The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors

<p>Abstract</p> <p>Background</p> <p><it>Zymomonas mobilis </it>produces near theoretical yields of ethanol and recombinant strains are candidate industrial microorganisms. To date, few studies have examined its responses to various stresses at the gene level. Hfq is a conserved bacterial member of the Sm-like family of RNA-binding proteins, coordinating a broad array of responses including multiple stress responses. In a previous study, we observed <it>Z. mobilis </it>ZM4 gene ZMO0347 showed higher expression under anaerobic, stationary phase compared to that of aerobic, stationary conditions.</p> <p>Results</p> <p>We generated a <it>Z. mobilis hfq </it>insertion mutant AcRIM0347 in an acetate tolerant strain (AcR) background and investigated its role in model lignocellulosic pretreatment inhibitors including acetate, vanillin, furfural and hydroxymethylfurfural (HMF). <it>Saccharomyces cerevisiae </it>Lsm protein (Hfq homologue) mutants and Lsm protein overexpression strains were also assayed for their inhibitor phenotypes. Our results indicated that all the pretreatment inhibitors tested in this study had a detrimental effect on both <it>Z. mobilis </it>and <it>S. cerevisiae</it>, and vanillin had the most inhibitory effect followed by furfural and then HMF for both <it>Z. mobilis </it>and <it>S. cerevisiae</it>. AcRIM0347 was more sensitive than the parental strain to the inhibitors and had an increased lag phase duration and/or slower growth depending upon the conditions. The <it>hfq </it>mutation in AcRIM0347 was complemented partially by trans-acting <it>hfq </it>gene expression. We also assayed growth phenotypes for <it>S. cerevisiae </it>Lsm protein mutant and overexpression phenotypes. Lsm1, 6, and 7 mutants showed reduced tolerance to acetate and other pretreatment inhibitors. <it>S. cerevisiae </it>Lsm protein overexpression strains showed increased acetate and HMF resistance as compared to the wild-type, while the overexpression strains showed greater inhibition under vanillin stress conditions.</p> <p>Conclusions</p> <p>We have shown the utility of the pKNOCK suicide plasmid for mutant construction in <it>Z. mobilis</it>, and constructed a Gateway compatible expression plasmid for use in <it>Z. mobilis </it>for the first time. We have also used genetics to show <it>Z. mobilis </it>Hfq and <it>S. cerevisiae </it>Lsm proteins play important roles in resisting multiple, important industrially relevant inhibitors. The conserved nature of this global regulator offers the potential to apply insights from these fundamental studies for further industrial strain development.</p

Star formation and dust extinction properties of local galaxies from AKARI-GALEX All-Sky Surveys: First results from most secure multiband sample from FUV to FIR

The AKARI All-Sky Survey provided the first bright point source catalog detected at 90um. Starting from this catalog, we selected galaxies by matching AKARI sources with those in the IRAS PSCz. Next, we have measured total GALEX FUV and NUV flux densities. Then, we have matched this sample with SDSS and 2MASS galaxies. By this procedure, we obtained the final sample which consists of 607 galaxies. If we sort the sample with respect to 90um, their average SED shows a coherent trend: the more luminous at 90um, the redder the global SED becomes. The M_r--NUV-r color-magnitude relation of our sample does not show bimodality, and the distribution is centered on the green valley between the blue cloud and red sequence seen in optical surveys. We have established formulae to convert FIR luminosity from AKARI bands to the total infrared (IR) luminosity L_TIR. With these formulae, we calculated the star formation directly visible with FUV and hidden by dust. The luminosity related to star formation activity (L_SF) is dominated by L_TIR even if we take into account the far-infrared (FIR) emission from dust heated by old stars. At high star formation rate (SFR) (> 20 Msun yr^-1), the fraction of directly visible SFR, SFR_FUV, decreases. We also estimated the FUV attenuation A_FUV from FUV-to-total IR (TIR) luminosity ratio. We also examined the L_TIR/L_FUV-UV slope (FUV- NUV) relation. The majority of the sample has L_TIR/L_FUV ratios 5 to 10 times lower than expected from the local starburst relation, while some LIRGs and all the ULIRGs of this sample have higher L_TIR/L_FUV ratios. We found that the attenuation indicator L_TIR/L_FUV is correlated to the stellar mass of galaxies, M*, but there is no correlation with specific SFR (SSFR), SFR/M*, and dust attenuation L_TIR/L_FUV. (abridged)Comment: 13 pages, 18 figures, accepted for publication in A&

A Multiwavelength Study of a Sample of 70 micron Selected Galaxies in the COSMOS Field I: Spectral Energy Distributions and Luminosities

We present a large robust sample of 1503 reliable and unconfused 70microm selected sources from the multiwavelength data set of the Cosmic Evolution Survey (COSMOS). Using the Spitzer IRAC and MIPS photometry, we estimate the total infrared luminosity, L_IR (8--1000 microns), by finding the best fit template from several different template libraries. The long wavelength 70 and 160 micron data allow us to obtain a reliable estimate of L_IR, accurate to within 0.2 and 0.05 dex, respectively. The 70 micron data point enables a significant improvement over the luminosity estimates possible with only a 24 micron detection. The full sample spans a wide range in L_IR, L_IR ~ 10^8-10^14 L_sun, with a median luminosity of 10^11.4 L_sun. We identify a total of 687 luminous, 303 ultraluminous, and 31 hyperluminous infrared galaxies (LIRGs, ULIRGs, and HyLIRGs) over the redshift range 0.01<z<3.5 with a median redshift of 0.5. Presented here are the full spectral energy distributions for each of the sources compiled from the extensive multiwavelength data set from the ultraviolet (UV) to the far-infrared (FIR). Using SED fits we find possible evidence for a subset of cooler ultraluminous objects than observed locally. However, until direct observations at longer wavelengths are obtained, the peak of emission and the dust temperature cannot be well constrained. We use these SEDs, along with the deep radio and X-ray coverage of the field, to identify a large sample of candidate active galactic nuclei (AGN). We find that the fraction of AGN increases strongly with L_IR, as it does in the local universe, and that nearly 70% of ULIRGs and all HyLIRGs likely host a powerful AGN.Comment: 31 pages including 31 figures and 6 tables. Accepted for publication in ApJ. The full resolution version is available here: http://www.ifa.hawaii.edu/~jeyhan/paperI/Kartaltepe_70mic_PaperI.pd

Star Formation Rate Indicators in Wide-Field Infrared Survey Preliminary Release

With the goal of investigating the degree to which theMIR luminosity in theWidefield Infrared Survey Explorer (WISE) traces the SFR, we analyze 3.4, 4.6, 12 and 22 {\mu}m data in a sample of {\guillemotright} 140,000 star-forming galaxies or star-forming regions covering a wide range in metallicity 7.66 < 12 + log(O/H) < 9.46, with redshift z < 0.4. These star-forming galaxies or star-forming regions are selected by matching the WISE Preliminary Release Catalog with the star-forming galaxy Catalog in SDSS DR8 provided by JHU/MPA 1.We study the relationship between the luminosity at 3.4, 4.6, 12 and 22 {\mu}m from WISE and H\alpha luminosity in SDSS DR8. From these comparisons, we derive reference SFR indicators for use in our analysis. Linear correlations between SFR and the 3.4, 4.6, 12 and 22 {\mu}m luminosity are found, and calibrations of SFRs based on L(3.4), L(4.6), L(12) and L(22) are proposed. The calibrations hold for galaxies with verified spectral observations. The dispersion in the relation between 3.4, 4.6, 12 and 22 {\mu}m luminosity and SFR relates to the galaxy's properties, such as 4000 {\deg}A break and galaxy color.Comment: 10 pages, 3 figure

Wet scavenging of soluble gases in DC3 deep convective storms using WRF-Chem simulations and aircraft observations

We examine wet scavenging of soluble trace gases in storms observed during the Deep Convective Clouds and Chemistry (DC3) field campaign. We conduct high-resolution simulations with the Weather Research and Forecasting model with Chemistry (WRF-Chem) of a severe storm in Oklahoma. The model represents well the storm location, size, and structure as compared with Next Generation Weather Radar reflectivity, and simulated CO transport is consistent with aircraft observations. Scavenging efficiencies (SEs) between inflow and outflow of soluble species are calculated from aircraft measurements and model simulations. Using a simple wet scavenging scheme, we simulate the SE of each soluble species within the error bars of the observations. The simulated SEs of all species except nitric acid (HNO_3) are highly sensitive to the values specified for the fractions retained in ice when cloud water freezes. To reproduce the observations, we must assume zero ice retention for formaldehyde (CH_2O) and hydrogen peroxide (H_2O_2) and complete retention for methyl hydrogen peroxide (CH_3OOH) and sulfur dioxide (SO_2), likely to compensate for the lack of aqueous chemistry in the model. We then compare scavenging efficiencies among storms that formed in Alabama and northeast Colorado and the Oklahoma storm. Significant differences in SEs are seen among storms and species. More scavenging of HNO_3 and less removal of CH_3OOH are seen in storms with higher maximum flash rates, an indication of more graupel mass. Graupel is associated with mixed-phase scavenging and lightning production of nitrogen oxides (NO_x), processes that may explain the observed differences in HNO_3 and CH_3OOH scavenging

miR-146a is a significant brake on autoimmunity, myeloproliferation, and cancer in mice

Excessive or inappropriate activation of the immune system can be deleterious to the organism, warranting multiple molecular mechanisms to control and properly terminate immune responses. MicroRNAs (miRNAs), ~22-nt-long noncoding RNAs, have recently emerged as key posttranscriptional regulators, controlling diverse biological processes, including responses to non-self. In this study, we examine the biological role of miR-146a using genetically engineered mice and show that targeted deletion of this gene, whose expression is strongly up-regulated after immune cell maturation and/or activation, results in several immune defects. Collectively, our findings suggest that miR-146a plays a key role as a molecular brake on inflammation, myeloid cell proliferation, and oncogenic transformation