The word landscape of the non-coding segments of the Arabidopsis thaliana genome

<p>Abstract</p> <p>Background</p> <p>Genome sequences can be conceptualized as arrangements of motifs or words. The frequencies and positional distributions of these words within particular non-coding genomic segments provide important insights into how the words function in processes such as mRNA stability and regulation of gene expression.</p> <p>Results</p> <p>Using an enumerative word discovery approach, we investigated the frequencies and positional distributions of all 65,536 different 8-letter words in the genome of <it>Arabidopsis thaliana</it>. Focusing on promoter regions, introns, and 3' and 5' untranslated regions (3'UTRs and 5'UTRs), we compared word frequencies in these segments to genome-wide frequencies. The statistically interesting words in each segment were clustered with similar words to generate motif logos. We investigated whether words were clustered at particular locations or were distributed randomly within each genomic segment, and we classified the words using gene expression information from public repositories. Finally, we investigated whether particular sets of words appeared together more frequently than others.</p> <p>Conclusion</p> <p>Our studies provide a detailed view of the word composition of several segments of the non-coding portion of the <it>Arabidopsis </it>genome. Each segment contains a unique word-based signature. The respective signatures consist of the sets of enriched words, 'unwords', and word pairs within a segment, as well as the preferential locations and functional classifications for the signature words. Additionally, the positional distributions of enriched words within the segments highlight possible functional elements, and the co-associations of words in promoter regions likely represent the formation of higher order regulatory modules. This work is an important step toward fully cataloguing the functional elements of the <it>Arabidopsis </it>genome.</p

Biogenic carbonate mercury and marine temperature records reveal global influence of Late Cretaceous Deccan Traps

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155784/1/Meyer_et_al_2019_Biogenic_carbonate_mercury.pd

A new Holocene eruptive history of Erebus volcano, Antarctica using cosmogenic 3He and 36Cl exposure ages

AbstractThe ages of recent effusive eruptions on Erebus volcano, Antarctica are poorly known. Published 40Ar/39Ar ages of the 10 youngest “post-caldera” lava flows are unreliable because of the young ages of the flows (<10 ka) and the presence of excess 40Ar. Here we use cosmogenic 3He and 36Cl to provide new ages for the 10 youngest flows and 3 older summit flows, including a newly recognized flow distinguished by its exposure age. Estimated eruption ages of the post-caldera flows, assuming no erosion or prior snow cover, range from 4.52 ± 0.08 ka to 8.50 ± 0.19 ka, using Lifton et al. (2014) to scale cosmogenic production rates. If the older Lal (1991)/Stone (2000) model is used to scale production rates, calculated ages are older by 16–25%. Helium-3 and chlorine-36 exposure ages measured on the same samples show excellent agreement. Helium-3 ages measured on clinopyroxene and olivine from the same samples are discordant, probably due in part to lower-than-expected 3He production rates in the Fe-rich olivine. Close agreement of multiple clinopyroxene 3He ages from each flow indicates that the effects of past snow coverage on the exposure ages have been minimal.The new cosmogenic ages differ considerably from published 40Ar/39Ar and 36Cl ages and reveal that the post-caldera flows were erupted during relatively brief periods of effusive activity spread over an interval of ∼4 ka. The average eruption rate over this interval is estimated to be 0.01 km3/ka. Because the last eruption was at least 4 ka ago, and the longest repose interval between the 10 youngest eruptions is ∼1 ka, we consider the most recent period of effusive activity to have ended

Building relationships and facilitating immigrant community integration: An evaluation of a Cultural Navigator Program

Despite the United States’ long history of immigration, large and small communities around the country struggle to integrate newcomers into the social, economic, cultural, and political spheres of society. Utilizing results from the program evaluation of one public library’s Cultural Navigator Program (CNP), the authors illustrate how communities and public institutions can promote integration and relationship building between newly arrived immigrants and long-time residents. Existing social networks, conceptualized in this article as social capital, within receiving communities were leveraged to build capacity among newly arrived immigrants and foster inclusivity and integration at the community level. As a place of intervention, public libraries are suggested as a safe and shared space where community integration can be fostered. The program model is provided as an approach to immigrant community integration. Insights derived from the evaluation inform a discussion on engaging approaches to immigrant integration. The CNP utilized community networks to deliberately and systematically facilitate integration and relationship building between newly arrived immigrants and community members. Lessons learned and recommendations for program evaluators and administrators are provided

Telomere Length Trajectory and Its Determinants in Persons with Coronary Artery Disease: Longitudinal Findings from the Heart and Soul Study

Background: Leukocyte telomere length, an emerging marker of biological age, has been shown to predict cardiovascular morbidity and mortality. However, the natural history of telomere length in patients with coronary artery disease has not been studied. We sought to investigate the longitudinal trajectory of telomere length, and to identify the independent predictors of telomere shortening, in persons with coronary artery disease. Methodology/Principal Findings: In a prospective cohort study of 608 individuals with stable coronary artery disease, we measured leukocyte telomere length at baseline, and again after five years of follow-up. We used multivariable linear and logistic regression models to identify the independent predictors of leukocyte telomere trajectory. Baseline and follow-up telomere lengths were normally distributed. Mean telomere length decreased by 42 base pairs per year (p,0.001). Three distinct telomere trajectories were observed: shortening in 45%, maintenance in 32%, and lengthening in 23 % of participants. The most powerful predictor of telomere shortening was baseline telomere length (OR per SD increase = 7.6; 95 % CI 5.5, 10.6). Other independent predictors of telomere shortening were age (OR per 10 years = 1.6; 95 % CI 1.3, 2.1), male sex (OR = 2.4; 95 % CI 1.3, 4.7), and waist-to-hip ratio (OR per 0.1 increase = 1.4; 95 % CI 1.0, 2.0). Conclusions/Significance: Leukocyte telomere length may increase as well as decrease in persons with coronary arter

Supplementing essential amino acids with the nitric oxide precursor, l-arginine, enhances skeletal muscle perfusion without impacting anabolism in older men

Postprandial limb blood flow and skeletal muscle microvascular perfusion reduce with aging. Here we tested the impact of providing bolus essential amino acids (EAA) in the presence and absence of the nitric oxide precursor, l-Arginine (ARG), upon skeletal muscle blood flow and anabolism in older men. Healthy young (YOUNG: 19.7 ± 0.5 y, N = 8) and older men (OLD, 70 ± 0.8 y, N = 8) received 15 g EAA or (older only) 15 g EAA +3 g ARG (OLD-ARG, 69.2 ± 1.2 y, N = 8). We quantified responses in muscle protein synthesis (MPS; incorporation of 13C phenylalanine into myofibrillar proteins), leg and muscle microvascular blood flow (Doppler/contrast enhanced ultrasound (CEUS)) and insulin/EAA in response to EEA ± ARG. Plasma EAA increased similarly across groups but argininemia was evident solely in OLD-ARG (∼320 mmol, 65 min post feed); increases in plasma insulin (to ∼13 IU ml−1) were similar across groups. Increases in femoral flow were evident in YOUNG >2 h after feeding; these effects were blunted in OLD and OLD-ARG. Increases in microvascular blood volume (MBV) occurred only in YOUNG and these effects were isolated to the early postprandial phase (+45% at ∼45 min after feeding) coinciding with detectable arterio-venous differences in EAA reflecting net uptake by muscle. Increases in microvascular flow velocity (MFV) and tissue perfusion (MBV × MFV) occurred (∼2 h) in YOUNG and OLD-ARG, but not OLD. Postprandial protein accretion was greater in YOUNG than OLD or OLD-ARG; the latter two groups being indistinguishable. Therefore, ARG rescues aspects of muscle perfusion in OLD without impacting anabolic blunting, perhaps due to the “rescue” being beyond the period of active EAA-uptake

Measurement of the top quark forward-backward production asymmetry and the anomalous chromoelectric and chromomagnetic moments in pp collisions at √s = 13 TeV

Abstract The parton-level top quark (t) forward-backward asymmetry and the anomalous chromoelectric (d̂ t) and chromomagnetic (μ̂ t) moments have been measured using LHC pp collisions at a center-of-mass energy of 13 TeV, collected in the CMS detector in a data sample corresponding to an integrated luminosity of 35.9 fb−1. The linearized variable AFB(1) is used to approximate the asymmetry. Candidate t t ¯ events decaying to a muon or electron and jets in final states with low and high Lorentz boosts are selected and reconstructed using a fit of the kinematic distributions of the decay products to those expected for t t ¯ final states. The values found for the parameters are AFB(1)=0.048−0.087+0.095(stat)−0.029+0.020(syst),μ̂t=−0.024−0.009+0.013(stat)−0.011+0.016(syst), and a limit is placed on the magnitude of | d̂ t| &lt; 0.03 at 95% confidence level. [Figure not available: see fulltext.