High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

Cis-regulatory modules (CRMs) function by binding sequence specific transcription factors, but the relationship between in vivo physical binding and the regulatory capacity of factor-bound DNA elements remains uncertain. We investigate this relationship for the well-studied Twist factor in Drosophila melanogaster embryos by analyzing genome-wide factor occupancy and testing the functional significance of Twist occupied regions and motifs within regions. Twist ChIP-seq data efficiently identified previously studied Twist-dependent CRMs and robustly predicted new CRM activity in transgenesis, with newly identified Twist-occupied regions supporting diverse spatiotemporal patterns (>74% positive, n = 31). Some, but not all, candidate CRMs require Twist for proper expression in the embryo. The Twist motifs most favored in genome ChIP data (in vivo) differed from those most favored by Systematic Evolution of Ligands by EXponential enrichment (SELEX) (in vitro). Furthermore, the majority of ChIP-seq signals could be parsimoniously explained by a CABVTG motif located within 50 bp of the ChIP summit and, of these, CACATG was most prevalent. Mutagenesis experiments demonstrated that different Twist E-box motif types are not fully interchangeable, suggesting that the ChIP-derived consensus (CABVTG) includes sites having distinct regulatory outputs. Further analysis of position, frequency of occurrence, and sequence conservation revealed significant enrichment and conservation of CABVTG E-box motifs near Twist ChIP-seq signal summits, preferential conservation of ±150 bp surrounding Twist occupied summits, and enrichment of GA- and CA-repeat sequences near Twist occupied summits. Our results show that high resolution in vivo occupancy data can be used to drive efficient discovery and dissection of global and local cis-regulatory logic

Globally sparse PLS regression

Volume 56 ; Print ISBN : 978-1-4614-8282-6Partial least squares (PLS) regression combines dimensionality reduction and prediction using a latent variable model. It provides better predictive ability than principle component analysis by taking into account both the independent and re- sponse variables in the dimension reduction procedure. However, PLS suffers from over-fitting problems for few samples but many variables. We formulate a new criterion for sparse PLS by adding a structured sparsity constraint to the global SIMPLS optimization. The constraint is a sparsity-inducing norm, which is useful for selecting the important variables shared among all the components. The optimization is solved by an augmented Lagrangian method to obtain the PLS components and to perform variable selection simultaneously. We propose a novel greedy algorithm to overcome the computation difficulties. Experiments demonstrate that our approach to PLS regression attains better performance with fewer selected predictor

Comparison of 2 high-throughput spectral techniques to predict differences in diet composition of grazing sheep and cattle

Diet composition can be estimated in free-ranging animals by the use of n-alkane and long-chain fatty alcohol concentrations in feces. However, this technique involves relatively laborious and costly analytical techniques. Two spectroscopy techniques were investigated as a way of determining whether dietary differences are likely, thus indicating whether the more expensive and labor-intensive techniques for more detailed analysis are justified. Fourier-transform infrared spectroscopy (FTIR) and front-face fluorescence emission spectroscopy (lambda(excitation) = 380 nm, lambda(emission) = 600 to 760 nm) were used to analyze fecal samples collected from 2 different breeds of cattle and sheep (4 groups in total, n = 6 per group) grazing moorland plants in 2 grazing sessions. These fecal samples were also analyzed for alkane and alcohol concentrations. Fourier-transform infrared spectra, particularly in the alkane regions, demonstrated clear separation between animal species. Fluorescence emission spectra showed similar separation; fluorophores were most likely chlorophylls and their derivatives. Multivariate analysis of all 3 data sets showed similar variation within and between groups of cattle and sheep, indicating differences in diet selection particularly between species, but also between breed and grazing session. Both spectroscopy methods showed utility in suggesting differences in diet composition that would be worth investigating using more detailed chemical analyses. Of the 2 techniques, the FTIR spectroscopy gave the better comparative results, being able to detect differences in sampling months that were detected with alkanes and alcohols that the fluorescence emission spectroscopy did not detect

Evolution of trace gases and particles emitted by a chaparral fire in California

Biomass burning (BB) is a major global source of trace gases and particles. Accurately representing the production and evolution of these emissions is an important goal for atmospheric chemical transport models. We measured a suite of gases and aerosols emitted from an 81 hectare prescribed fire in chaparral fuels on the central coast of California, US on 17 November 2009. We also measured physical and chemical changes that occurred in the isolated downwind plume in the first ~4 h after emission. The measurements were carried out onboard a Twin Otter aircraft outfitted with an airborne Fourier transform infrared spectrometer (AFTIR), aerosol mass spectrometer (AMS), single particle soot photometer (SP2), nephelometer, LiCor CO_2 analyzer, a chemiluminescence ozone instrument, and a wing-mounted meteorological probe. Our measurements included: CO_2; CO; NO_x; NH_3; non-methane organic compounds; organic aerosol (OA); inorganic aerosol (nitrate, ammonium, sulfate, and chloride); aerosol light scattering; refractory black carbon (rBC); and ambient temperature, relative humidity, barometric pressure, and three-dimensional wind velocity. The molar ratio of excess O_3 to excess CO in the plume (ΔO_3/ΔCO) increased from −5.13 (±1.13) × 10^(−3) to 10.2 (±2.16) × 10^(−2) in ~4.5 h following smoke emission. Excess acetic and formic acid (normalized to excess CO) increased by factors of 1.73 ± 0.43 and 7.34 ± 3.03 (respectively) over the same time since emission. Based on the rapid decay of C_2H_4 we infer an in-plume average OH concentration of 5.27 (±0.97) × 10^6 molec cm^(−3), consistent with previous studies showing elevated OH concentrations in biomass burning plumes. Ammonium, nitrate, and sulfate all increased over the course of 4 h. The observed ammonium increase was a factor of 3.90 ± 2.93 in about 4 h, but accounted for just ~36% of the gaseous ammonia lost on a molar basis. Some of the gas phase NH_3 loss may have been due to condensation on, or formation of, particles below the AMS detection range. NO_x was converted to PAN and particle nitrate with PAN production being about two times greater than production of observable nitrate in the first ~4 h following emission. The excess aerosol light scattering in the plume (normalized to excess CO_2) increased by a factor of 2.50 ± 0.74 over 4 h. The increase in light scattering was similar to that observed in an earlier study of a biomass burning plume in Mexico where significant secondary formation of OA closely tracked the increase in scattering. In the California plume, however, ΔOA/ΔCO_2 decreased sharply for the first hour and then increased slowly with a net decrease of ~20% over 4 h. The fraction of thickly coated rBC particles increased up to ~85% over the 4 h aging period. Decreasing OA accompanied by increased scattering/particle coating in initial aging may be due to a combination of particle coagulation and evaporation processes. Recondensation of species initially evaporated from the particles may have contributed to the subsequent slow rise in OA. We compare our results to observations from other plume aging studies and suggest that differences in environmental factors such as smoke concentration, oxidant concentration, actinic flux, and RH contribute significantly to the variation in plume evolution observations

A Flux-Limited Sample of z~1 Ly-alpha Emitting Galaxies in the CDFS

We describe a method for obtaining a flux-limited sample of Ly-alpha emitters from GALEX grism data. We show that the multiple GALEX grism images can be converted into a three-dimensional (two spatial axes and one wavelength axis) data cube. The wavelength slices may then be treated as narrowband images and searched for emission-line galaxies. For the GALEX NUV grism data, the method provides a Ly-alpha flux-limited sample over the redshift range z=0.67-1.16. We test the method on the Chandra Deep Field South field, where we find 28 Ly-alpha emitters with faint continuum magnitudes (NUV>22) that are not present in the GALEX pipeline sample. We measure the completeness by adding artificial emitters and measuring the fraction recovered. We find that we have an 80% completeness above a Ly-alpha flux of 10^-15 erg/cm^2/s. We use the UV spectra and the available X-ray data and optical spectra to estimate the fraction of active galactic nuclei in the selection. We report the first detection of a giant Ly-alpha blob at z<1, though we find that these objects are much less common at z=1 than at z=3. Finally, we compute limits on the z~1 Ly-alpha luminosity function and confirm that there is a dramatic evolution in the luminosity function over the redshift range z=0-1.Comment: 18 pages, in press at The Astrophysical Journa

Effect of lifestyle factors on Staphylococcus aureus gut colonization in Swedish and Italian infants

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Abstract basins of attraction

Abstract basins appear naturally in different areas of several complex variables. In this survey we want to describe three different topics in which they play an important role, leading to interesting open problems

Screening of antioxidant properties of the apple juice using the front-face synchronous fluorescence and chemometrics

Fluorescence spectroscopy is gaining increasing attention in food analysis due to its higher sensitivity and selectivity as compared to other spectroscopic techniques. Synchronous scanning fluorescence technique is particularly useful in studies of multi-fluorophoric food samples, providing a further improvement of selectivity by reduction in the spectral overlapping and suppressing light-scattering interferences. Presently, we study the feasibility of the prediction of the total phenolics, flavonoids, and antioxidant capacity using front-face synchronous fluorescence spectra of apple juices. Commercial apple juices from different product ranges were studied. Principal component analysis (PCA) applied to the unfolded synchronous fluorescence spectra was used to compare the fluorescence of the entire sample set. The regression analysis was performed using partial least squares (PLS1 and PLS2) methods on the unfolded total synchronous and on the single-offset synchronous fluorescence spectra. The best calibration models for all of the studied parameters were obtained using the PLS1 method for the single-offset synchronous spectra. The models for the prediction of the total flavonoid content had the best performance; the optimal model was obtained for the analysis of the synchronous fluorescence spectra at Delta lambda = 110 nm (R (2) = 0.870, residual predictive deviation (RPD) = 2.7). The optimal calibration models for the prediction of the total phenolic content (Delta lambda = 80 nm, R (2) = 0.766, RPD = 2.0) and the total antioxidant capacity (Delta lambda = 70 nm, R (2) = 0.787, RPD = 2.1) had only an approximate predictive ability. These results demonstrate that synchronous fluorescence could be a useful tool in fast semi-quantitative screening for the antioxidant properties of the apple juices.info:eu-repo/semantics/publishedVersio