Altered Ecosystem Nitrogen Dynamics as a Consequence of Land Cover Change in Tallgrass Prairie

ABSTRACT.-Inre cent decades, substantial areas of North American tallgrass prairie have been lost to the establishment and expansion of woodlands and forests, including those dominated by eastern redcedar (Juniperus virginiana). This shift in dominant plant life form, from C4 grasses to coniferous trees, may be accompanied by changes in productivity, standing stocks of biomass and nutrients and biogeochemical cycles. The goal of this study was to quantify and compare major pools and fluxes of nitrogen in recently established (5 80 y) redcedar forests and adjacent native grasslands. Three former grassland sites in the Flint Hills region of Kansas that developed closed-canopy redcedar forests in the recent past were paired with adjacent grassland sites on similar soil type and topographic position (n = 3 sites/land cover type), and selected soil and plant nitrogen pools and fluxes were measured in replicate plots (n = 6/site) along transects in each forest or grassland site over a 20-mo period. We found few significant differences in median soil inorganic N pools or net N mineralization rates between the forest and grassland sites, though there was a trend for greater concentrations of inorganic N in grassland sites on most sample dates, and cumulative growing season net N mineralization averaged 15% less in forest sites (14.3 kg N-ha-1\u27yr-1) than in grassland sites (16.9 kg N-ha-\u27.yr-1). Mean aboveground plant productivity of forest sites (9162 kg ha-1 yr-1) was about 2.5X greater than that of comparable grasslands (similar soils and topographic position), in spite of similar levels of soil N availability. This resulted in an ecosystem-level nitrogen use efficiency (ANPP:litterfall N) in forests that was more than double that of the grasslands they replaced. Additional changes in N cycling associated with redcedar forest development included large accumulations of N in aboveground biomass and transfer to the forest floor via litterfall; redcedar aboveground biomass contained 617 kg N/ ha, forest floor litter N was 253 kg N/ha, and litterfall N flux was 41 kg ha-l\u27yr-1. These are substantial increases in aboveground biomass N accumulation, surface litter N inputs, and surface litter N accumulation compared to the native grasslands characteristic of this region. These fundamental shifts in ecosystem patterns and processes have the potential to alter regional biogeochemistry and both nitrogen and carbon storage throughout areas of the eastern Central Plains where coverage of redcedars is increasing

Cdc53p acts in concert with Cdc4p and Cdc34p to control the G1 to S phase transition and identifies a conserved family of proteins

Regulation of cell cycle progression occurs in part through the targeted degradation of both activating and inhibitory subunits of the cyclin-dependent kinases. During G1, CDC4, encoding a WD-40 repeat protein, and CDC34, encoding a ubiquitin-conjugating enzyme, are involved in the destruction of these regulators. Here we describe evidence indicating that CDC53 also is involved in this process. Mutations in CDC53 cause a phenotype indistinguishable from those of cdc4 and cdc34 mutations, numerous genetic interactions are seen between these genes, and the encoded proteins are found physically associated in vivo. Cdc53p defines a large family of proteins found in yeasts, nematodes, and humans whose molecular functions are uncharacterized. These results suggest a role for this family of proteins in regulating cell cycle proliferation through protein degradation

The role of ecotypic variation and the environment on biomass and nitrogen in a dominant prairie grass

Citation: Mendola, M. L., Baer, S. G., Johnson, L. C., & Maricle, B. R. (2015). The role of ecotypic variation and the environment on biomass and nitrogen in a dominant prairie grass. Ecology, 96(9), 2433-2445. doi:10.1890/14-1492.1Knowledge of the relative strength of evolution and the environment on a phenotype is required to predict species responses to environmental change and decide where to source plant material for ecological restoration. This information is critically needed for dominant species that largely determine the productivity of the central U.S. grassland. We established a reciprocal common garden experiment across a longitudinal gradient to test whether ecotypic variation interacts with the environment to affect growth and nitrogen (N) storage in a dominant grass. We predicted plant growth would increase from west to east, corresponding with increasing precipitation, but differentially among ecotypes due to local adaptation in all ecotypes and a greater range of growth response in ecotypes originating from west to east. We quantified aboveground biomass, root biomass, belowground net primary production (BNPP), root C:N ratio, and N storage in roots of three ecotypes of Andropogon gerardii collected from and reciprocally planted in central Kansas, eastern Kansas, and southern Illinois. Only the ecotype from the most mesic region (southern Illinois) exhibited more growth from west to east. There was evidence for local adaptation in the southern Illinois ecotype by means of the local vs. foreign contrast within a site and the home vs. away contrast when growth in southern Illinois was compared to the most distant site in central Kansas. Root biomass of the eastern Kansas ecotype was higher at home than at either away site. The ecotype from the driest region, central Kansas, exhibited the least response across the environmental gradient, resulting in a positive relationship between the range of biomass response and precipitation in ecotype region of origin. Across all sites, ecotypes varied in root C: N ratio (highest in the driest-origin ecotype) and N storage in roots (highest in the most mesic-origin ecotype). The low and limited range of biomass, higher C: N ratio of roots, and lower N storage in the central Kansas ecotype relative to the southern Illinois ecotype suggests that introducing ecotypes of A. gerardii from much drier regions into highly mesic prairie would reduce productivity and alter belowground ecosystem processes under a wide range of conditions

Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii

Citation: Raithel, S., Johnson, L., Galliart, M., Brown, S., Shelton, J., Herndon, N., & Bello, N. M. (2016). Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii. Bmc Genomics, 17, 16. doi:10.1186/s12864-016-2442-7Background: Differential expression (DE) analysis of RNA-seq data still poses inferential challenges, such as handling of transcripts characterized by low expression levels. In this study, we use a plasmode-based approach to assess the relative performance of alternative inferential strategies on RNA-seq transcripts, with special emphasis on transcripts characterized by a small number of read counts, so-called low-count transcripts, as motivated by an ecological application in prairie grasses. Big bluestem (Andropogon gerardii) is a wide-ranging dominant prairie grass of ecological and agricultural importance to the US Midwest while edaphic subspecies sand bluestem (A. gerardii ssp. Hallii) grows exclusively on sand dunes. Relative to big bluestem, sand bluestem exhibits qualitative phenotypic divergence consistent with enhanced drought tolerance, plausibly associated with transcripts of low expression levels. Our dataset consists of RNA-seq read counts for 25,582 transcripts (60 % of which are classified as low-count) collected from leaf tissue of individual plants of big bluestem (n = 4) and sand bluestem (n = 4). Focused on low-count transcripts, we compare alternative ad-hoc data filtering techniques commonly used in RNA-seq pipelines and assess the inferential performance of recently developed statistical methods for DE analysis, namely DESeq2 and edgeR robust. These methods attempt to overcome the inherently noisy behavior of low-count transcripts by either shrinkage or differential weighting of observations, respectively. Results: Both DE methods seemed to properly control family-wise type 1 error on low-count transcripts, whereas edgeR robust showed greater power and DESeq2 showed greater precision and accuracy. However, specification of the degree of freedom parameter under edgeR robust had a non-trivial impact on inference and should be handled carefully. When properly specified, both DE methods showed overall promising inferential performance on low-count transcripts, suggesting that ad-hoc data filtering steps at arbitrary expression thresholds may be unnecessary. A note of caution is in order regarding the approximate nature of DE tests under both methods. Conclusions: Practical recommendations for DE inference are provided when low-count RNA-seq transcripts are of interest, as is the case in the comparison of subspecies of bluestem grasses. Insights from this study may also be relevant to other applications focused on transcripts of low expression levels

Revising Neutrino Oscillation Parameter Space With Direct Flavor-Changing Interactions

We formulate direct, neutrino flavor-changing interactions in a framework that fits smoothly with the parameterization of two-and three-state mixing of massive neutrino states. We show that even small direct interaction strengths could have important consequences for the interpretation of currently running and proposed oscillation experiments. The oscillation amplitude and the borders of the allowed regions in two-and three-flavor mixing parameter space can be sensitieve to the presence of direct interactions when the transition probability is small. We use extensively the high sensitivity of the NOMAD experiment to illustrate potentially large effects from small, direct flavor violation. In the purely leptonic sector, we find that the clean muon neutrino and electron neutrino beams from a muon collider could provide the sharpest tests of direct flavor violation.Comment: 16 pages, 10 figure

Altered hippocampal epigenetic regulation underlying reduced cognitive development in response to early life environmental insults

The hippocampus is involved in learning and memory and undergoes significant growth and maturation during the neonatal period. Environmental insults during this developmental timeframe can have lasting effects on brain structure and function. This study assessed hippocampal DNA methylation and gene transcription from two independent studies reporting reduced cognitive development stemming from early life environmental insults (iron deficiency and porcine reproductive and respiratory syndrome virus (PRRSv) infection) using porcine biomedical models. In total, 420 differentially expressed genes (DEGs) were identified between the reduced cognition and control groups, including genes involved in neurodevelopment and function. Gene ontology (GO) terms enriched for DEGs were associated with immune responses, angiogenesis, and cellular development. In addition, 116 differentially methylated regions (DMRs) were identified, which overlapped 125 genes. While no GO terms were enriched for genes overlapping DMRs, many of these genes are known to be involved in neurodevelopment and function, angiogenesis, and immunity. The observed altered methylation and expression of genes involved in neurological function suggest reduced cognition in response to early life environmental insults is due to altered cholinergic signaling and calcium regulation. Finally, two DMRs overlapped with two DEGs, VWF and LRRC32, which are associated with blood brain barrier permeability and regulatory T-cell activation, respectively. These results support the role of altered hippocampal DNA methylation and gene expression in early life environmentally-induced reductions in cognitive development across independent studies.</p

Extending Sensitivity for Low-Mass Neutral Heavy Lepton Searches

We point out the importance of two-body final states of weak isosinglet neutral heavy leptons predicted in several models of new physics beyond the standard model. We concentrate on muon-type neutral heavy leptons $L_\mu^0$ with mass $M<2$ GeV which can be searched for with increased sensitivity at a new round of neutrino experiments at CERN and Fermilab. Providing explicit decay rate formulae for the $e e \nu$, $e\mu \nu$, $\mu \mu \nu$, $\pi \mu$, $\rho \mu$, and $a_1\mu$ final states, we use general scaling features to estimate sensitivity of $L_\mu^0$ searches in current and future experiments, emphasizing the importance of the $\pi \mu$ decay mode.Comment: 14 pages, 8 figure

Pulse‐labeling studies of carbon cycling in arctic tundra ecosystems: Contribution of photosynthates to soil organic matter

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95486/1/gbc827.pd

"I know that you know that I know": neural substrates associated with social cognition deficits in DM1 patients

Myotonic dystrophy type-1 (DM1) is a genetic multi-systemic disorder involving several organs including the brain. Despite the heterogeneity of this condition, some patients with non-congenital DM1 can present with minimal cognitive impairment on formal testing but with severe difficulties in daily-living activities including social interactions. One explanation for this paradoxical mismatch can be found in patients' dysfunctional social cognition, which can be assessed in the framework of the Theory of Mind (ToM). We hypothesize here that specific disease driven abnormalities in DM1 brains may result in ToM impairments. We recruited 20 DM1 patients who underwent the "Reading the Mind in the Eyes" and the ToM-story tests. These patients, together with 18 healthy controls, also underwent resting-state functional MRI. A composite Theory of Mind score was computed for all recruited patients and correlated with their brain functional connectivity. This analysis provided the patients' "Theory of Mind-network", which was compared, for its topological properties, with that of healthy controls. We found that DM1 patients showed deficits in both tests assessing ToM. These deficits were associated with specific patterns of abnormal connectivity between the left inferior temporal and fronto-cerebellar nodes in DM1 brains. The results confirm the previous suggestions of ToM dysfunctions in patients with DM1 and support the hypothesis that difficulties in social interactions and personal relationships are a direct consequence of brain abnormalities, and not a reaction symptom. This is relevant not only for a better pathophysiological comprehension of DM1, but also for non-pharmacological interventions to improve clinical aspects and impact on patients' success in life