While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a ...large part, on the activation and repression of regulatory sequences, including transcriptional enhancers. Transcriptional enhancers can be located tens of kilobases from their target genes, but display characteristic chromatin and DNA features, allowing their identification by genome-wide profiling. Here we show that integration of chromatin characteristics can be applied to predict distal enhancer candidates in Zea mays, thereby providing a basis for a better understanding of gene regulation in this important crop plant.
To predict transcriptional enhancers in the crop plant maize (Zea mays L. ssp. mays), we integrated available genome-wide DNA methylation data with newly generated maps for chromatin accessibility and histone 3 lysine 9 acetylation (H3K9ac) enrichment in young seedling and husk tissue. Approximately 1500 intergenic regions, displaying low DNA methylation, high chromatin accessibility and H3K9ac enrichment, were classified as enhancer candidates. Based on their chromatin profiles, candidate sequences can be classified into four subcategories. Tissue-specificity of enhancer candidates is defined based on the tissues in which they are identified and putative target genes are assigned based on tissue-specific expression patterns of flanking genes.
Our method identifies three previously identified distal enhancers in maize, validating the new set of enhancer candidates and enlarging the toolbox for the functional characterization of gene regulation in the highly repetitive maize genome.
We present a statistical analysis of the environments of 11 supernovae (SNe) which occurred in six nearby galaxies (z ... 0.016). All galaxies were observed with MUSE, the high spatial resolution ...integral-field spectrograph mounted to the 8 m VLT UT4. These data enable us to map the full spatial extent of host galaxies up to ~3 effective radii. In this way, not only can one characterize the specific host environment of each SN, one can compare their properties with stellar populations within the full range of other environments within the host. We present a method that consists of selecting all H II regions found within host galaxies from 2D extinction-corrected H alpha emission maps. These regions are then characterized in terms of their H alpha equivalent widths, star formation rates and oxygen abundances. Identifying H II regions spatially coincident with SN explosion sites, we are thus able to determine where within the distributions of host galaxy e.g. metallicities and ages each SN is found, thus providing new constraints on SN progenitor properties. This initial pilot study using MUSE opens the way for a revolution in SN environment studies where we are now able to study multiple environment SN progenitor dependencies using a single instrument and single pointing. (ProQuest: ... denotes formulae/symbols omitted.)
The significance and cause of the decline in biomass burning across the Americas after ad 1500 is a topic of considerable debate. We synthesized charcoal records (a proxy for biomass burning) from ...the Americas and from the remainder of the globe over the past 2000 years, and compared these with paleoclimatic records and population reconstructions. A distinct post-ad 1500 decrease in biomass burning is evident, not only in the Americas, but also globally, and both are similar in duration and timing to ‘Little Ice Age’ climate change. There is temporal and spatial variability in the expression of the biomass-burning decline across the Americas but, at a regional–continental scale, ‘Little Ice Age’ climate change was likely more important than indigenous population collapse in driving this decline.
Oxamniquine resistance evolved in the human blood fluke (Schistosoma monsoni) in Brazil in the 1970s. We crossed parental parasites differing -500-fold in drug response, determined drug sensitivity ...and marker segregation in clonally derived second-generation progeny, and identified a single quantitative trait locus (logarithm of odds = 31) on chromosome 6. A sulfotransferase was identified as the causative gene by using RNA interference knockdown and biochemical complementation assays, and we subsequently demonstrated independent origins of loss-of-f unction mutations in field-derived and laboratory-selected resistant parasites. These results demonstrate the utility of linkage mapping in a human helminth parasite, while crystallographic analyses of protein-drug interactions illuminate the mode of drug action and provide a framework for rational design of oxamniquine derivatives that kill both 5. monsoni and 5. haematobium, the two species responsible for >99% of schistosomiasis cases worldwide.
In January 2003, the US Environmental Protection Agency sponsored a “roundtable discussion” to develop a consensus on the relationship between eutrophication and harmful algal blooms (HABs), ...specifically targeting those relationships for which management actions may be appropriate. Academic, federal, and state agency representatives were in attendance. The following seven statements were unanimously adopted by attendees based on review and analysis of current as well as pertinent previous data:
(1)
Degraded water quality from increased nutrient pollution promotes the development and persistence of many HABs and is one of the reasons for their expansion in the U.S. and other nations;
(2)
The composition–not just the total quantity–of the nutrient pool impacts HABs;
(3)
High-biomass blooms must have exogenous nutrients to be sustained;
(4)
Both chronic and episodic nutrient delivery promote HAB development;
(5)
Recently developed tools and techniques are already improving the detection of some HABs, and emerging technologies are rapidly advancing toward operational status for the prediction of HABs and their toxins;
(6)
Experimental studies are critical to further the understanding about the role of nutrients in HABs expression, and will strengthen prediction and mitigation of HABs; and
(7)
Management of nutrient inputs to the watershed can lead to significant reduction in HABs.
Supporting evidence and pertinent examples for each consensus statement are provided herein.
Single-electron circuits of the future, consisting of a network of quantum dots, will require a mechanism to transport electrons from one functional part of the circuit to another. For example, in a ...quantum computer decoherence and circuit complexity can be reduced by separating quantum bit (qubit) manipulation from measurement and by providing a means of transporting electrons between the corresponding parts of the circuit. Highly controlled tunnelling between neighbouring dots has been demonstrated, and our ability to manipulate electrons in single- and double-dot systems is improving rapidly. For distances greater than a few hundred nanometres, neither free propagation nor tunnelling is viable while maintaining confinement of single electrons. Here we show how a single electron may be captured in a surface acoustic wave minimum and transferred from one quantum dot to a second, unoccupied, dot along a long, empty channel. The transfer direction may be reversed and the same electron moved back and forth more than sixty times-a cumulative distance of 0.25 mm-without error. Such on-chip transfer extends communication between quantum dots to a range that may allow the integration of discrete quantum information processing components and devices.
ABSTRACT We present the first results of the High Cadence Transient Survey (HiTS), a survey for which the objective is to detect and follow-up optical transients with characteristic timescales from ...hours to days, especially the earliest hours of supernova (SN) explosions. HiTS uses the Dark Energy Camera and a custom pipeline for image subtraction, candidate filtering and candidate visualization, which runs in real-time to be able to react rapidly to the new transients. We discuss the survey design, the technical challenges associated with the real-time analysis of these large volumes of data and our first results. In our 2013, 2014, and 2015 campaigns, we detected more than 120 young SN candidates, but we did not find a clear signature from the short-lived SN shock breakouts (SBOs) originating after the core collapse of red supergiant stars, which was the initial science aim of this survey. Using the empirical distribution of limiting magnitudes from our observational campaigns, we measured the expected recovery fraction of randomly injected SN light curves, which included SBO optical peaks produced with models from Tominaga et al. (2011) and Nakar & Sari (2010). From this analysis, we cannot rule out the models from Tominaga et al. (2011) under any reasonable distributions of progenitor masses, but we can marginally rule out the brighter and longer-lived SBO models from Nakar & Sari (2010) under our best-guess distribution of progenitor masses. Finally, we highlight the implications of this work for future massive data sets produced by astronomical observatories, such as LSST.
Context:
Phthalates are ubiquitous environmental chemicals. Fetal exposure to certain phthalates e.g. di-n-butyl phthalate (DBP) causes masculinization disorders in rats, raising concern for similar ...effects in humans. We investigated whether DBP exposure impairs steroidogenesis by the human fetal testis.
Objective:
The aim of the study was to determine effects of DBP exposure on testosterone production by normally growing human fetal testis xenografts.
Design:
Human fetal testes (14–20 wk gestation; n = 12) were xenografted into castrate male nude mice that were treated for 4–21 d with vehicle, or 500 mg/kg · d DBP, or monobutyl phthalate (active metabolite of DBP); all mice were treated with human chorionic gonadotropin to mimic normal human pregnancy. Rat fetal testis xenografts were exposed for 4 d to DBP as a positive control.
Main Outcome Measures:
Testosterone production was assessed by measuring host serum testosterone and seminal vesicle (SV) weights at termination, plus testis gene expression (rats).
Results:
Human fetal testis xenografts showed similar survival (∼80%) and total graft weight (8.6 vs. 10.1 mg) in vehicle and DBP-exposed hosts, respectively. Serum testosterone (0.56 vs. 0.64 ng/ml; P > 0.05) and SV weight (67.2 vs. 81.9 mg; P > 0.05) also did not differ. Exposure to monobutyl phthalate gave similar results. In contrast, exposure of rat fetal xenografts to DBP significantly reduced SV weight and testis Cyp11a1/StAR mRNA expression and lowered testosterone levels, confirming that DBP exposure can inhibit steroidogenesis in xenografts, further validating the negative findings on testosterone production in the human.
Conclusions:
Exposure of human fetal testes to DBP is unlikely to impair testosterone production as it does in rats. This has important safety and regulatory implications.
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