Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance

BACKGROUND: Molecular and genomic surveillance is becoming increasingly used to track malaria control and elimination efforts. Blood samples can be collected as whole blood and stored at - 20 degrees C until DNA extraction, or as dried blood spots (DBS), circumventing the need for a cold chain. Despite the wide use of either method, systematic comparisons of how the method of blood sample preservation affects the limit of detection (LOD) of molecular diagnosis and the proportion of DNA recovered for downstream applications are lacking. METHODS: Extractions based on spin columns, magnetic beads, Tween-Chelex, and direct PCR without prior extraction were compared for whole blood and dried blood spots (DBS) using dilution series of Plasmodium falciparum culture samples. Extracted DNA was quantified by qPCR and droplet digital PCR (ddPCR). RESULTS: DNA recovery was 5- to 10-fold higher for whole blood compared to DBS, resulting in a 2- to 3-fold lower LOD for both extraction methods compared to DBS. For whole blood, a magnetic bead-based method resulted in a DNA recovery rate of 88-98% when extracting from whole blood compared to 17-33% for a spin-column based method. For extractions from DBS, the magnetic bead-based method resulted in 8-20% DNA recovery, while the spin-column based method resulted in only 2% DNA recovery. The Tween-Chelex method was superior to other methods with 15-21% DNA recovery, and even more sensitive than extractions from whole blood samples. The direct PCR method was found to have the lowest LOD overall for both, whole blood and DBS. CONCLUSIONS: Pronounced differences in LOD and DNA yield need to be considered when comparing prevalence estimates based on molecular methods and when selecting sampling protocols for other molecular surveillance applications

A Measurement of Newton's Gravitational Constant

A precision measurement of the gravitational constant $G$ has been made using a beam balance. Special attention has been given to determining the calibration, the effect of a possible nonlinearity of the balance and the zero-point variation of the balance. The equipment, the measurements and the analysis are described in detail. The value obtained for G is 6.674252(109)(54) 10^{-11} m3 kg-1 s-2. The relative statistical and systematic uncertainties of this result are 16.3 10^{-6} and 8.1 10^{-6}, respectively.Comment: 26 pages, 20 figures, Accepted for publication by Phys. Rev.

Obtaining the equation of motion for a fermionic particle in a generalized Lorentz-violating system framework

Using a generalized procedure for obtaining the dispersion relation and the equation of motion for a propagating fermionic particle, we examine previous claims for a preferred axis at $n_{\mu}$($\equiv(1,0,0,1)$), $n^{2}=0$ embedded in the framework of very special relativity (VSR). We show that, in a relatively high energy scale, the corresponding equation of motion is reduced to a conserving lepton number chiral equation previously predicted in the literature. Otherwise, in a relatively low energy scale, the equation is reduced to the usual Dirac equation for a free propagating fermionic particle. It is accomplished by the suggestive analysis of some special cases where a nonlinear modification of the action of the Lorentz group is generated by the addition of a modified conformal transformation which, meanwhile, preserves the structure of the ordinary Lorentz algebra in a very peculiar way. Some feasible experiments, for which Lorentz violating effects here pointed out may be detectable, are suggested.Comment: 10 page

A scheme with two large extra dimensions confronted with neutrino physics

We investigate a particle physics model in a six-dimensional spacetime, where two extra dimensions form a torus. Particles with Standard Model charges are confined by interactions with a scalar field to four four-dimensional branes, two vortices accommodating ordinary type fermions and two antivortices accommodating mirror fermions. We investigate the phenomenological implications of this multibrane structure by confronting the model with neutrino physics data.Comment: LATEX, 24 pages, 9 figures, minor changes in the tex

Observation of two time scales in the ferromagnetic manganite La(1-x)Ca(x)MnO(3), x = 0.3

We report new zero-field muon spin relaxation and neutron spin echo measurements in ferromagnetic (FM) (La,Ca)MnO3 which taken together suggest two spatially separated regions in close proximity possessing very different Mn-ion spin dynamics. One region corresponds to an extended cluster which displays 'critical slowing down' near Tc and an increasing volume fraction below Tc. The second region possesses more slowly fluctuating spins and a decreasing volume fraction below Tc. These data are discussed in terms of the growth of small polarons into overlapping regions of correlated spins below Tc, resulting in a microscopically inhomogeneous FM transition.Comment: 10 pages, 3 figure

Muon Spin Relaxation Study of (La, Ca)MnO3

We report predominantly zero field muon spin relaxation measurements in a series of Ca-doped LaMnO_3 compounds which includes the colossal magnetoresistive manganites. Our principal result is a systematic study of the spin-lattice relaxation rates 1/T_1 and magnetic order parameters in the series La_{1-x}Ca_xMnO_3, x = 0.0, 0.06, 0.18, 0.33, 0.67 and 1.0. In LaMnO_3 and CaMnO_3 we find very narrow critical regions near the Neel temperatures T_N and temperature independent 1/T_1 values above T_N. From the 1/T_1 in LaMnO_3 we derive an exchange integral J = 0.83 meV which is consistent with the mean field expression for T_N. All of the doped manganites except CaMnO_3 display anomalously slow, spatially inhomogeneous spin-lattice relaxation below their ordering temperatures. In the ferromagnetic (FM) insulating La_{0.82}Ca_{0.18}MnO_3 and ferromagnetic conducting La_{0.67}Ca_{0.33}MnO_3 systems we show that there exists a bi-modal distribution of \muSR rates \lambda_f and \lambda_s associated with relatively 'fast' and 'slow' Mn fluctuation rates, respectively. A physical picture is hypothesized for these FM phases in which the fast Mn rates are due to overdamped spin waves characteristic of a disordered FM, and the slower Mn relaxation rates derive from distinct, relatively insulating regions in the sample. Finally, likely muon sites are identified, and evidence for muon diffusion in these materials is discussed.Comment: 21 pages, 17 figure

Effects of habitat composition and landscape structure on worker foraging distances of five bumblebee species

Bumblebees (Bombus spp.) are important pollinators of both crops and wild flowers. Their contribution to this essential ecosystem service has been threatened over recent decades by changes in land use, which have led to declines in their populations. In order to design effective conservation measures it is important to understand the effects of variation in landscape composition and structure on the foraging activities of worker bumblebees. This is because the viability of individual colonies is likely to be affected by the trade-off between the energetic costs of foraging over greater distances and the potential gains from access to additional resources. We used field surveys, molecular genetics and fine resolution remote sensing to estimate the locations of wild bumblebee nests and to infer foraging distances across a 20 km2 agricultural landscape in southern England. We investigated five species, including the rare B. ruderatus and ecologically similar but widespread B. hortorum. We compared worker foraging distances between species and examined how variation in landscape composition and structure affected foraging distances at the colony level. Mean worker foraging distances differed significantly between species. Bombus terrestris, B. lapidarius and B. ruderatus exhibited significantly greater mean foraging distances (551 m, 536 m, 501 m, respectively) than B. hortorum and B. pascuorum (336 m, 272 m, respectively). There was wide variation in worker foraging distances between colonies of the same species, which was in turn strongly influenced by the amount and spatial configuration of available foraging habitats. Shorter foraging distances were found for colonies where the local landscape had high coverage and low fragmentation of semi-natural vegetation, including managed agri-environmental field margins. The strength of relationships between different landscape variables and foraging distance varied between species, for example the strongest relationship for B. ruderatus being with floral cover of preferred forage plants. Our findings suggest that favourable landscape composition and configuration has the potential to minimise foraging distances across a range of bumblebee species. There is thus potential for improvements in the design and implementation of landscape management options, such as agri-environment schemes, aimed at providing foraging habitat for bumblebees and enhancing crop pollination services