Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation

Indexación: Web of Science.Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia. These core gene families are absent in the closest extant genus Thermithiobacillus tepidarius that subtends the Acidithiobacillus genus and roots the deepest in this class. The predicted proteins encoded by these core gene families are not detected by a BLAST search in the NCBI non-redundant database of more than 90 million proteins using a relaxed cut-off of 1.0e(-5). None of the five families has a clear functional prediction. However, bioinformatic scrutiny, using pI prediction, motif/domain searches, cellular location predictions, genomic context analyses, and chromosome topology studies together with previously published transcriptomic and proteomic data, suggests that some may have functions associated with membrane remodeling during cell division perhaps in response to pH stress. Despite the high level of amino acid sequence conservation within each family, there is sufficient nucleotide variation of the respective genes to permit the use of the DNA sequences to distinguish different species of Acidithiobacillus, making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to the Acidithiobacillus genus, they can also be leveraged as probes to detect the genus in environmental metagenomes and metatranscriptomes, including industrial biomining operations, and acid mine drainage (AMD).http://journal.frontiersin.org/article/10.3389/fmicb.2016.02035/ful

The effects of long-day lighting and removal of young leaves on tomato yield

While low intensity long-day (LD) lighting has been shown to enhance the growth of young plants under low light levels, its effect on the yield of a long-season glasshouse tomato crop has not been previously examined. LD were provided by the use of tungsten lamps (2.8 μmol m-2 s-1 at approx. 0.5 m from the ground) between 04.00 h to sunrise and from sunset until 20.00 h (GMT). LD lighting increased leaf chlorophyll contents, and the numbers of flowers and fruits set per truss when the plants were young. However, this treatment did not affect the total yield of tomatoes. Different leaf removal treatments were applied within each glasshouse compartment. A previous experiment had shown that reducing the leaf area index (LAI) from 5.2 to 2.6, by removing old leaves, did not affect yield. It was also thought that removal of young leaves reduced the total vegetative sink-strength and favoured assimilate partitioning into the fruit. Therefore, removal of young leaves could increase fruit yield. In the present experiments, one-third of the leaves were removed in March (those immediately below each truss) and, subsequently, every third leaf was removed at an early stage of its development. This reduced the LAI from 4.1 to 2.9 and resulted in a loss of yield from 3 – 4 weeks after leaf removal until the end of the experiment, at which point there was an 8% loss of cumulative yield due to a reduction in the average number of fruits set per truss and in mean fruit weight. We postulate that the light which would have been intercepted by young photosynthetically-efficient leaves at the top of the canopy was intercepted instead by older leaves which were less efficient, reducing overall net canopy photosynthesis

Produtividade da agricultura: resultados para o Brasil e estados selecionados.

Este trabalho analisa a produtividade da agricultura nos anos recentes, em especial no período de 2000 a 2012. O artigo estima indicadores de produtividade não apenas para o Brasil, mas também para uma seleção de estados. Estes foram escolhidos pela sua relevância na produção nacional de grãos e carnes. Para isso, foram escolhidos os estados da Bahia, Minas Gerais, São Paulo, Paraná, Rio Grande do Sul, Mato Grosso e Goiás. Utilizou-se o conceito de produtividade total dos fatores (PTF) porque ele oferece uma definição mais abrangente de produtividade do que medidas que comparam o produto a apenas um insumo, como trabalho ou terra. Esta última forma de mensuração da produtividade é chamada produtividade parcial. A PTF considera, em sua definição, a reunião de todos os produtos das lavouras e da pecuária e os relaciona com todos os insumos usados na produção

A Study of Nine High-Redshift Clusters of Galaxies: IV. Photometry and Sp ectra of Clusters 1324+3011 and 1604+4321

New photometric and spectroscopic observations of galaxies in the directions of three distant clusters are presented as part of our on-going high-redshift cluster survey. The clusters are CL1324+3011 at z = 0.76, CL1604+4304 at z = 0.90, and CL1604+4321 at z = 0.92. The observed x-ray luminosities in these clusters are at least a factor of 3 smaller than those observed in clusters with similar velocity dispersions at z <= 0.4. These clusters contain a significant population of elliptical-like galaxies, although these galaxies are not nearly as dominant as in massive clusters at z <= 0.5. We also find a large population of blue cluster members. Defining an active galaxy as one in which the rest equivalent width of [OII] is greater than 15 Angstroms, the fraction of active cluster galaxies, within the central 1.0 Mpc, is 45%. In the field population, we find that 65% of the galaxies with redshifts between z = 0.40 and z = 0.85 are active, while the fraction is 79% for field galaxies at z > 0.85. The star formation rate normalized by the rest AB B-band magnitude, SFRN, increases as the redshift increases at a given evolving luminosity. At a given redshift, however, SFRN decreases linearly with increasing luminosity indicating a remarkable insensitivity of the star formation rate to the intrinsic luminosity of the galaxy over the range -18 >= ABB >= -22. Cluster galaxies in the central 1 Mpc regions exhibit depressed star formation rates. We are able to measure significant evolution in the B-band luminosity function over the range 0.1 <= z <= 1. The characteristic luminosity increases by a factor of 3 with increasing redshift over this range.Comment: 64 pages, 18 figures, accepted for publication in the Astronomical Journal on May 25, 2001. Scheduled to appear in Sept 2001 issu

Absolute Proper Motion of the Fornax Dwarf Spheroidal Galaxy from Photographic and HST WFPC2 Data

We have measured the absolute proper motion of the Fornax dwarf spheroidal galaxy from a combination of photographic plate material and HST WFPC2 data that provide a time baseline of up to 50 years. The extragalactic reference frame consists of 8 QSO images and 48 galaxies. The absolute proper motion is mu_alpha cos(delta) = 0.59 +-0.16 mas/yr and mu_delta = -0.15 +- 0.16 mas/yr. The corresponding orbit of Fornax is polar, with an eccentricity of 0.27, and a radial period of 4.5 Gyr. Fornax's current location is near pericenter. The direction of the motion of Fornax supports the notion that Fornax belongs to the Fornax-LeoI-LeoII-Sculptor-Sextans stream as hypothesized by Lynden-Bell (1976, 1982) and Majewski (1994). According to our orbit determination, Fornax crossed the Magellanic plane \~190 Myr ago, a time that coincides with the termination of the star-formation process in Fornax. We propose that ram-pressure stripping due to the passage of Fornax through a gaseous medium denser than the typical intragalactic medium left behind from the LMC may have caused the end of star formation in Fornax. The excess, anomalous clouds within the South Galactic pole region of the Magellanic Stream whose origin has long been debated in the literature as constituents of either the Magellanic Stream or of the extragalactic Sculptor group, are found to lie along the orbit of Fornax. We speculate that these clouds are stripped material from Fornax as the dwarf crossed the Magellanic Clouds' orbit.Comment: Accepted for publication in Astronomical Journal. The version with high resolution figures can be found at ftp://pegasus.astro.yale.edu/pub/dana/paper

The BTC40 Survey for Quasars at 4.8 < z < 6

The BTC40 Survey for high-redshift quasars is a multicolor search using images obtained with the Big Throughput Camera (BTC) on the CTIO 4-m telescope in V, I, and z filters to search for quasars at redshifts of 4.8 < z < 6. The survey covers 40 sq. deg. in B, V, & I and 36 sq. deg. in z. Limiting magnitudes (3 sigma) reach to V = 24.6, I = 22.9 and z = 22.9. We used the (V-I) vs. (I-z) two-color diagram to select high-redshift quasar candidates from the objects classified as point sources in the imaging data. Follow-up spectroscopy with the AAT and CTIO 4-m telescopes of candidates having I < 21.5 has yielded two quasars with redshifts of z = 4.6 and z = 4.8 as well as four emission line galaxies with z = 0.6. Fainter candidates have been identified down to I = 22 for future spectroscopy on 8-m class telescopes.Comment: 27 pages, 8 figures; Accepted for publication in the Astronomical Journa

An X-ray Selected Galaxy Cluster at z=1.26

We report the discovery of an X-ray luminous galaxy cluster at z=1.26. RXJ0848.9+4452 was selected as an X-ray cluster candidate in the ROSAT Deep Cluster Survey, on the basis of its spatial extent. Deep optical and near-IR imaging have revealed a galaxy overdensity around the peak of the X-ray emission, with a significant excess of red objects with J-K colors typical of elliptical galaxies at z>1. Spectroscopic observations at the Keck II telescope have secured 6 galaxy redshifts in the range 1.257=1.261), within a 35 arcsec radius around the peak X-ray emission. This system lies only 4.2 arcmin away (5.0 h^{-1}_{50} comoving Mpc, q_0=0.5) from the galaxy cluster ClG J0848+4453, which was identified by Stanford et al. (1997) at z=1.273 in a near-IR field galaxy survey, and is also known to be X-ray luminous. Assuming that the X-ray emission is entirely due to hot intra-cluster gas, both these systems have similar rest frame luminosities L_x ~=1x10^{44} ergs/s (0.5-2.0 keV band). In combination with our spectrophotometric data for the entire 30 arcmin^2 field, this suggests the presence of a superstructure, consisting of two collapsed, possibly virialized clusters, the first detected to date at z>1.Comment: To appear in The Astronomical Journal, 24 pages, 8 figures, 1 color jpg plate (fig.7), see http://www.eso.org/~prosati/lynx/plate_fig7.jp

Regularization of image reconstruction in ultrasound computed tomography

We propose two regularizations techniques for a bent-ray (BR) tracing algorithm to reconstruct the speed of sound maps of breast tissues in an Ultrasound Computed Tomography (USCT) system. When high frequencies are employed, the use of BR is a good approximation to describe the propagation of the front of the pressure wave. The quantitative accuracy of the images reconstructed with the BR algorithm was evaluated without any kind of regularization, and with two regularization methods. The regularizations were based on some available a priori information, namely the known higher and lower values of the speed of sound expected in the breast tissues, and the maps of the internal structures obtained from the standard reflection ultrasound (US) imaging. The use of the proposed regularizations in the implemented algorithm improves the convergence and quality of the resulting images, although further improvements are still possible. These methods will help obtaining quantitative US images in a reasonable amount of time, expanding the possibilities and applications of this technique

Expert-Augmented Machine Learning

Machine Learning is proving invaluable across disciplines. However, its success is often limited by the quality and quantity of available data, while its adoption by the level of trust that models afford users. Human vs. machine performance is commonly compared empirically to decide whether a certain task should be performed by a computer or an expert. In reality, the optimal learning strategy may involve combining the complementary strengths of man and machine. Here we present Expert-Augmented Machine Learning (EAML), an automated method that guides the extraction of expert knowledge and its integration into machine-learned models. We use a large dataset of intensive care patient data to predict mortality and show that we can extract expert knowledge using an online platform, help reveal hidden confounders, improve generalizability on a different population and learn using less data. EAML presents a novel framework for high performance and dependable machine learning in critical applications