Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences

The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing protocols are, however, limited by the fraction of the 16S rRNA gene that is interrogated and therefore limit the resolution and quality of the profiling. To address this, we present the design of a novel protocol for shotgun Illumina sequencing of the bacterial 16S rRNA gene, optimized to capture more than 90% of sequences in the Greengenes database and with nearly twice the resolution of existing protocols. Using several in silico and experimental datasets, we demonstrate that despite the presence of multiple variable and conserved regions, the resulting shotgun sequences can be used to accurately quantify the diversity of complex microbial communities. The reconstruction of a significant fraction of the 16S rRNA gene also enabled high precision (>90%) in species-level identification thereby opening up potential application of this approach for clinical microbial characterization.Comment: 17 pages, 2 tables, 2 figures, supplementary materia

Standards for Documenting Finite-Fault Earthquake Rupture Models

In this article, we propose standards for documenting and disseminating finite‐fault earthquake rupture models, and related data and metadata. A comprehensive documentation of the rupture models, a detailed description of the data processing steps, and facilitating the access to the actual data that went into the earthquake source inversion are required to promote follow‐up research and to ensure interoperability, transparency, and reproducibility of the published slip‐inversion solutions. We suggest a formatting scheme that describes the kinematic rupture process in an unambiguous way to support subsequent research. We also provide guidelines on how to document the data, metadata, and data processing. The proposed standards and formats represent a first step to establishing best practices for comprehensively documenting input and output of finite‐fault earthquake source studies

Integrin-mediated adhesion regulates membrane order

The properties of cholesterol-dependent domains (lipid rafts) in cell membranes have been controversial. Because integrin-mediated cell adhesion and caveolin both regulate trafficking of raft components, we investigated the effects of adhesion and caveolin on membrane order. The fluorescent probe Laurdan and two-photon microscopy revealed that focal adhesions are highly ordered; in fact, they are more ordered than caveolae or domains that stain with cholera toxin subunit B (CtxB). Membrane order at focal adhesion depends partly on phosphorylation of caveolin1 at Tyr14, which localizes to focal adhesions. Detachment of cells from the substratum triggers a rapid, caveolin-independent decrease in membrane order, followed by a slower, caveolin-dependent decrease that correlates with internalization of CtxB-stained domains. Endocytosed CtxB domains also become more fluid. Thus, membrane order is highly dependent on caveolae and focal adhesions. These results show that lipid raft properties are conferred by assembly of specific protein complexes. The ordered state within focal adhesions may have important consequences for signaling at these sites

The peri-implant phenotype

This commentary proposes a definition for the term - peri- implant phenotype- and provides a comprehensive description of all its components.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154670/1/jper10524.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154670/2/jper10524_am.pd

An exploration of the pedagogies employed to integrate knowledge in work-integrated learning

This article describes a three‐sector, national research project that investigated the integration aspect of work‐integrated learning (WIL). The context for this study is three sectors of New Zealand higher education: business and management, sport, and science and engineering, and a cohort of higher educational institutions that offer WIL/cooperative education in variety of ways. The aims of this study were to investigate the pedagogical approaches in WIL programs that are currently used by WIL practitioners in terms of learning, and the integration of academic‐workplace learning. The research constituted a series of collective case studies, and there were two main data sources — interviews with three stakeholder groups (namely employers, students, and co‐op practitioners), and analyses of relevant documentation (e.g., course/paper outlines, assignments on reflective practice, portfolio of learning, etc.). The research findings suggest that there is no consistent mechanism by which placement coordinators, off‐campus supervisors, or mentors seek to employ or develop pedagogies to foster learning and the integration of knowledge. Learning, it seems, occurs by means of legitimate peripheral participation with off‐campus learning occurring as a result of students working alongside professionals in their area via an apprenticeship model of learning. There is no evidence of explicit attempts to integrate on‐ and off‐campus learning, although all parties felt this would and should occur. However, integration is implicitly or indirectly fostered by a variety of means such as the use of reflective journals

Twisting waves increase the visibility of nonlinear behaviour

Nonlinear behaviour for acoustic systems is readily measured at high acoustic pressures in gasses or bulk materials. However, at low acoustic pressures non-linear effects are not commonly observed. We find that by phase structuring acoustics beams, one observes evidence of non-linear behaviour at an acoustic pressure of 66.78 dB lower than non-structured beams in room temperature air. A bespoke 28-element ultrasonic phased array antenna was developed to generate short pulses that carry orbital angular momentum and are propagated over a short air channel. When sampling small areas of the wavefront, we observed a distinctive change in the frequency components near phase singularities. At these phase singularities the local propagation path is screwed, resulting in the collection signals from pulses traveling along different paths across the aperture of a microphone. The usually negligible frequency chirping that arises from nonlinear behaviour in air interfere at these singularity points and produce a distinctive distortion of the acoustic pulse. Simple physical movement in the system or super-sonic wave speeds do not yield similar results. Such distortions in measured frequency response near phase singularities could lead to errors for SONAR or acoustic communication systems, where received signals are integrated over a finite-area detector. With further development this behaviour could potentially lead to accurate measurement techniques for determining a material's nonlinear properties at lower acoustic pressure

Darwin -— an experimental astronomy mission to search for extrasolar planets

As a response to ESA call for mission concepts for its Cosmic Vision 2015–2025 plan, we propose a mission called Darwin. Its primary goal is the study of terrestrial extrasolar planets and the search for life on them. In this paper, we describe different characteristics of the instrument