ZO' phonons) are observed.Comment: 18 pages, 4 figures, research articl

A GENERALIZED STOCHASTIC DOMINANCE PROGRAM FOR THE IBM PC

A microcomputer program to perform Generalized Stochastic Dominance (GSD), Quasi-Second Degree Dominance (SSD), and Quasi-First Degree Stochastic Dominance (FSD) is described. The program is designed to run on IBM-compatible personal computers with a Hercules or CGA graphics adapter. It is menu-driven and has options for GSD, quasi-FSD, quasi-SSD, graphics, and calculations of premiums associated with use of dominant distributions.Research and Development/Tech Change/Emerging Technologies,

Probabilistic models to describe the dynamics of migrating microbial communities

In all but the most sterile environments bacteria will reside in fluid being transported through conduits and some of these will attach and grow as biofilms on the conduit walls. The concentration and diversity of bacteria in the fluid at the point of delivery will be a mix of those when it entered the conduit and those that have become entrained into the flow due to seeding from biofilms. Examples include fluids through conduits such as drinking water pipe networks, endotracheal tubes, catheters and ventilation systems. Here we present two probabilistic models to describe changes in the composition of bulk fluid microbial communities as they are transported through a conduit whilst exposed to biofilm communities. The first (discrete) model simulates absolute numbers of individual cells, whereas the other (continuous) model simulates the relative abundance of taxa in the bulk fluid. The discrete model is founded on a birth-death process whereby the community changes one individual at a time and the numbers of cells in the system can vary. The continuous model is a stochastic differential equation derived from the discrete model and can also accommodate changes in the carrying capacity of the bulk fluid. These models provide a novel Lagrangian framework to investigate and predict the dynamics of migrating microbial communities. In this paper we compare the two models, discuss their merits, possible applications and present simulation results in the context of drinking water distribution systems. Our results provide novel insight into the effects of stochastic dynamics on the composition of non-stationary microbial communities that are exposed to biofilms and provides a new avenue for modelling microbial dynamics in systems where fluids are being transported

High-frequency performance of Schottky source/drain silicon pMOS devices

A radio-frequency performance of 85-nm gate-length p-type Schottky barrier (SB) with PtSi source/drain materials is investigated. The impact of silicidation annealing temperature on the high-frequency behavior of SB MOSFETs is analyzed using an extrinsic small-signal equivalent circuit. It is demonstrated that the current drive and the gate transconductance strongly depend on the silicidation anneal temperature, whereas the unity-gain cutoff frequency of the measured devices remains nearly unchanged

The Rarita-Schwinger spin-3/2 equation in a nonuniform, central potential

The equations of motion for a massive spin-3/2 Rarita-Schwinger field in a finite-range, central, Lorentz scalar potential are developed. It is shown that the resulting density may not be everywhere positive definite.Comment: 9 pages, RevTe