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

Stable water isotopes in HadCM3: isotopic signature of El Nino-Southern Oscillation and the tropical amount effect

Stable water isotopes have been added to the full hydrological cycle of the Hadley Centre Climate model (HadCM3) coupled atmosphere-ocean GCM. Simulations of delta O-18 in precipitation and at the ocean surface compare well with observations for the present-day climate. The model has been used to investigate the isotopic anomalies associated with ENSO; it is found that the anomalous delta O-18 in precipitation is correlated with the anomalous precipitation amount in accordance with the "amount effect.'' The El Nino delta O-18 anomaly at the ocean surface is largest in coastal regions because of the mixing of ocean water and the more depleted runoff from the land surface. Coral delta O-18 anomalies were estimated, using an established empirical relationship, and generally reflect ocean surface delta O-18 anomalies in coastal regions and sea surface temperatures away from the coast. The spatial relationship between tropical precipitation and delta O-18 was investigated for the El Nino anomaly simulated by HadCM3. Weighting the El Nino precipitation anomaly by the precipitation amount at each grid box gave a large increase in the spatial correlation between tropical precipitation and delta O-18. This improvement was most apparent over land points and between 10 and 20 degrees of latitude

The impact of a seasonally ice free Arctic Ocean on the temperature, precipitation and surface mass balance of Svalbard

The observed decline in summer sea ice extent since the 1970s is predicted to continue until the Arctic Ocean is seasonally ice free during the 21st Century. This will lead to a much perturbed Arctic climate with large changes in ocean surface energy flux. Svalbard, located on the present day sea ice edge, contains many low lying ice caps and glaciers and is expected to experience rapid warming over the 21st Century. The total sea level rise if all the land ice on Svalbard were to melt completely is 0.02 m. The purpose of this study is to quantify the impact of climate change on Svalbard’s surface mass balance (SMB) and to determine, in particular, what proportion of the projected changes in precipitation and SMB are a result of changes to the Arctic sea ice cover. To investigate this a regional climate model was forced with monthly mean climatologies of sea surface temperature (SST) and sea ice concentration for the periods 1961–1990 and 2061–2090 under two emission scenarios. In a novel forcing experiment, 20th Century SSTs and 21st Century sea ice were used to force one simulation to investigate the role of sea ice forcing. This experiment results in a 3.5 m water equivalent increase in Svalbard’s SMB compared to the present day. This is because over 50 % of the projected increase in winter precipitation over Svalbard under the A1B emissions scenario is due to an increase in lower atmosphere moisture content associated with evaporation from the ice free ocean. These results indicate that increases in precipitation due to sea ice decline may act to moderate mass loss from Svalbard’s glaciers due to future Arctic warming

Simultaneous Multicolor Detection of Faint Galaxies in the Hubble Deep Field

We present a novel way to detect objects when multiband images are available. Typically, object detection is performed in one of the available bands or on a somewhat arbitrarily co-added image. Our technique provides an almost optimal way to use all the color information available. We build up a composite image of the N passbands where each pixel value corresponds to the probability that the given pixel is just sky. By knowing the probability distribution of sky pixels (a chi-square distribution with N degrees of freedom), the data can be used to derive the distribution of pixels dominated by object flux. From the two distributions an optimal segmentation threshold can be determined. Clipping the probability image at this threshold yields a mask, where pixels unlikely to be sky are tagged. After using a standard connected-pixel criterion, the regions of this mask define the detected objects. Applying this technique to the Hubble Deep Field data, we find that we can extend the detection limit of the data below that possible using linearly co-added images. We also discuss possible ways of enhancing object detection probabilities for certain well defined classes of objects by using various optimized linear combinations of the pixel fluxes (optimal subspace filtering).Comment: 8 pages, 5 figures (4 postscript, 1 JPEG). To be published in A

Shock and statistical acceleration of energetic particles in the interplanetary medium

Definite evidence for particle acceleration in the solar wind came around a decade ago. Two likely sources are known to exist: particles may be accelerated by the turbulence resulting from the superposition of Alfven and Magnetosonic waves (Statistical Acceleration) or they may be accelerated directly at shock fronts formed by the interaction of fast and slow solar wind (CIR's) or by traveling shocks due to sporadic coronal mass ejections. Naurally both mechanisms may be operative. In this work the acceleration problem was tackled numerically using Helios 1 and 2 data to create a realistic representation of the Heliospheric plasma. Two 24 hour samples were used: one where there are only wave like fluctuations of the field (Day 90 Helios 1) and another with a shock present in it (Day 92 of Helios 2) both in 1976 during the STIP 2 interval. Transport coefficients in energy space have been calculated for particles injected in each sample and the effect of the shock studied in detail

A closer look at the role of the fruit and vegetable planting restriction provision on land use in the United States

Current U.S. farm programs make payments to farmers based in part on historical base acres planted in particular program crops such as corn, soybeans, cotton, wheat and soybeans. Eligibility for payments includes regulations on the crops allowed to be grown on base acres, and there are restrictions on planting horticultural crops on such base acres. The fruits and planting restriction on base acres has potentially influenced the number of acres planted to fruits and vegetables over the past two decades. This research carefully examines the effects of planting restrictions applied to vegetables and program crops, using county-level data in the United States in 1982, 1987, 1992 and 1997. The paper employs the difference-indifference (DiD) approach to estimate acreage response to planting restrictions. The results show planting restrictions crowded out land used for growing fruits and vegetables, most notably in the Great Lakes region that produces processing vegetables.Crop Production/Industries, Land Economics/Use,