Multi‐century stasis in C3 and C4 grass distributions across the contiguous United States since the industrial revolution

AimsUnderstanding the functional response of ecosystems to past global change is crucial to predicting performance in future environments. One sensitive and functionally significant attribute of grassland ecosystems is the percentage of species that use the C4 versus C3 photosynthetic pathway. Grasses using C3 and C4 pathways are expected to have different responses to many aspects of anthropogenic environmental change that have followed the industrial revolution, including increases in temperature and atmospheric CO2, changes to land management and fire regimes, precipitation seasonality, and nitrogen deposition. In spite of dramatic environmental changes over the past 300 years, it is unknown if the C4 grass percentage in grasslands has shifted.LocationContiguous United States of America.MethodsHere, we used stable carbon isotope data (i.e. δ13C) from 30 years of soil samples, as well as herbivore tissues that date to 1739 CE, to reconstruct coarse‐grain C3 and C4 grass composition in North American grassland sites to compare with modern vegetation. We spatially resampled these three datasets to a shared 100‐km grid, allowing comparison of δ13C values at a resolution and extent common for climate model outputs and biogeographical studies.ResultsAt this spatial grain, the bison tissue proxy was superior to the soil proxy because the soils reflect integration of local carbon inputs, whereas bison sample vegetation across landscapes. Bison isotope values indicate that historical grassland photosynthetic‐type composition was similar to modern vegetation.Main conclusionsDespite major environmental change, comparing modern plot vegetation data to three centuries of bison δ13C data revealed that the biogeographical distribution of C3 and C4 grasses has not changed significantly since the 1700s. This is particularly surprising given the expected CO2 fertilization of C3 grasses. Our findings highlight the critical importance of capturing the full range of physiological, ecological and demographical processes in biosphere models predicting future climates and ecosystems.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/139065/1/jbi13061.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139065/2/jbi13061_am.pd

Assessing earth system model predictions of C-4 grass cover in North America: From the glacial era to the end of this century

Aim C-4 grasses are distinct from C-3 grasses, because C-4 grasses respond in a different manner to light, temperature, CO2 and nitrogen and often have higher resource-use efficiencies. C-3 and C-4 grasses are typically represented in earth system models (ESMs) by different plant functional types (PFTs). The ability of ESMs to capture C-4 grass biogeography and ecology across differing time periods is important to assess, given the crucial role they play in ecosystems and their divergent responses to global change. Location North America. Time periods Last Glacial Maximum (LGM), historical modern period (ca. 1850) and end of this century. Major taxa studied C-4 grasses. Methods Proxy data representing relative cover and productivity of C-4 grasses were collated, including carbon isotope ratios of soil carbon and animal grazer tissue, and vegetation plot data in undisturbed grasslands. We selected available model predictions of C-4 PFT percentage cover. Models were compared against one another and assessed against proxy data at key time points: the LGM, the historical modern period before widespread grassland conversion to agriculture, and the end of this century. Results We highlight large differences among model predictions of percentage C-4 grass cover across North America: all pairwise combinations have correlations < .5, and most are < .2. Models also do not capture spatial patterns of the percentage C-4 grass cover from proxy data, during either the LGM or the historical modern period. Models generally under-predict percentage C-4 grass cover, particularly during the historical modern period. Main conclusions Earth system models do not accurately represent the biogeography of C-4 grasses across a range of time-scales, and their outputs do not agree with one another. We suggest model improvements to represent this crucial functional type better, including more collection and greater integration of C-3 and C-4 grass trait data, explicit representations of tree-grass competition for water, and a greater focus on disturbance ecology

Targeted redox inhibition of protein phosphatase 1 by Nox4 regulates eIF2a-mediated stress signaling

Source: doi: 10.15252/embj.201592394Phosphorylation of translation initiation factor 2α (eIF2α) attenuates global protein synthesis but enhances translation of activating transcription factor 4 (ATF4) and is a crucial evolutionarily conserved adaptive pathway during cellular stresses. The serine–threonine protein phosphatase 1 (PP1) deactivates this pathway whereas prolonging eIF2α phosphorylation enhances cell survival. Here, we show that the reactive oxygen species‐generating NADPH oxidase‐4 (Nox4) is induced downstream of ATF4, binds to a PP1‐targeting subunit GADD34 at the endoplasmic reticulum, and inhibits PP1 activity to increase eIF2α phosphorylation and ATF4 levels. Other PP1 targets distant from the endoplasmic reticulum are unaffected, indicating a spatially confined inhibition of the phosphatase. PP1 inhibition involves metal center oxidation rather than the thiol oxidation that underlies redox inhibition of protein tyrosine phosphatases. We show that this Nox4‐regulated pathway robustly enhances cell survival and has a physiologic role in heart ischemia–reperfusion and acute kidney injury. This work uncovers a novel redox signaling pathway, involving Nox4–GADD34 interaction and a targeted oxidative inactivation of the PP1 metal center, that sustains eIF2α phosphorylation to protect tissues under stress

The wavelength dependence of interstellar polarization in the Local Hot Bubble

The properties of dust in the interstellar medium (ISM) nearest the Sun are poorly understood because the low column densities of dust toward nearby stars induce little photometric reddening, rendering the grains largely undetectable. Stellar polarimetry offers one pathway to deducing the properties of this diffuse material. Here we present multi-wavelength aperture polarimetry measurements of seven bright stars chosen to probe interstellar polarization near the edge of the Local Hot Bubble (LHB) – an amorphous region of relatively low-density interstellar gas and dust extending ∼70–150 pc from the Sun. The measurements were taken using the HIgh Precision Polarimetric Instrument (HIPPI) on the 3.9-m Anglo-Australian Telescope. HIPPI is an aperture stellar polarimeter with a demonstrated sensitivity of 4.3 parts-per-million (ppm). Of the stars observed two are polarized to a much greater degree than the others; they have a wavelength of maximum polarization (λmax) of ∼550 ± 20 nm – similar to that of stars beyond the LHB – and we conclude that they are in the wall of the LHB. The remaining five stars have polarizations of ∼70–160 ppm, of these four have a much bluer λmax, ∼350 ± 50 nm. Bluer values of λmax may indicate grains shocked during the evolution of the Loop I Superbubble. The remaining star, HD 4150 is not well fit by a Serkowski curve, and may be intrinsically polarized.JPM acknowledges research support by the Ministry of Science and Technology of Taiwan under grants MOST104-2628-M-001-004-MY3 and MOST107-2119-M-001-031-MY3, and Academia Sinica grant AS-IA-106-M03

Whence the interstellar magnetic field shaping the heliosphere?

Measurements of starlight polarized by aligned interstellar dust grains are used to probe the relation between the orientation of the ambient interstellar magnetic field (ISMF) and the ISMF traced by the ribbons of energetic neutral atoms discovered by the Interstellar Boundary Explorer spacecraft. We utilize polarization data, many acquired specifically for this study, to trace the configuration of the ISMF within 40 pc. A statistical analysis yields a best-fit ISMF orientation, B (magpol), aligned with Galactic coordinates l = 42 degrees, b = 49 degrees. Further analysis shows the ISMF is more orderly for "downfield" stars located over 90 degrees from B (magpol). The data subset of downfield stars yields an orientation for the nearby ISMF at ecliptic coordinates lambda, beta approximate to 219 degrees +/- 15 degrees, 43 degrees +/- 9 degrees (Galactic coordinates l, b approximate to 40 degrees, 56 degrees, +/- 17 degrees). This best-fit ISMF orientation from polarization data is close to the field direction obtained from ribbon models. This agreement suggests that the ISMF shaping the heliosphere belongs to an extended ordered magnetic field. Extended filamentary structures are found throughout the sky. A previously discovered filament traversing the heliosphere nose region, "Filament A," extends over 300 degrees of the sky, and crosses the upwind direction of interstellar dust flowing into the heliosphere. Filament A overlaps the locations of the Voyager kilohertz emissions, three quasar intraday variables, cosmic microwave background (CMB) components, and the inflow direction of interstellar grains sampled by Ulysses and Galileo. These features are likely located in the upstream outer heliosheath where ISMF drapes over the heliosphere, suggesting Filament A coincides with a dusty magnetized plasma. A filament 55 degrees long is aligned with a possible shock interface between local interstellar clouds. A dark spot in the CMB is seen within 5 degrees of the filament and within 10 degrees of the downfield ISMF direction. Two large magnetic arcs are centered on the directions of the heliotail. The overlap between CMB components and the aligned dust grains forming Filament A indicates the configuration of dust entrained in the ISMF interacting with the heliosphere provides a measurable foreground to the CMB

Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana-exposed to more than a decade of regular ivermectin treatment-have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread.Pooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR.This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT) whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic drift rather than genetic selection of SOR is the underlying driver of population differentiation, which has significant implications for the emergence and potential spread of SOR within and between these parasite populations

Chapter 11: Challenges in and Principles for Conducting Systematic Reviews of Genetic Tests used as Predictive Indicators

In this paper, we discuss common challenges in and principles for conducting systematic reviews of genetic tests. The types of genetic tests discussed are those used to 1). determine risk or susceptibility in asymptomatic individuals; 2). reveal prognostic information to guide clinical management in those with a condition; or 3). predict response to treatments or environmental factors. This paper is not intended to provide comprehensive guidance on evaluating all genetic tests. Rather, it focuses on issues that have been of particular concern to analysts and stakeholders and on areas that are of particular relevance for the evaluation of studies of genetic tests. The key points include:The general principles that apply in evaluating genetic tests are similar to those for other prognostic or predictive tests, but there are differences in how the principles need to be applied or the degree to which certain issues are relevant.A clear definition of the clinical scenario and an analytic framework is important when evaluating any test, including genetic tests.Organizing frameworks and analytic frameworks are useful constructs for approaching the evaluation of genetic tests.In constructing an analytic framework for evaluating a genetic test, analysts should consider preanalytic, analytic, and postanalytic factors; such factors are useful when assessing analytic validity.Predictive genetic tests are generally characterized by a delayed time between testing and clinically important events.Finding published information on the analytic validity of some genetic tests may be difficult. Web sites (FDA or diagnostic companies) and gray literature may be important sources.In situations where clinical factors associated with risk are well characterized, comparative effectiveness reviews should assess the added value of using genetic testing along with known factors compared with using the known factors alone.For genome-wide association studies, reviewers should determine whether the association has been validated in multiple studies to minimize both potential confounding and publication bias. In addition, reviewers should note whether appropriate adjustments for multiple comparisons were used

Gel mobility shift scanning of pectin-inducible promoter from Penicillium griseoroseum reveals the involvement of a CCAAT element in the expression of a polygalacturonase gene

Previous reports have described pgg2, a polygalacturonase-encoding gene of Penicillium griseoroseum, as an attractive model for transcriptional regulation studies, due to its high expression throughout several in vitro growth conditions, even in the presence of non-inducing sugars such as sucrose. A search for regulatory motifs in the 5' upstream regulatory sequence of pgg2 identified a putative CCAAT box that could justify this expression profile. This element, located 270 bp upstream of the translational start codon, was tested as binding target for regulatory proteins. Analysis of a 170 bp promoter fragment by electrophoretic mobility shift assay (EMSA) with nuclear extracts prepared from mycelia grown in pectin-containing culture medium revealed a high mobility complex that was subsequently confirmed by analyzing it with a double-stranded oligonucleotide spanning the CCAAT motif. A substitution in the core sequence for GTAGG partially abolished the formation of specific complexes, showing the involvement of the CCAAT box in the regulation of the polygalacturonase gene studied