Optimizing a PCR protocol for cpn60-based microbiome profiling of samples variously contaminated with host genomic DNA.

The current recommended protocol for chaperonin-60 (cpn60) universal target based microbiome profiling includes universal PCR of microbiome samples across an annealing temperature gradient to maximize the diversity of sequences amplified. However, the value of including this gradient approach has not been formally evaluated since the optimization of a modified universal PCR primer cocktail for cpn60 PCR. PCR conditions that maximize representation of the microbiome while minimizing PCR-associated distortion of the community structure, especially in samples containing large amounts of host genomic DNA are critical. The goal of this study was to measure the effects of PCR annealing temperature and the ratio of host to bacterial DNA on the outcome of microbiota analysis, using pig microbiota as a model environment.Six samples were chosen with an anticipated range of ratios of pig to bacterial genomic DNA, and universal cpn60 PCR amplification with an annealing temperature gradient was used to create libraries for pyrosequencing, resulting in 426,477 sequences from the six samples. The sequences obtained were classified as target (cpn60) or non-target based on the percent identity of their closest match to the cpnDB reference database, and target sequences were further processed to create microbiome profiles for each sample at each annealing temperature. Annealing temperature affected the amount of PCR product generated, with more product generated at higher temperatures. Samples containing proportionally more host genomic DNA yielded more non-target reads, especially at lower annealing temperatures. However, microbiome composition for each sample across the annealing temperature gradient remained consistent at both the phylum and operational taxonomic unit levels. Although some microbial sequences were detected at only one annealing temperature, these sequences accounted for a minority of the total microbiome.These results indicate that PCR annealing temperature does have an affect on cpn60 based microbiome profiles, but that most of the differences are due to differences in detection of low abundance sequences. Higher annealing temperatures resulted in larger amounts of PCR product and lower amounts of non-target sequence amplification, especially in samples containing proportionally large amounts of host DNA. Taken together these results provide important information to guide decisions about experimental design for cpn60 based microbiome studies

Phylogeny Of Lampridiform Fishes

A survey of characters defining the Neoteleostei, Eurypterygii, Ctenosquamata, Acanthomorpha, Paracanthopterygii and Acanthopterygii convincingly places the Lampridiformes within the acanthomorph clade. Lampridiforms are primitive with respect to the Percomorpha but their precise placement among basal acanthomorphs remains unclear. In the absence of a specific sister-group hypothesis, Polymixia, percopsiform and beryciform taxa were used as outgroups in a cladistic analysis of the order. Monophyly of Lampridiformes is supported by four apomorphies; three are correlated modifications related to the evolution of a unique feeding mechanism in which the maxilla slides forward with the premaxilla during jaw protrusion. The Veliferidae are the sister group of all other lampridiforms. The deep-bodied (bathysomous) lampridiforms are not monophyletic because Lampris is the sister group of the elongate (taeniosomous) families. Stylephorus is placed as the sister group of all other taeniosomous families. The Radiicephalidae are hypothesized to be the sister group of the Lophotidae, a clade that forms the sister group of the Replecidae + Trachipteridae. Ateleopodid, mirapinnid, and eutaeniiophorid fishes are not lampridiforms. DaggerBajaichthys is allied with living lampridiform fishes but daggerPharmacichthys is not a lampridiform. The affinities of daggerAipichthys and daggerBathysomous are unknown

Numerical Calculations of Acoustic Emission

A computer program [1] which solves the partial differential equations for sound propagation numerically is applied to the study of problems in acoustic emission. The program uses finite difference techniques to calculate sound fields due to distributions of sources in complex geometries in two dimensions. The potential to handle more complex geometries and to model more realistic sources is the main advantage of this type of calculation over the analytic calculations. The main disadvantage of the numerical technique is the cost of obtaining results since a large main frame computer or supercomputer is required

A new neolepadid cirripede from a Pleistocene cold seep, Krishna-Godavari Basin, offshore India

Valves of a thoracican cirripede belonging to a new species of the Neolepadidae, Ashinkailepas indica Gale sp. nov. are described from a Late Pleistocene cold seep (52.6 ka), cored in the Krishna-Godavari Basin, offshore from the eastern coast of India. This constitutes the first fossil record of the genus, and its first occurrence in the Indian Ocean. Other fossil records of the Neolepadidae (here elevated to full family status) are discussed, and it is concluded that only Stipilepas molerensis from the Eocene of Denmark, is correctly referred to the family. Cladistic analysis of the Neolepadidae supports a basal position for Ashinkailepas, as deduced independently from molecular studies, and the Lower Cretaceous brachylepadid genus Pedupycnolepas is identified as sister taxon to Neolepadidae. Neolepadids are not Mesozoic relics as claimed, preserved in association with the highly specialised environments of cold seeps and hydrothermal vents, but are rather an early Cenozoic offshoot from the clade which also gave rise to the sessile cirripedes

A NITROGEN-ENRICHED NEBULA AROUND P-CYGNI

We have detected extended nebular emission in [S II]λλ6716,6731, [N II] λ6584,6584andHα on a long-slit spectrum offset by 9 arcsec from P Cyg. Anomalously strong [Ni II]λ6666.8 emission was also detected. The [S II] doublet ratio yields an electron density of 600 cm–3. The [N II] and [S II] lines have been used to derive an N/S ratio which is insensitive to the adopted value of electron temperature. The N/S ratio is 33 ± 5 by number, five times higher than solar, implying that the material has undergone CN-cycle processing which has converted most of the original carbon into nitrogen

Direct electronic measurement of the spin Hall effect

The generation, manipulation and detection of spin-polarized electrons in nanostructures define the main challenges of spin-based electronics[1]. Amongst the different approaches for spin generation and manipulation, spin-orbit coupling, which couples the spin of an electron to its momentum, is attracting considerable interest. In a spin-orbit-coupled system, a nonzero spin-current is predicted in a direction perpendicular to the applied electric field, giving rise to a "spin Hall effect"[2-4]. Consistent with this effect, electrically-induced spin polarization was recently detected by optical techniques at the edges of a semiconductor channel[5] and in two-dimensional electron gases in semiconductor heterostructures[6,7]. Here we report electrical measurements of the spin-Hall effect in a diffusive metallic conductor, using a ferromagnetic electrode in combination with a tunnel barrier to inject a spin-polarized current. In our devices, we observe an induced voltage that results exclusively from the conversion of the injected spin current into charge imbalance through the spin Hall effect. Such a voltage is proportional to the component of the injected spins that is perpendicular to the plane defined by the spin current direction and the voltage probes. These experiments reveal opportunities for efficient spin detection without the need for magnetic materials, which could lead to useful spintronics devices that integrate information processing and data storage.Comment: 5 pages, 4 figures. Accepted for publication in Nature (pending format approval

Dynamics of Fundamental Matter in N=2* Yang-Mills Theory

We study the dynamics of quenched fundamental matter in $\mathcal{N}=2^\ast$ supersymmetric large $N$ SU(N) Yang-Mills theory at zero temperature. Our tools for this study are probe D7-branes in the holographically dual $\mathcal{N}=2^\ast$ Pilch-Warner gravitational background. Previous work using D3-brane probes of this geometry has shown that it captures the physics of a special slice of the Coulomb branch moduli space of the gauge theory, where the $N$ constituent D3-branes form a dense one dimensional locus known as the enhancon, located deep in the infrared. Our present work shows how this physics is supplemented by the physics of dynamical flavours, revealed by the D7-branes embeddings we find. The Pilch-Warner background introduces new divergences into the D7-branes free energy, which we are able to remove with a single counterterm. We find a family of D7-brane embeddings in the geometry and discuss their properties. We study the physics of the quark condensate, constituent quark mass, and part of the meson spectrum. Notably, there is a special zero mass embedding that ends on the enhancon, which shows that while the geometry acts repulsively on the D7-branes, it does not do so in a way that produces spontaneous chiral symmetry breaking.Comment: 24 pages, 8 figures. Corrected typos, added comment about counterterm. To appear in JHE

Correlated physical and mental health summary scores for the SF-36 and SF-12 Health Survey, V.1

<p>Abstract</p> <p>Background</p> <p>The SF-36 and SF-12 summary scores were derived using an uncorrelated (orthogonal) factor solution. We estimate SF-36 and SF-12 summary scores using a correlated (oblique) physical and mental health factor model.</p> <p>Methods</p> <p>We administered the SF-36 to 7,093 patients who received medical care from an independent association of 48 physician groups in the western United States. Correlated physical health (PCS_c) and mental health (MCS_c) scores were constructed by multiplying each SF-36 scale z-score by its respective scoring coefficient from the obliquely rotated two factor solution. PCS_c-12 and MCS_c-12 scores were estimated using an approach similar to the one used to derive the original SF-12 summary scores.</p> <p>Results</p> <p>The estimated correlation between SF-36 PCS_cand MCS_cscores was 0.62. There were far fewer negative factor scoring coefficients for the oblique factor solution compared to the factor scoring coefficients produced by the standard orthogonal factor solution. Similar results were found for PCS_c-12, and MCS_c-12 summary scores.</p> <p>Conclusion</p> <p>Correlated physical and mental health summary scores for the SF-36 and SF-12 derived from an obliquely rotated factor solution should be used along with the uncorrelated summary scores. The new scoring algorithm can reduce inconsistent results between the SF-36 scale scores and physical and mental health summary scores reported in some prior studies.</p> <p>(Subscripts C = correlated and UC = uncorrelated)</p

Clinical applications and limitations of current ovarian stem cell research: a review

The publication of a report in Nature in 2004 by the Tilly group suggesting that mouse ovaries are capable of generating oocytes de novo post-natally, has sparked interest in a problem long thought to have been resolved from classical studies in a variety of mammalian species. Within a nearly two year time period, laboratories around the world have taken up the challenge to dogma raised by this initial report, either to test this concept in an experimental basic science setting or give direction to clinical applications that could result, were the original premises of this work in the mouse valid for extrapolation to humans. This review provides a status report for this promising area of research, (1) to summarize recent findings in the literature with respect to the validity of the original hypothesis proffered by the Tilly group, and, (2) to gauge the potential utility of ovarian stem cells as a treatment for certain forms of human infertility