Plant Diversity, Soil Microbial Communities, And Ecosystem Function: Are There Any Links?

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/117152/1/ecy20038482042.pd

The Peaks Formalism and the Formation of Cold Dark Matter Haloes

We use two cosmological simulations of structure formation to study the conditions under which dark matter haloes emerge from the linear density field. Our analysis focuses on matching sites of halo collapse to local density maxima, or "peaks", in the initial conditions of the simulations and provides a crucial test of the central ansatz of the peaks formalism. By identifying peaks on a variety of smoothed, linearly extrapolated density fields we demonstrate that as many as ~70% of well-resolved dark matter haloes form preferentially near peaks whose characteristic masses are similar to that of the halo, with more massive haloes showing a stronger tendency to reside near peaks initially. We identify a small but significant fraction of haloes that appear to evolve from peaks of substantially lower mass than that of the halo itself. We refer to these as "peakless haloes" for convenience. By contrasting directly the properties of these objects with the bulk of the proto-halo population we find two clear differences: 1) their initial shapes are significantly flatter and more elongated than the predominantly triaxial majority, and 2) they are, on average, more strongly compressed by tidal forces associated with their surrounding large scale structure. Using the two-point correlation function we show that peakless haloes tend to emerge from highly clustered regions of the initial density field implying that, at fixed mass, the accretion geometry and mass accretion histories of haloes in highly clustered environments differ significantly from those in the field. This may have important implications for understanding the origin of the halo assembly bias, of galaxy properties in dense environments and how environment affects the morphological transformation of galaxies near groups and rich galaxy clusters.Comment: 13 pages, 11 figures, published in MNRA

The spatial and velocity bias of linear density peaks and proto-haloes in the Lambda cold dark matter cosmology

We use high resolution N-body simulations to investigate the Lagrangian bias of cold dark matter haloes within the LCDM cosmology. Our analysis focuses on "proto-haloes", which we identify in the simulation initial conditions with the subsets of particles belonging to individual redshift-zero haloes. We then calculate the number-density and velocity-divergence fields of proto-haloes and estimate their auto spectral densities. We also measure the corresponding cross spectral densities with the linear matter distribution. We use our results to test a Lagrangian-bias model presented by Desjacques and Sheth which is based on the assumption that haloes form out of local density maxima of a specific height. Our comparison validates the predicted functional form for the scale-dependence of the bias for both the density and velocity fields. We also show that the bias coefficients are accurately predicted for the velocity divergence. On the contrary, the theoretical values for the density bias parameters do not accurately match the numerical results as a function of halo mass. This is likely due to the simplistic assumptions that relate virialized haloes to density peaks of a given height in the model. We also detect appreciable stochasticity for the Lagrangian density bias, even on very large scales. These are not included in the model at leading order but correspond to higher order corrections.Comment: 10 pages, 4 figures. Matches version accepted for publication in MNRA

DETECTING AND QUANTIFYING REDUCTIVE DECHLORINATION DURING MONITORED NATURAL ATTENUATION AT THE SAVANNAH RIVER CBRP SITE

Various attenuation mechanisms control the destruction, stabilization, and/or removal of contaminants from contaminated subsurface systems. Measuring the rates of the controlling attenuation mechanisms is a key to employing mass balance as a means to evaluate and monitor the expansion, stability and subsequent shrinkage of a contaminant plume. A team of researchers investigated the use of push-pull tests for measuring reductive dechlorination rates in situ at sites with low chlorinated solvent concentrations (<1 ppm). The field research also examined the synergistic use of a suite of geochemical and microbial assays. Previous push-pull tests applied to environmental remediation objectives focused on general hydrological characterization or on designing bioremediation systems by examining the response of the subsurface to stimulation. In this research, the push-pull technique was tested to determine its ''low-range'' sensitivity and uncertainty. Can these tests quantify relatively low attenuation rates representative of natural attenuation? The results of this research indicate that push-pull testing will be useful for measurement of in situ reductive dechlorination rates for chlorinated solvents at ''Monitored Natural Attenuation'' (MNA) sites. Further, using principal component analysis and other techniques, the research confirmed the usefulness of multiple lines of evidence in site characterization and in upscaling measurements made in individual wells--especially for sites where there is a geochemical gradient or varying geochemical regimes within the contaminant plume

Myogenic progenitors contribute to open but not closed fracture repair

<p>Abstract</p> <p>Background</p> <p>Bone repair is dependent on the presence of osteocompetent progenitors that are able to differentiate and generate new bone. Muscle is found in close association with orthopaedic injury, however its capacity to make a cellular contribution to bone repair remains ambiguous. We hypothesized that myogenic cells of the MyoD-lineage are able to contribute to bone repair.</p> <p>Methods</p> <p>We employed a <it>MyoD</it>-Cre⁺:Z/AP⁺conditional reporter mouse in which all cells of the MyoD-lineage are permanently labeled with a <it>human alkaline phosphatase (hAP) </it>reporter. We tracked the contribution of MyoD-lineage cells in mouse models of tibial bone healing.</p> <p>Results</p> <p>In the absence of musculoskeletal trauma, MyoD-expressing cells are limited to skeletal muscle and the presence of reporter-positive cells in non-muscle tissues is negligible. In a closed tibial fracture model, there was no significant contribution of hAP⁺cells to the healing callus. In contrast, open tibial fractures featuring periosteal stripping and muscle fenestration had up to 50% of hAP⁺cells detected in the open fracture callus. At early stages of repair, many hAP⁺cells exhibited a chondrocyte morphology, with lesser numbers of osteoblast-like hAP⁺cells present at the later stages. Serial sections stained for hAP and type II and type I collagen showed that MyoD-lineage cells were surrounded by cartilaginous or bony matrix, suggestive of a functional role in the repair process. To exclude the prospect that osteoprogenitors spontaneously express MyoD during bone repair, we created a metaphyseal drill hole defect in the tibia. No hAP⁺staining was observed in this model suggesting that the expression of MyoD is not a normal event for endogenous osteoprogenitors.</p> <p>Conclusions</p> <p>These data document for the first time that muscle cells can play a significant secondary role in bone repair and this knowledge may lead to important translational applications in orthopaedic surgery.</p> <p>Please see related article: <url>http://www.biomedcentral.com/1741-7015/9/136</url></p

In Situ Microbial Community Control of the Stability of Bio-reduced Uranium

In aerobic aquifers typical of many Department of Energy (DOE) legacy waste sites, uranium is present in the oxidized U(VI) form which is more soluble and thus more mobile. Field experiments at the Old Rifle UMTRA site have demonstrated that biostimulation by electron donor addition (acetate) promotes biological U(VI) reduction (2). However, U(VI) reduction is reversible and oxidative dissolution of precipitated U(IV) after the cessation of electron donor addition remains a critical issue for the application of biostimulation as a treatment technology. Despite the potential for oxidative dissolution, field experiments at the Old Rifle site have shown that rapid reoxidation of bio-reduced uranium does not occur and U(VI) concentrations can remain at approximately 20% of background levels for more than one year. The extent of post-amendment U(VI) removal and the maintenance of bioreduced uranium may result from many factors including U(VI) sorption to iron-containing mineral phases, generation of H2S or FeS0.9, or the preferential sorption of U(VI) by microbial cells or biopolymers, but the processes controlling the reduction and in situ reoxidation rates are not known. To investigate the role of microbial community composition in the maintenance of bioreduced uranium, in-well sediment incubators (ISIs) were developed allowing field deployment of amended and native sediments during on-going experiments at the site. Field deployment of the ISIs allows expedient interrogation of microbial community response to field environmental perturbations and varying geochemical conditions

Galaxy And Mass Assembly (GAMA): stellar mass estimates

This paper describes the first catalogue of photometrically derived stellar mass estimates for intermediate-redshift (z < 0.65; median z= 0.2) galaxies in the Galaxy And Mass Assembly (GAMA) spectroscopic redshift survey. These masses, as well as the full set of ancillary stellar population parameters, will be made public as part of GAMA data release 2. Although the GAMA database does include near-infrared (NIR) photometry, we show that the quality of our stellar population synthesis fits is significantly poorer when these NIR data are included. Further, for a large fraction of galaxies, the stellar population parameters inferred from the optical-plus-NIR photometry are formally inconsistent with those inferred from the optical data alone. This may indicate problems in our stellar population library, or NIR data issues, or both; these issues will be addressed for future versions of the catalogue. For now, we have chosen to base our stellar mass estimates on optical photometry only. In light of our decision to ignore the available NIR data, we examine how well stellar mass can be constrained based on optical data alone. We use generic properties of stellar population synthesis models to demonstrate that restframe colour alone is in principle a very good estimator of stellar mass-to-light ratio, M*/Li. Further, we use the observed relation between restframe (g−i) and M*/Li for real GAMA galaxies to argue that, modulo uncertainties in the stellar evolution models themselves, (g−i) colour can in practice be used to estimate M*/Li to an accuracy of ≲0.1 dex (1σ). This ‘empirically calibrated' (g−i)-M*/Li relation offers a simple and transparent means for estimating galaxies' stellar masses based on minimal data, and so provides a solid basis for other surveys to compare their results to z≲0.4 measurements from GAM

Galaxy and Mass Assembly: FUV, NUV, ugrizYJHK Petrosian, Kron and Sérsic photometry

In order to generate credible 0.1-2 μm spectral energy distributions, the Galaxy and Mass Assembly (GAMA) project requires many gigabytes of imaging data from a number of instruments to be reprocessed into a standard format. In this paper, we discuss the software infrastructure we use, and create self-consistent ugrizYJHK photometry for all sources within the GAMA sample. Using UKIDSS and SDSS archive data, we outline the pre-processing necessary to standardize all images to a common zero-point, the steps taken to correct for the seeing bias across the data set and the creation of gigapixel-scale mosaics of the three 4 × 12 deg2 GAMA regions in each filter. From these mosaics, we extract source catalogues for the GAMA regions using elliptical Kron and Petrosian matched apertures. We also calculate Sérsic magnitudes for all galaxies within the GAMA sample using sigma, a galaxy component modelling wrapper for galfit 3. We compare the resultant photometry directly and also calculate the r-band galaxy luminosity function for all photometric data sets to highlight the uncertainty introduced by the photometric method. We find that (1) changing the object detection threshold has a minor effect on the best-fitting Schechter parameters of the overall population (M*± 0.055 mag, α± 0.014, ϕ*± 0.0005 h3 Mpc−3); (2) there is an offset between data sets that use Kron or Petrosian photometry, regardless of the filter; (3) the decision to use circular or elliptical apertures causes an offset in M* of 0.20 mag; (4) the best-fitting Schechter parameters from total-magnitude photometric systems (such as SDSS modelmag or Sérsic magnitudes) have a steeper faint-end slope than photometric systems based upon Kron or Petrosian measurements; and (5) our Universe's total luminosity density, when calculated using Kron or Petrosian r-band photometry, is underestimated by at least 15 per cen

TERT promoter mutations are highly recurrent in SHH subgroup medulloblastoma

Telomerase reverse transcriptase (TERT) promoter mutations were recently shown to drive telomerase activity in various cancer types, including medulloblastoma. However, the clinical and biological implications of TERT mutations in medulloblastoma have not been described. Hence, we sought to describe these mutations and their impact in a subgroup-specific manner. We analyzed the TERT promoter by direct sequencing and genotyping in 466 medulloblastomas. The mutational distributions were determined according to subgroup affiliation, demographics, and clinical, prognostic, and molecular features. Integrated genomics approaches were used to identify specific somatic copy number alterations in TERT promoter-mutated and wild-type tumors. Overall, TERT promoter mutations were identified in 21 % of medulloblastomas. Strikingly, the highest frequencies of TERT mutations were observed in SHH (83 %; 55/66) and WNT (31 %; 4/13) medulloblastomas derived from adult patients. Group 3 and Group 4 harbored this alteration in <5 % of cases and showed no association wit