The Rain Forests of Home: an Atlas of People and Place

pdf contains 31 page

Using biosolids to enhance phytoremediation of oil-contaminated soil

While the plant rhizosphere and associated microbial processes have been shown to amplify the degradation rate of chemical residues in soils, phytoremediation can be a slow process. The objective of this greenhouse study was to determine if the addition of biosolids as an organic soil amendment would enhance growth of plants in oil-contaminated soil and thus potentially increase effectiveness of phytoremediation. Pearl millet (Pennisetum glaucum (L.) R. Br.) or sudangrass (Sorghum sudanense (Piper) Stapf (Piper)) was grown in a Captina silt loam (finesilty, siliceous, mesic Typic Fragiudults) contaminated with 5% crude oil (v/w) and amended with 24 g biosolids/kg soil. Addition of biosolids enhanced oil degradation after 10 weeks as indicated by the lower carbon (C) content in the oil-contaminated soil that was amended with biosolids compared to the C content of the oil-contaminated soil only. The addition of biosolids to the oil-contaminated soil resulted in a significant increase in plant shoot biomass. Pearl millet plus biosolids produced more root biomass, root length, root surface area, and root diameter than sudangrass plus biosolids in the oil-contaminated soil. The addition of biosolids also increased the amount of nitrogen (N) and phosphorus (P) in the soil. The results suggest that the addition of biosolids could increase potential for remediation of oil-contaminated soil

Ultrafast Spin Density Wave Transition in Chromium Governed by Thermalized Electron Gas

The energy and momentum selectivity of time- and angle-resolved photoemission spectroscopy is exploited to address the ultrafast dynamics of the antiferromagnetic spin density wave (SDW) transition photoexcited in epitaxial thin films of chromium. We are able to quantitatively extract the evolution of the SDW order parameter Δ through the ultrafast phase transition and show that Δ is governed by the transient temperature of the thermalized electron gas, in a mean field description. The complete destruction of SDW order on a sub-100 fs time scale is observed, much faster than for conventional charge density wave materials. Our results reveal that equilibrium concepts for phase transitions such as the order parameter may be utilized even in the strongly nonadiabatic regime of ultrafast photoexcitation

Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus

BACKGROUND: The interpandemic evolution of the influenza A virus hemagglutinin (HA) protein is commonly considered a paragon of rapid evolutionary change under positive selection in which amino acid replacements are fixed by virtue of their effect on antigenicity, enabling the virus to evade immune surveillance. RESULTS: We performed phylogenetic analyses of the recently obtained large and relatively unbiased samples of the HA sequences from 1995–2005 isolates of the H3N2 and H1N1 subtypes of influenza A virus. Unexpectedly, it was found that the evolution of H3N2 HA includes long intervals of generally neutral sequence evolution without apparent substantial antigenic change ("stasis" periods) that are characterized by an excess of synonymous over nonsynonymous substitutions per site, lack of association of amino acid replacements with epitope regions, and slow extinction of coexisting virus lineages. These long periods of stasis are punctuated by shorter intervals of rapid evolution under positive selection during which new dominant lineages quickly displace previously coexisting ones. The preponderance of positive selection during intervals of rapid evolution is supported by the dramatic excess of amino acid replacements in the epitope regions of HA compared to replacements in the rest of the HA molecule. In contrast, the stasis intervals showed a much more uniform distribution of replacements over the HA molecule, with a statistically significant difference in the rate of synonymous over nonsynonymous substitution in the epitope regions between the two modes of evolution. A number of parallel amino acid replacements – the same amino acid substitution occurring independently in different lineages – were also detected in H3N2 HA. These parallel mutations were, largely, associated with periods of rapid fitness change, indicating that there are major limitations on evolutionary pathways during antigenic change. The finding that stasis is the prevailing modality of H3N2 evolution suggests that antigenic changes that lead to an increase in fitness typically result from epistatic interactions between several amino acid substitutions in the HA and, perhaps, other viral proteins. The strains that become dominant due to increased fitness emerge from low frequency strains thanks to the last amino acid replacement that completes the set of replacements required to produce a significant antigenic change; no subset of substitutions results in a biologically significant antigenic change and corresponding fitness increase. In contrast to H3N2, no clear intervals of evolution under positive selection were detected for the H1N1 HA during the same time span. Thus, the ascendancy of H1N1 in some seasons is, most likely, caused by the drop in the relative fitness of the previously prevailing H3N2 lineages as the fraction of susceptible hosts decreases during the stasis intervals. CONCLUSION: We show that the common view of the evolution of influenza virus as a rapid, positive selection-driven process is, at best, incomplete. Rather, the interpandemic evolution of influenza appears to consist of extended intervals of stasis, which are characterized by neutral sequence evolution, punctuated by shorter intervals of rapid fitness increase when evolutionary change is driven by positive selection. These observations have implications for influenza surveillance and vaccine formulation; in particular, the possibility exists that parallel amino acid replacements could serve as a predictor of new dominant strains. REVIEWERS: Ron Fouchier (nominated by Andrey Rzhetsky), David Krakauer, Christopher Le

Separating the influence of temperature, drought, and fire on interannual variability in atmospheric CO 2

The response of the carbon cycle in prognostic Earth system models (ESMs) contributes significant uncertainty to projections of global climate change. Quantifying contributions of known drivers of interannual variability in the growth rate of atmospheric carbon dioxide (CO 2 ) is important for improving the representation of terrestrial ecosystem processes in these ESMs. Several recent studies have identified the temperature dependence of tropical net ecosystem exchange (NEE) as a primary driver of this variability by analyzing a single, globally averaged time series of CO 2 anomalies. Here we examined how the temporal evolution of CO 2 in different latitude bands may be used to separate contributions from temperature stress, drought stress, and fire emissions to CO 2 variability. We developed atmospheric CO 2 patterns from each of these mechanisms during 1997–2011 using an atmospheric transport model. NEE responses to temperature, NEE responses to drought, and fire emissions all contributed significantly to CO 2 variability in each latitude band, suggesting that no single mechanism was the dominant driver. We found that the sum of drought and fire contributions to CO 2 variability exceeded direct NEE responses to temperature in both the Northern and Southern Hemispheres. Additional sensitivity tests revealed that these contributions are masked by temporal and spatial smoothing of CO 2 observations. Accounting for fires, the sensitivity of tropical NEE to temperature stress decreased by 25% to 2.9 ± 0.4 Pg C yr −1  K −1 . These results underscore the need for accurate attribution of the drivers of CO 2 variability prior to using contemporary observations to constrain long‐term ESM responses. Key Points Accurate attribution of CO 2 variability is required to constrain coupled models Combined influence of drought and fire exceed ecosystem responses to temperature Temporal and spatial smoothing of CO 2 observations masks variability from firePeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/109962/1/gbc20215.pd

Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918

The H1N1 subtype of influenza A virus has caused substantial morbidity and mortality in humans, first documented in the global pandemic of 1918 and continuing to the present day. Despite this disease burden, the evolutionary history of the A/H1N1 virus is not well understood, particularly whether there is a virological basis for several notable epidemics of unusual severity in the 1940s and 1950s. Using a data set of 71 representative complete genome sequences sampled between 1918 and 2006, we show that segmental reassortment has played an important role in the genomic evolution of A/H1N1 since 1918. Specifically, we demonstrate that an A/H1N1 isolate from the 1947 epidemic acquired novel PB2 and HA genes through intra-subtype reassortment, which may explain the abrupt antigenic evolution of this virus. Similarly, the 1951 influenza epidemic may also have been associated with reassortant A/H1N1 viruses. Intra-subtype reassortment therefore appears to be a more important process in the evolution and epidemiology of H1N1 influenza A virus than previously realized

Correlations between life-detection techniques and implications for sampling site selection in planetary analog missions

We conducted an analog sampling expedition under simulated mission constraints to areas dominated by basaltic tephra of the Eldfell and Fimmvörðuháls lava fields (Iceland). Sites were selected to be “homogeneous” at a coarse remote sensing resolution (10–100 m) in apparent color, morphology, moisture, and grain size, with best-effort realism in numbers of locations and replicates. Three different biomarker assays (counting of nucleic-acid-stained cells via fluorescent microscopy, a luciferin/luciferase assay for adenosine triphosphate, and quantitative polymerase chain reaction (qPCR) to detect DNA associated with bacteria, archaea, and fungi) were characterized at four nested spatial scales (1 m, 10 m, 100 m, and >1 km) by using five common metrics for sample site representativeness (sample mean variance, group F tests, pairwise t tests, and the distribution-free rank sum H and u tests). Correlations between all assays were characterized with Spearman's rank test. The bioluminescence assay showed the most variance across the sites, followed by qPCR for bacterial and archaeal DNA; these results could not be considered representative at the finest resolution tested (1 m). Cell concentration and fungal DNA also had significant local variation, but they were homogeneous over scales of >1 km. These results show that the selection of life detection assays and the number, distribution, and location of sampling sites in a low biomass environment with limited a priori characterization can yield both contrasting and complementary results, and that their interdependence must be given due consideration to maximize science return in future biomarker sampling expeditions

Galaxy Zoo: Passive Red Spirals

We study the spectroscopic properties and environments of red spiral galaxies found by the Galaxy Zoo project. By carefully selecting face-on, disk dominated spirals we construct a sample of truly passive disks (not dust reddened, nor dominated by old stellar populations in a bulge). As such, our red spirals represent an interesting set of possible transition objects between normal blue spirals and red early types. We use SDSS data to investigate the physical processes which could have turned these objects red without disturbing their morphology. Red spirals prefer intermediate density regimes, however there are no obvious correlations between red spiral properties and environment - environment alone is not sufficient to determine if a spiral will become red. Red spirals are a small fraction of spirals at low masses, but are a significant fraction at large stellar masses - massive galaxies are red independent of morphology. We confirm that red spirals have older stellar popns and less recent star formation than the main spiral population. While the presence of spiral arms suggests that major star formation cannot have ceased long ago, we show that these are not recent post-starbursts, so star formation must have ceased gradually. Intriguingly, red spirals are ~4 times more likely than normal spirals to host optically identified Seyfert or LINER, with most of the difference coming from LINERs. We find a curiously large bar fraction in the red spirals suggesting that the cessation of star formation and bar instabilities are strongly correlated. We conclude by discussing the possible origins. We suggest they may represent the very oldest spiral galaxies which have already used up their reserves of gas - probably aided by strangulation, and perhaps bar instabilities moving material around in the disk.Comment: MNRAS in press, 20 pages, 15 figures (v3