Soil Microbial Dynamics and Biogeochemistry in Tropical Forests and Pastures, Southwestern Costa Rica

Tropical rain forest ecosystems are currently undergoing unprecedented rates of land conversion and land use change. Recent research suggests these activities profoundly influence nutrient cycling, but the principal mechanisms driving variation in nutrient status following land conversion are still not well understood. In this study, we used soils of varying fertility (oxisols and mollisols) in Costa Rica to investigate how conversion of tropical rain forest to cattle pasture affects the size and function of the microbial community, and to explore possible relationships between microbial dynamics and biogeochemistry. Our pasture sites are relatively lightly managed, and total pools of carbon (C), nitrogen (N), and phosphorus (P) were not significantly different from their forest counterparts. However, pools of available elements were different; most notably, plant available forms of P were significantly lower in the oxisol pasture than in the oxisol forest site. In addition, we found that land conversion led to fundamental changes in the size and activity of the soil microbial community. Microbial biomass was consistently higher in forests than in pastures, particularly in the oxisol sites, where it was more than twice the pasture value. Forest sites were also characterized by a microbial community that was more active, responded more rapidly to carbon substrate additions, and showed strong seasonal variation. Our results provide evidence that changes in biogeochemical cycling following land conversion observed here and elsewhere may be directly related to changes in microbial community structure and function

Growth of Nanocrystalline MoSe2 Monolayers on Epitaxial Graphene from Amorphous Precursors

A new approach to the growth of MoSe2 thin films on epitaxial graphene on SiC(0001) by the use of modulated elemental reactants (MER) precursors has been reported. The synthesis applies a two-step process, where first an amorphous precursor is deposited on the substrate which self-assembles upon annealing. Films with a nominal thickness of about 1ML are successfully grown on epitaxial graphene monolayer as well as buffer layer samples. Characterization of the films is performed using XPS, LEED, AFM, and Raman spectroscopy. The films are nanocrystalline and show randomly rotated domains. This approach opens up an avenue to synthesize a number of new van-der-Waals systems on epitaxial graphene and other substrates

Two distinct modes for propagation of histone PTMs across the cell cycle

Epigenetic states defined by chromatin can be maintained through mitotic cell division. However, it remains unknown how histone-based information is transmitted. Here we combine nascent chromatin capture (NCC) and triple-SILAC (stable isotope labeling with amino acids in cell culture) labeling to track histone modifications and histone variants during DNA replication and across the cell cycle. We show that post-translational modifications (PTMs) are transmitted with parental histones to newly replicated DNA. Di- and trimethylation marks are diluted twofold upon DNA replication, as a consequence of new histone deposition. Importantly, within one cell cycle, all PTMs are restored. In general, new histones are modified to mirror the parental histones. However, H3K9 trimethylation (H3K9me3) and H3K27me3 are propagated by continuous modification of parental and new histones because the establishment of these marks extends over several cell generations. Together, our results reveal how histone marks propagate and demonstrate that chromatin states oscillate within the cell cycle

Forecasting the potential of weak lensing magnification to enhance LSST large-scale structure analyses

Recent works have shown that weak lensing magnification must be included in upcoming large-scale structure analyses, such as for the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST), to avoid biasing the cosmological results. In this work we investigate whether including magnification has a positive impact on the precision of the cosmological constraints, as well as being necessary to avoid bias. We forecast this using an LSST mock catalog and a halo model to calculate the galaxy power spectra. We find that including magnification has little effect on the precision of the cosmological parameter constraints for an LSST galaxy clustering analysis, where the halo model parameters are additionally constrained by the galaxy luminosity function. In particular, we find that for the LSST gold sample ($i < 25.3$) including weak lensing magnification only improves the galaxy clustering constraint on $\Omega_{\rm{m}}$ by a factor of 1.03, and when using a very deep LSST mock sample ($i<26.5$) by a factor of 1.3. Since magnification predominantly contributes to the clustering measurement and provides similar information to that of cosmic shear, this improvement would be reduced for a combined galaxy clustering and shear analysis. We also confirm that not modelling weak lensing magnification will catastrophically bias the cosmological results from LSST. Magnification must therefore be included in LSST large-scale structure analyses even though it does not significantly enhance the precision of the cosmological constraints.Comment: v2: Version accepted in MNRAS. Minor clarifications, conclusions unchange

Immunohistochemical characterization of bipolar cells in four distantly related avian species

Visual (and probably also magnetic) signal processing starts at the first synapse, at which photoreceptors contact different types of bipolar cells, thereby feeding information into different processing channels. In the chicken retina, 15 and 22 different bipolar cell types have been identified based on serial electron microscopy and single‐cell transcriptomics, respectively. However, immunohistochemical markers for avian bipolar cells were only anecdotally described so far. Here, we systematically tested 12 antibodies for their ability to label individual bipolar cells in the bird retina and compared the eight most suitable antibodies across distantly related species, namely domestic chicken, domestic pigeon, common buzzard, and European robin, and across retinal regions. While two markers (GNB3 and EGFR) labeled specifically ON bipolar cells, most markers labeled in addition to bipolar cells also other cell types in the avian retina. Staining pattern of four markers (CD15, PKCα, PKCβ, secretagogin) was species‐specific. Two markers (calbindin and secretagogin) showed a different expression pattern in central and peripheral retina. For the chicken and European robin, we found slightly more ON bipolar cell somata in the inner nuclear layer than OFF bipolar cell somata. In contrast, OFF bipolar cells made more ribbon synapses than ON bipolar cells in the inner plexiform layer of these species. Finally, we also analyzed the photoreceptor connectivity of selected bipolar cell types in the European robin retina. In summary, we provide a catalog of bipolar cell markers for different bird species, which will greatly facilitate analyzing the retinal circuitry of birds on a larger scale

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7. Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000 quasar spectra (g<22) will constrain BAO over the redshift range 2.15<z<3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyman alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance D_A to an accuracy of 1.0% at redshifts z=0.3 and z=0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyman alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D_A(z) and H^{-1}(z) parameters to an accuracy of 1.9% at z~2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.Comment: 49 pages, 16 figures, accepted by A

The Eighth Data Release of the Sloan Digital Sky Survey: First Data from SDSS-III

The Sloan Digital Sky Survey (SDSS) started a new phase in August 2008, with new instrumentation and new surveys focused on Galactic structure and chemical evolution, measurements of the baryon oscillation feature in the clustering of galaxies and the quasar Ly alpha forest, and a radial velocity search for planets around ~8000 stars. This paper describes the first data release of SDSS-III (and the eighth counting from the beginning of the SDSS). The release includes five-band imaging of roughly 5200 deg^2 in the Southern Galactic Cap, bringing the total footprint of the SDSS imaging to 14,555 deg^2, or over a third of the Celestial Sphere. All the imaging data have been reprocessed with an improved sky-subtraction algorithm and a final, self-consistent photometric recalibration and flat-field determination. This release also includes all data from the second phase of the Sloan Extension for Galactic Understanding and Evolution (SEGUE-2), consisting of spectroscopy of approximately 118,000 stars at both high and low Galactic latitudes. All the more than half a million stellar spectra obtained with the SDSS spectrograph have been reprocessed through an improved stellar parameters pipeline, which has better determination of metallicity for high metallicity stars.Comment: Astrophysical Journal Supplements, in press (minor updates from submitted version

The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey

The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T_eff<5000 K and in metallicity estimates for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SDSS-III Sloan Extension for Galactic Understanding and Exploration-2 (SEGUE-2). The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) along with another year of data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at http://www.sdss3.org/dr

Informed consent for MRI and fMRI research: Analysis of a sample of Canadian consent documents

<p>Abstract</p> <p>Background</p> <p>Research ethics and the measures deployed to ensure ethical oversight of research (e.g., informed consent forms, ethics review) are vested with extremely important ethical and practical goals. Accordingly, these measures need to function effectively in real-world research and to follow high level standards.</p> <p>Methods</p> <p>We examined approved consent forms for Magnetic Resonance Imaging (MRI) and functional Magnetic Resonance Imaging (fMRI) studies approved by Canadian research ethics boards (REBs).</p> <p>Results</p> <p>We found evidence of variability in consent forms in matters of physical and psychological risk reporting. Approaches used to tackle the emerging issue of incidental findings exposed extensive variability between and within research sites.</p> <p>Conclusion</p> <p>The causes of variability in approved consent forms and studies need to be better understood. However, mounting evidence of administrative and practical hurdles within current ethics governance systems combined with potential sub-optimal provision of information to and protection of research subjects support other calls for more scrutiny of research ethics practices and applicable revisions.</p