Flow cytometry for enrichment and titration in massively parallel DNA sequencing

Massively parallel DNA sequencing is revolutionizing genomics research throughout the life sciences. However, the reagent costs and labor requirements in current sequencing protocols are still substantial, although improvements are continuously being made. Here, we demonstrate an effective alternative to existing sample titration protocols for the Roche/454 system using Fluorescence Activated Cell Sorting (FACS) technology to determine the optimal DNA-to-bead ratio prior to large-scale sequencing. Our method, which eliminates the need for the costly pilot sequencing of samples during titration is capable of rapidly providing accurate DNA-to-bead ratios that are not biased by the quantification and sedimentation steps included in current protocols. Moreover, we demonstrate that FACS sorting can be readily used to highly enrich fractions of beads carrying template DNA, with near total elimination of empty beads and no downstream sacrifice of DNA sequencing quality. Automated enrichment by FACS is a simple approach to obtain pure samples for bead-based sequencing systems, and offers an efficient, low-cost alternative to current enrichment protocols

High Spatial Resolution Studies of Epithermal Neutron Emission from the Lunar Poles: Constraints on Hydrogen Mobility

The data from the collimated sensors of the LEND instrument are shown to be of exceptionally high quality. Counting uncertainties are about 0.3% relative and are shown to be the only significant source of random error, thus conclusions based on small differences in count rates are valid. By comparison with the topography of Shoemaker crater, the spatial resolution of the instrument is shown to be consistent with the design value of 5 km for the radius of the circle over which half the counts from the lunar surface would be determined. The observed epithermal-neutron suppression factor due to the hydrogen deposit in Shoemaker crater of 0.25 plus or minus 0.04 cps is consistent with the collimated field-of-view rate of 1.7 cps estimated by Mitrofanov et al. (2010a). The statistical significance of the neutron suppressed regions (NSRs) relative to the larger surrounding polar region is demonstrated, and it is shown that they are not closely related to the permanently shadowed regions. There is a significant increase in H content in the polar regions independent of the H content of the NSRs. The non-NSR H content increases directly with latitude, and the rate of increase is virtually identical at both poles. There is little or no increase with latitude outside the polar region. Various mechanisms to explain this steep increase in the non-NSR polar H with latitude are investigated, and it is suggested that thermal volatilization is responsible for the increase because it is minimized at the low surface temperatures close to the poles

Global Maps of Lunar Neutron Fluxes from the LEND Instrument

The latest neutron spectrometer measurements with the Lunar Exploration Neutron Detector (LEND) onboard the Lunar Reconnaissance Orbiter (LRO) are presented. It covers more than 1 year of mapping phase starting on 15 September 2009. In our analyses we have created global maps showing regional variations in the flux of thermal (energy range 0.5 MeV), and compared these fluxes to variances in soil elemental composition, and with previous results obtained by the Lunar Prospector Neutron Spectrometer (LPNS). We also processed data from LEND collimated detectors and derived a value for the collimated signal of epithermal neutrons based on the comparative analysis with the LEND omnidirectional detectors. Finally, we have compared our final (after the data reduction) global epithermal neutron map with LPNS data

Testing Lunar Permanently Shadowed Regions for Water Ice: LEND Results from LRO

We use measurements from the Lunar Exploration Neutron Detector (LEND) collimated sensors during more than one year of the mapping phase of NASA's Lunar Reconnaissance Orbiter (LRO) mission to make estimates of the epithermal neutron flux within known large Permanently Shadowed Regions (PSRs). These are compared with the local neutron background measured outside PSRs in sunlit regions. Individual and collective analyses of PSR properties have been performed. Only three large PSRs, Shoemaker and Cabeus in the south and Rozhdestvensky U in the north, have been found to manifest significant neutron suppression. All other PSRs have much smaller suppression, only a few percent, if at all. Some even display an excess of neutron emission in comparison to the sunlit vicinity around them. Testing PSRs collectively, we have not found any average suppression for them. Only the group of 18 large PSRs, with area >200 square kilometers, show a marginal effect of small average suppression, approx. 2%, with low statistical confidence. An approx. 2% suppression corresponds to approx. 125 ppm of hydrogen taking into account the global neutron suppression near the lunar poles and assuming a homogeneous H distribution in depth in the regolith. This means that all PSRs, except those in Shoemaker, Cabeus and Rozhdestvensky U craters, do not contain any significant amount of hydrogen in comparison with sunlit areas around them at the same latitude

Topographically Induced Thermal Effects on Lunar Hydrogen Distributions: Correlated Observations from the LRO LEND and LOLA Instruments

The question of whether water exists on the Moon's surface has long been an enigma to Lunar researchers. Largely, this was due to the thermally extreme lunar surface environment that would seem to preclude any long term maintenance, manufacture, transport or accumulation of hydrogen (H) volatiles over most of the lunar surface. As a result, for many years the cold permanent shadow regions (PSR) in the bottoms of craters near the lunar poles appeared to provide the basic conditions at least for maintenance of lunar hydrogen. Importantly, recent discoveries indicate that there is some hydrogen at the poles. However, the picture of the lunar hydrogen budget may be more complex than the PSR hypothesis has suggested. This evidence comes from observations by the Lunar Exploration Neutron Detector (LEND) onboard the Lunar Reconnaissance Orbiter (LRO) that inclici1te 1) some H concentrations lie outside PSR and 2) though a few of the larger PSR's have high hydrogen, PSR does not appear to be an independent factor influencing the large-scale suppression of polar epithermals observed by LEND and the Lunar Prospector Neutron Spectrometer. In this research we investigate the possibility that the thermal contrast between pole-facing and equator facing-slopes is a factor influencing the surface distributions of lunar H. We perform this bulk correlated observation and study by developing a thermal proxy from slope data of the Lunar Orbiting Laser Altimeter (LOLA) digital elevation model (DEM) which is registered with the collimated LEND epithermal map. From the LOLA transforms we impose a thermal functional decomposition and systematic statistical analysis of the LEND epithermal map. Our hypothesis testing suggests in most high latitude bands studied> +/- 45 deg: Epithermal rates in pole-facing slopes are significantly lower than epithermal rates in equivalent equator-facing slopes. As a control study, we find that there is no statistically significant difference between equivalent east and west facing slopes. This finding suggests topographic modulation of insolation is a factor influencing the lunar H budget. Importantly, this result is consistent with observations in terrestrial, Martian research

Thermoregulation of foraging honeybees on flowering plants: seasonal variability and influence of radiative heat gain

1. During nectar and pollen foraging in a temperate climate, honeybees are exposed to a broad range of ambient temperatures, challenging their thermoregulatory ability. The body temperature that the bees exhibit results from endothermic heat production, exogenous heat gain from solar radiation, and heat loss. In addition to profitability of foraging, season was suggested to have a considerable influence on thermoregulation. To assess the relative importance of these factors, the thermoregulatory behaviour of foragers on 33 flowering plants in dependence on season and environmental factors was investigated

Asteroids' physical models from combined dense and sparse photometry and scaling of the YORP effect by the observed obliquity distribution

The larger number of models of asteroid shapes and their rotational states derived by the lightcurve inversion give us better insight into both the nature of individual objects and the whole asteroid population. With a larger statistical sample we can study the physical properties of asteroid populations, such as main-belt asteroids or individual asteroid families, in more detail. Shape models can also be used in combination with other types of observational data (IR, adaptive optics images, stellar occultations), e.g., to determine sizes and thermal properties. We use all available photometric data of asteroids to derive their physical models by the lightcurve inversion method and compare the observed pole latitude distributions of all asteroids with known convex shape models with the simulated pole latitude distributions. We used classical dense photometric lightcurves from several sources and sparse-in-time photometry from the U.S. Naval Observatory in Flagstaff, Catalina Sky Survey, and La Palma surveys (IAU codes 689, 703, 950) in the lightcurve inversion method to determine asteroid convex models and their rotational states. We also extended a simple dynamical model for the spin evolution of asteroids used in our previous paper. We present 119 new asteroid models derived from combined dense and sparse-in-time photometry. We discuss the reliability of asteroid shape models derived only from Catalina Sky Survey data (IAU code 703) and present 20 such models. By using different values for a scaling parameter cYORP (corresponds to the magnitude of the YORP momentum) in the dynamical model for the spin evolution and by comparing synthetics and observed pole-latitude distributions, we were able to constrain the typical values of the cYORP parameter as between 0.05 and 0.6.Comment: Accepted for publication in A&A, January 15, 201

Mayday SeaSight: Combined Analysis of Deep Sequencing and Microarray Data

Recently emerged deep sequencing technologies offer new high-throughput methods to quantify gene expression, epigenetic modifications and DNA-protein binding. From a computational point of view, the data is very different from that produced by the already established microarray technology, providing a new perspective on the samples under study and complementing microarray gene expression data. Software offering the integrated analysis of data from different technologies is of growing importance as new data emerge in systems biology studies. Mayday is an extensible platform for visual data exploration and interactive analysis and provides many methods for dissecting complex transcriptome datasets. We present Mayday SeaSight, an extension that allows to integrate data from different platforms such as deep sequencing and microarrays. It offers methods for computing expression values from mapped reads and raw microarray data, background correction and normalization and linking microarray probes to genomic coordinates. It is now possible to use Mayday's wealth of methods to analyze sequencing data and to combine data from different technologies in one analysis

Spectroscopic survey of Kepler stars. I. HERMES/Mercator observations of A- and F-type stars

The Kepler space mission provided near-continuous and high-precision photometry of about 207 000 stars, which can be used for asteroseismology. However, for successful seismic modeling it is equally important to have accurate stellar physical parameters. Therefore, supplementary ground-based data are needed. We report the results of the analysis of high-resolution spectroscopic data of A- and F-type stars from the Kepler field, which were obtained with the HERMES spectrograph on the Mercator telescope. We determined spectral types, atmospheric parameters and chemical abundances for a sample of 117 stars. Hydrogen Balmer, Fe i, and Fe ii lines were used to derive effective temperatures, surface gravities, and microturbulent velocities. We determined chemical abundances and projected rotational velocities using a spectrum synthesis technique. The atmospheric parameters obtained were compared with those from the Kepler Input Catalogue (KIC), confirming that the KIC effective temperatures are underestimated for A stars. Effective temperatures calculated by spectral energy distribution fitting are in good agreement with those determined from the spectral line analysis. The analysed sample comprises stars with approximately solar chemical abundances, as well as chemically peculiar stars of the Am, Ap, and λ Boo types. The distribution of the projected rotational velocity, vsin i, is typical for A and F stars and ranges from 8 to about 280 km s−1, with a mean of 134 km s−1

Evidence for the Sequestration of Hydrogen-Bearing Volatiles Towards the Moons Southern Pole-Facing Slopes

The Lunar Exploration Neutron Detector (LEND) onboard the Lunar Reconnaissance Orbiter (LRO) detects a widespread suppression of the epithermal neutron leakage flux that is coincident with the pole-facing slopes (PFS) of the Moon's southern hemisphere. Suppression of the epithermal neutron flux is consistent with an interpretation of enhanced concentrations of hydrogen-bearing volatiles within the upper meter of the regolith. Localized flux suppression in PFS suggests that the reduced solar irradiation and lowered temperature on PFS constrains volatility to a greater extent than in surrounding regions. Epithermal neutron flux mapped with LEND's Collimated Sensor for Epithermal Neutrons (CSETN) was analyzed as a function of slope geomorphology derived from the Lunar Orbiting Laser Altimeter (LOLA) and the results compared to co-registered maps of diurnally averaged temperature from the Diviner Lunar Radiometer Experiment and an averaged illumination map derived from LOLA. The suppression in the average south polar epithermal neutron flux on equator-facing slopes (EFS) and PFS (85-90 deg S) is 3.3 +/- 0.04% and 4.3 +/- 0.05% respectively (one-sigma-uncertainties), relative to the average count-rate in the latitude band 45-90 deg S. The discrepancy of 1.0 +/- 0.06% between EFS and PFS neutron flux corresponds to an average of approximately 23 parts-per-million-by-weight (ppmw) more hydrogen on PFS than on EFS. Results show that the detection of hydrogen concentrations on PFS is dependent on their spatial scale. Epithermal flux suppression on large scale PFS was found to be enhanced to 5.2 +/- 0.13%, a discrepancy of approximately 45 ppmw hydrogen relative to equivalent EFS. Enhanced poleward hydration of PFS begins between 50 deg S and 60 deg S latitude. Polar regolith temperature contrasts do not explain the suppression of epithermal neutrons on pole-facing slopes. The Supplemental on-line materials include supporting results derived from the uncollimated Lunar Prospector Neutron Spectrometer and the LEND Sensor for Epithermal Neutrons