Microbial stress. From sensing to intracellular and population responses

We initially devised this Research Topic (RT) as a valuable initiative to collect high-quality scientific articles from the participants of the 4th European Federation of Biotechnology (EFB) Microbial Stress meeting held in Kinsale, Ireland, April 2018. The scope of the RT is based on the scientific content of that “Microbial Stress: from Systems to Molecules and back” meeting. Indeed, over 40% of the articles eventually accepted for publication were contributed by meeting participants, but notably the remaining 60% was contributed by authors that work in this field. The collection of 22 original research and 2 review articles, contributed by 163 authors collectively, deal with the many different aspects of the microbial responses to biotic and abiotic stresses, relevant to many fields: from host-pathogen interactions to biotechnology, from bioremediation to food processing, from molecular and single-cell to population studies. The RT showcases the rapid developments of the microbial stress research on a range of microorganisms and stress conditions, and confirms that understanding microbial physiology under stress can be a trigger for the development of new methodologies as well as helping to integrate the knowledge from many different microbiological fields of research. The retrospective analysis of the articles contributed to this RT allowed them to be assigned to one of four main sub-topics: (i) impact of weak organic acids and low pH on micro-organisms, from clinical to biotechnological contexts; (ii) adaptive responses in microbial pathogens to abiotic/environmental stress; (iii) oxidative and metal stress, from clinical to bioremediation contexts, and (iv) regulation of transcription and translation under stress, from epigenetic aspects to the role of second messengers and sRNA

Aid and government fiscal behavior: assessing recent evidence

This paper reviews evidence published in the last 10 years that has added to our understanding of the effects of aid on government spending and tax effort in recipient countries, with a discussion of when (general) budget support is a fiscally efficient aid modality. Three generalizations are permitted by the evidence: aid finances government spending; the extent to which aid is fungible is over-stated and even where it is fungible this does not appear to make the aid less effective; and there is no systematic effect of aid on tax effort. Beyond these conclusions effects are country-specific

Disentangling the influence of environment, host specificity and thallus differentiation on bacteria communities in siphonous green seaweeds

Siphonous green seaweeds, such as Caulerpa, are among the most morphologically complex algae with differentiated algal structures (morphological niches). Caulerpa is also host to a rich diversity of bacterial endo- and epibionts. The degree to which these bacterial communities are species-, or even niche-specific remains largely unknown. To address this, we investigated the diversity of bacteria associated to different morphological niches of both native and invasive species of Caulerpa from different geographic locations along the Turkish coastline of the Aegean sea. Associated bacteria were identified using the 16S rDNA marker gene for three morphological niches, such as the endobiome, epibiome, and rhizobiome. Bacterial community structure was explored and deterministic factors behind bacterial variation were investigated. Of the total variation, only 21 .5% could be explained. Pronounced differences in bacterial community composition were observed and variation was partly explained by a combination of host species, biogeography and nutrient levels. The majority of the explained bacterial variation within the algal holobiont was attributed to the micro-environments established by distinct morphological niches. This study further supports the hypothesis that the bacterial assembly is largely stochastic in nature and bacterial community structure is most likely linked to functional genes rather than taxonomy

General methods for evolutionary quantitative genetic inference from generalized mixed models

P.d.V. was supported by a doctoral studentship from the French Ministère de la Recherche et de l’Enseignement Supérieur. H.S. was supported by an Emmy Noether fellowship from the German Research Foundation (SCHI 1188/1-1). S.N. is supported by a Future Fellowship, Australia (FT130100268). M.M. is supported by a University Research Fellowship from the Royal Society (London). The collection of the Soay sheep data is supported by the National Trust for Scotland and QinetQ, with funding from the Natural Environment Research Council, the Royal Society, and the Leverhulme Trust.Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioural traits, have inherently non-normal distributions. The generalised linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for non-normal traits. However, whereas GLMMs provide inference on a statistically-convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGGLMM. We show that known formulae for quantities such as heritability of traits with Binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation, and apply our approach to data from a wild pedigreed vertebrate population.Publisher PDFPeer reviewe

A GALEX Ultraviolet Imaging Survey of Galaxies in the Local Volume

We present results from a GALEX ultraviolet (UV) survey of a complete sample of 390 galaxies within ~11 Mpc of the Milky Way. The UV data are a key component of the composite Local Volume Legacy (LVL), an ultraviolet-to-infrared imaging program designed to provide an inventory of dust and star formation in nearby spiral and irregular galaxies. The ensemble dataset is an especially valuable resource for studying star formation in dwarf galaxies, which comprise over 80% of the sample. We describe the GALEX survey programs which obtained the data and provide a catalog of far-UV (~1500 Angstroms) and near-UV (~2200 Angstroms) integrated photometry. General UV properties of the sample are briefly discussed. We compute two measures of the global star formation efficiency, the SFR per unit HI gas mass and the SFR per unit stellar mass, to illustrate the significant differences that can arise in our understanding of dwarf galaxies when the FUV is used to measure the SFR instead of H-alpha. We find that dwarf galaxies may not be as drastically inefficient in coverting gas into stars as suggested by prior H-alpha studies. In this context, we also examine the UV properties of late-type dwarf galaxies that appear to be devoid of star formation because they were not detected in previous H-alpha narrowband observations. Nearly all such galaxies in our sample are detected in the FUV, and have FUV SFRs that fall below the limit where the H-alpha flux is robust to Poisson fluctuations in the formation of massive stars. The UV colors and star formation efficiencies of H-alpha-undetected, UV-bright dwarf irregulars appear to be relatively unremarkable with respect to those exhibited by the general population of star-forming galaxies.Comment: submitted to ApJS, revised per referee's comments; accepted Oct. 30 w/o further revision; 37 pages; figure 6 omitted due to size; figure available from http://users.obs.carnegiescience.edu/jlee/paper

Evolution of the UV Excess in Early-Type Galaxies

We examine the UV emission from luminous early-type galaxies as a function of redshift. We perform a stacking analysis using Galaxy Evolution Explorer (GALEX) images of galaxies in the NOAO Deep Wide Field Survey (NDWFS) Bo\"otes field and examine the evolution in the UV colors of the average galaxy. Our sample, selected to have minimal ongoing star formation based on the optical to mid-IR SEDs of the galaxies, includes 1843 galaxies spanning the redshift range $0.05\leq z\leq0.65$. We find evidence that the strength of the UV excess decreases, on average, with redshift, and our measurements also show moderate disagreement with previous models of the UV excess. Our results show little evolution in the shape of the UV continuum with redshift, consistent either with the binary model for the formation of Extreme Horizontal Branch (EHB) stars or with no evolution in EHB morphology with look-back time. However, the binary formation model predicts that the strength of the UV excess should also be relatively constant, in contradiction with our measured results. Finally, we see no significant influence of a galaxy's environment on the strength of its UV excess.Comment: 30 pages, 10 figures; accepted by ApJ. Modified from original version to reflect referee's comment

A 125 GeV Higgs Boson Mass and Gravitino Dark Matter in R-invariant Direct Gauge Mediation

We discuss the SM-like Higgs boson mass in the MSSM in an R-invariant direct gauge mediation model with the gravitino mass in the O(1) keV range. The gravitino dark matter scenario in this mass range is a good candidate for a slightly warm dark matter. We show that the Higgs boson mass around 125 GeV suggested by the ATLAS and CMS experiments can be easily achieved in the direct gauge mediation model with this gravitino mass range.Comment: 15 pages, 6 figures; v2: section 5 added (version accepted for the publication of PLB

Extremely Inefficient Star Formation in the Outer Disks of Nearby Galaxies

(Abridged) We combine data from The HI Nearby Galaxy Survey and the GALEX Nearby Galaxy Survey to study the relationship between atomic hydrogen (HI) and far-ultraviolet (FUV) emission outside the optical radius (r25) in 17 spiral and 5 dwarf galaxies. In this regime, HI is likely to represent most of the ISM and FUV emission to trace recent star formation with little bias due to extinction, so that the two quantities closely trace the underlying relationship between gas and star formation rate (SFR). The azimuthally averaged HI and FUV intensities both decline with increasing radius in this regime, with the scale length of the FUV profile typically half that of the HI profile. Despite the mismatch in profiles, there is a significant spatial correlation (at 15" resolution) between local FUV and HI intensities; near r25 this correlation is quite strong, in fact stronger than anywhere inside r25, and shows a decline towards larger radii. The star formation efficiency (SFE) - defined as the ratio of FUV/HI and thus the inverse of the gas depletion time - decreases with galactocentric radius across the outer disks, though much shallower than across the optical disks. On average, we find the gas depletion times to be well above a Hubble time (~10^11 yr). We observe a clear relationship between FUV/HI and HI column in the outer disks, with the SFE increasing with increasing HI column. Despite observing systematic variations in FUV/HI, we find no clear evidence for step-function type star formation thresholds. When compared with results from inside r25, we find outer disk star formation to be distinct in several ways: it is extremely inefficient (depletion times of many Hubble times) with column densities and SFRs lower than found anywhere inside the optical disks. It appears that the HI column is one of, perhaps even the key environmental factor in setting the SFR in outer galaxy disks.Comment: Accepted for Publication in The Astronomical Journa

The Recent Star Formation in NGC 6822: an Ultraviolet Study

We characterize the star formation in the low-metallicity galaxy NGC 6822 over the past few hundred million years, using GALEX far-UV (FUV, 1344-1786 A) and near-UV (NUV, 1771-2831 A) imaging, and ground-based Ha imaging. From GALEX FUV image, we define 77 star-forming (SF) regions with area >860 pc^2, and surface brightness <=26.8 mag(AB)arcsec^-2, within 0.2deg (1.7kpc) of the center of the galaxy. We estimate the extinction by interstellar dust in each SF region from resolved photometry of the hot stars it contains: E(B-V) ranges from the minimum foreground value of 0.22mag up to 0.66+-0.21mag. The integrated FUV and NUV photometry, compared with stellar population models, yields ages of the SF complexes up to a few hundred Myr, and masses from 2x10^2 Msun to 1.5x10^6 Msun. The derived ages and masses strongly depend on the assumed type of interstellar selective extinction, which we find to vary across the galaxy. The total mass of the FUV-defined SF regions translates into an average star formation rate (SFR) of 1.4x10^-2 Msun/yr over the past 100 Myr, and SFR=1.0x10^-2 Msun/yr in the most recent 10 Myr. The latter is in agreement with the value that we derive from the Ha luminosity, SFR=0.008 Msun/yr. The SFR in the most recent epoch becomes higher if we add the SFR=0.02 Msun/yr inferred from far-IR measurements, which trace star formation still embedded in dust (age <= a few Myr).Comment: Accepted for publication in ApJ, 21 pages, 6 figures, 3 table