Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy

Aim To use parallel array pyrosequencing to deconvolute mixtures of mitochondrial DNA (mtDNA) sequence and provide high resolution analysis of mtDNA heteroplasmy. Methods The hypervariable segment 1 (HV1) of the mtDNA control region was analyzed from 30 individuals using the 454 GS Junior instrument. Mock mixtures were used to evaluate the system’s ability to deconvolute mixtures and to reliably detect heteroplasmy, including heteroplasmic differences between 5 family members of the same maternal lineage. Amplicon sequencing was performed on polymerase chain reaction (PCR) products generated with primers that included multiplex identifiers (MID) and adaptors for pyrosequencing. Data analysis was performed using NextGENe® software. The analysis of an autosomal short tandem repeat (STR) locus (D18S51) and a Y-STR locus (DYS389 I/II) was performed simultaneously with a portion of HV1 to illustrate that multiplexing can encompass different markers of forensic interest. Results Mixtures, including heteroplasmic variants, can be detected routinely down to a component ratio of 1:250 (20 minor variant copies with a coverage rate of 5000 sequences) and can be readily detected down to 1:1000 (0.1%) with expanded coverage. Amplicon sequences from D18S51, DYS389 I/II, and the second half of HV1 were successfully partitioned and analyzed. Conclusions The ability to routinely deconvolute mtDNA mixtures down to a level of 1:250 allows for high resolution analysis of mtDNA heteroplasmy, and for differentiation of individuals from the same maternal lineage. The pyrosequencing approach results in poor resolution of homopolymeric sequences, and PCR/sequencing artifacts require a filtering mechanism similar to that for STR stutter and spectral bleed through. In addition, chimeric sequences from jumping PCR must be addressed to make the method operational

Characterisation of an Advanced Nickel Based Superalloy Post Cold Work by Swaging

Cylindrical bars of the advanced nickel based superalloy RR1000 were subjected to swaging to induce approximately 30% cold work. Grain size analysis demonstrated a distinct modification to the microstructure whilst electron back scattered diffraction (EBSD) measurements confirmed the evolution of a relatively strong texture parallel with the longitudinal bar axis. Intragranular strain damage was identified. The effects of the swaging on bulk mechanical properties are illustrated across a range of test temperatures

Boson stars in massive dilatonic gravity

We study equilibrium configurations of boson stars in the framework of a class scalar-tensor theories of gravity with massive gravitational scalar (dilaton). In particular we investigate the influence of the mass of the dilaton on the boson star structure. We find that the masses of the boson stars in presence of dilaton are close to those in general relativity and they are sensitive to the ratio of the boson mass to the dilaton mass within a typical few percent. It turns out also that the boson star structure is mainly sensitive to the mass term of the dilaton potential rather to the exact form of the potential.Comment: 9 pages, latex, 9 figures, one figure dropped, new comments added, new references added, typos correcte

Rapid production of 87^{87}Rb BECs in a combined magnetic and optical potential

We describe an apparatus for quickly and simply producing \Rb87 Bose-Einstein condensates. It is based on a magnetic quadrupole trap and a red detuned optical dipole trap. We collect atoms in a magneto-optical trap (MOT) and then capture the atom in a magnetic quadrupole trap and force rf evaporation. We then transfer the resulting cold, dense cloud into a spatially mode-matched optical dipole trap by lowering the quadrupole field gradient to below gravity. This technique combines the efficient capture of atoms from a MOT into a magnetic trap with the rapid evaporation of optical dipole traps; the approach is insensitive to the peak quadrupole gradient and the precise trapping beam waist. Our system reliably produces a condensate with $N\approx2\times10^6$ atoms every 16\second

Thermal gradient-induced forces on geodetic reference masses for LISA

The low frequency sensitivity of space-borne gravitational wave observatories will depend critically on the geodetic purity of the trajectories of orbiting test masses. Fluctuations in the temperature difference across the enclosure surrounding the free-falling test mass can produce noisy forces through several processes, including the radiometric effect, radiation pressure, and outgassing. We present here a detailed experimental investigation of thermal gradient-induced forces for the LISA gravitational wave mission and the LISA Pathfinder, employing high resolution torsion pendulum measurements of the torque on a LISA-like test mass suspended inside a prototype of the LISA gravitational reference sensor that will surround the test mass in orbit. The measurement campaign, accompanied by numerical simulations of the radiometric and radiation pressure effects, allows a more accurate and representative characterization of thermal-gradient forces in the specific geometry and environment relevant to LISA free-fall. The pressure dependence of the measured torques allows clear identification of the radiometric effect, in quantitative agreement with the model developed. In the limit of zero gas pressure, the measurements are most likely dominated by outgassing, but at a low level that does not threaten the LISA sensitivity goals.Comment: 21 pages, 16 figures, submitted to Physical Review

The State of the World’s Urban Ecosystems: what can we learn from trees, fungi and bees?

Trees are a foundation for biodiversity in urban ecosystems and therefore must be able to withstand global change and biological challenges over decades and even centuries to prevent urban ecosystems from deteriorating. Tree quality and diversity should be prioritized over simply numbers to optimize resilience to these challenges. Successful establishment and renewal of trees in cities must also consider belowground (e.g., mycorrhizas) and aboveground (e.g., pollinators) interactions to ensure urban ecosystem longevity, biodiversity conservation and continued provision of the full range of ecosystem services provided by trees. Positive interactions with nature inspire people to live more sustainable lifestyles that are consistent with stopping biodiversity loss and to participate in conservation actions such as tree‐planting and supporting pollinators. Interacting with nature simultaneously provides mental and physical health benefits to people. Since most people live in cities, here we argue that urban ecosystems provide important opportunities for increasing engagement with nature and educating people about biodiversity conservation. While advocacy on biodiversity must communicate in language that is relevant to a diverse audience, over‐simplified messaging, may result in unintended negative outcomes. For example, tree planting actions typically focus on numbers rather than diversity while the call to save bees has inspired unsustainable proliferation of urban beekeeping that may damage wild bee conservation through increased competition for limited forage in cities and disease spread. Ultimately multiple ecosystem services must be considered (and measured) to optimize their delivery in urban ecosystems and messaging to promote the value of nature in cities must be made widely available and more clearly defined

Modified Brans-Dicke theory of gravity from five-dimensional vacuum

We investigate, in the context of five-dimensional (5D) Brans-Dicke theory of gravity, the idea that macroscopic matter configurations can be generated from pure vacuum in five dimensions, an approach first proposed in the framework of general relativity. We show that the 5D Brans-Dicke vacuum equations when reduced to four dimensions lead to a modified version of Brans-Dicke theory in four dimensions (4D). As an application of the formalism, we obtain two five-dimensional extensions of four-dimensional O'Hanlon and Tupper vacuum solution and show that they lead two different cosmological scenarios in 4D.Comment: 9 page

Self-similar cosmological solutions with a non-minimally coupled scalar field

We present self-similar cosmological solutions for a barotropic fluid plus scalar field with Brans-Dicke-type coupling to the spacetime curvature and an arbitrary power-law potential energy. We identify all the fixed points in the autonomous phase-plane, including a scaling solution where the fluid density scales with the scalar field's kinetic and potential energy. This is related by a conformal transformation to a scaling solution for a scalar field with exponential potential minimally coupled to the spacetime curvature, but non-minimally coupled to the barotropic fluid. Radiation is automatically decoupled from the scalar field, but energy transfer between the field and non-relativistic dark matter can lead to a change to an accelerated expansion at late times in the Einstein frame. The scalar field density can mimic a cosmological constant even for steep potentials in the strong coupling limit.Comment: 10 pages, 1 figure, revtex version to appear in Phys Rev D, references adde

Naked Singularity Formation In f(R) Gravity

We study the gravitational collapse of a star with barotropic equation of state $p=w\rho$ in the context of $f({\mathcal R})$ theories of gravity. Utilizing the metric formalism, we rewrite the field equations as those of Brans-Dicke theory with vanishing coupling parameter. By choosing the functionality of Ricci scalar as $f({\mathcal R})=\alpha{\mathcal R}^{m}$, we show that for an appropriate initial value of the energy density, if $\alpha$ and $m$ satisfy certain conditions, the resulting singularity would be naked, violating the cosmic censorship conjecture. These conditions are the ratio of the mass function to the area radius of the collapsing ball, negativity of the effective pressure, and the time behavior of the Kretschmann scalar. Also, as long as parameter $\alpha$ obeys certain conditions, the satisfaction of the weak energy condition is guaranteed by the collapsing configuration.Comment: 15 pages, 4 figures, to appear in GR