Comparative metagenomics of Daphnia symbionts

BACKGROUND: Shotgun sequences of DNA extracts from whole organisms allow a comprehensive assessment of possible symbionts. The current project makes use of four shotgun datasets from three species of the planktonic freshwater crustaceans Daphnia: one dataset from clones of D. pulex and D. pulicaria and two datasets from one clone of D. magna. We analyzed these datasets with three aims: First, we search for bacterial symbionts, which are present in all three species. Second, we search for evidence for Cyanobacteria and plastids, which had been suggested to occur as symbionts in a related Daphnia species. Third, we compare the metacommunities revealed by two different 454 pyrosequencing methods (GS 20 and GS FLX). RESULTS: In all datasets we found evidence for a large number of bacteria belonging to diverse taxa. The vast majority of these were Proteobacteria. Of those, most sequences were assigned to different genera of the Betaproteobacteria family Comamonadaceae. Other taxa represented in all datasets included the genera Flavobacterium, Rhodobacter, Chromobacterium, Methylibium, Bordetella, Burkholderia and Cupriavidus. A few taxa matched sequences only from the D. pulex and the D. pulicaria datasets: Aeromonas, Pseudomonas and Delftia. Taxa with many hits specific to a single dataset were rare. For most of the identified taxa earlier studies reported the finding of related taxa in aquatic environmental samples. We found no clear evidence for the presence of symbiotic Cyanobacteria or plastids. The apparent similarity of the symbiont communities of the three Daphnia species breaks down on a species and strain level. Communities have a similar composition at a higher taxonomic level, but the actual sequences found are divergent. The two Daphnia magna datasets obtained from two different pyrosequencing platforms revealed rather similar results. CONCLUSION: Three clones from three species of the genus Daphnia were found to harbor a rich community of symbionts. These communities are similar at the genus and higher taxonomic level, but are composed of different species. The similarity of these three symbiont communities hints that some of these associations may be stable in the long-term

Candida auris Identification and Rapid Antifungal Susceptibility Testing Against Echinocandins by MALDI-TOF MS

Candida auris was first reported in an ear swab from Japan in 2009; it then promptly spread over five continents and turned into a global nosocomial problem. The main challenges faced by many researchers are the mis-identification by conventional methods in clinical laboratories and failure in treatment. About 90% of C. auris strains are intrinsically resistant to fluconazole (FLU), and it is developing resistance to multiple classes of available antifungals. Echinocandins are the most potent class of antifungals against C. auris; however, reduced susceptibility to one or many echinocandin drugs has been recently observed. Thus, the main issues addressed in this paper are the fast and accurate identification of C. auris derived from Sabouraud dextrose agar and blood culture bottles as well as the rapid antifungal susceptibility test by MALDI-TOF MS. This study successfully identified all isolates of C. auris (n = 50) by MALDI-TOF MS, with an average log score of ≥ 2. An accuracy of 100% was found on both agar plate and blood culture bottles. MALDI Biotyper antibiotic susceptibility test-rapid assay (MBT ASTRA) was used for rapid antifungal susceptibility testing (AFST). A comparison between MBT ASTRA and the Clinical and Laboratory Standards Institute guidelines (CLSI) detected a sensitivity and specificity of 100% and 98% for anidulafungin, and 100% and 95.5% for micafungin, respectively. A categorical agreement of 98% and 96% was calculated for the two methods. For caspofungin, sensitivity and specificity of 100 and 73% were found, respectively, with a categorical agreement of 82%. MBT ASTRA has the great potential to detect C. auris isolates non-susceptible against echinocandin antifungals within 6 h, which makes it a promising candidate for AFST in clinical laboratories in the future

First impressions and perceived roles: Palestinian perceptions on foreign aid

This paper summarizes some results of a wider research on foreign aid that was conducted in the West Bank and Gaza Strip in 2010. It seeks to describe the impressions and feelings of Palestinian aid beneficiaries as well as the roles and functions they attached to foreign aid. To capture and measure local perceptions on Western assistance a series of individual in depth interviews and few focus group interviews were conducted in the Palestinian territories. The interview transcripts were processed by content analysis. As research results show — from the perspective of aid beneficiaries — foreign aid is more related to human dignity than to any economic development. All this implies that frustration with the ongoing Israeli-Palestinian conflict inevitably embraces the donor policies and practices too

A missing dimension in measures of vaccination impacts

Immunological protection, acquired from either natural infection or vaccination, varies among hosts, reflecting underlying biological variation and affecting population-level protection. Owing to the nature of resistance mechanisms, distributions of susceptibility and protection entangle with pathogen dose in a way that can be decoupled by adequately representing the dose dimension. Any infectious processes must depend in some fashion on dose, and empirical evidence exists for an effect of exposure dose on the probability of transmission to mumps-vaccinated hosts [1], the case-fatality ratio of measles [2], and the probability of infection and, given infection, of symptoms in cholera [3]. Extreme distributions of vaccine protection have been termed leaky (partially protects all hosts) and all-or-nothing (totally protects a proportion of hosts) [4]. These distributions can be distinguished in vaccine field trials from the time dependence of infections [5]. Frailty mixing models have also been proposed to estimate the distribution of protection from time to event data [6], [7], although the results are not comparable across regions unless there is explicit control for baseline transmission [8]. Distributions of host susceptibility and acquired protection can be estimated from dose-response data generated under controlled experimental conditions [9]–[11] and natural settings [12], [13]. These distributions can guide research on mechanisms of protection, as well as enable model validity across the entire range of transmission intensities. We argue for a shift to a dose-dimension paradigm in infectious disease science and community health

The rise and fall of the Type Ib supernova iPTF13bvn - Not a massive Wolf-Rayet star

Context. We investigate iPTF13bvn, a core-collapse (CC) supernova (SN) in the nearby spiral galaxy NGC 5806. This object was discovered by the intermediate Palomar Transient Factory (iPTF) very close to the estimated explosion date and was classified as a stripped-envelope CC SN, likely of Type Ib. Furthermore, a possible progenitor detection in pre-explosion Hubble Space Telescope (HST) images was reported, making this the only SN Ib with such an identification. Based on the luminosity and color of the progenitor candidate, as well as on early-time spectra and photometry of the SN, it was argued that the progenitor candidate is consistent with a single, massive Wolf-Rayet (WR) star. Aims. We aim to confirm the progenitor detection, to robustly classify the SN using additional spectroscopy, and to investigate if our follow-up photometric and spectroscopic data on iPTF13bvn are consistent with a single-star WR progenitor scenario. Methods. We present a large set of observational data, consisting of multi-band light curves (UBVRI, g′r′i′z′) and optical spectra. We perform standard spectral line analysis to track the evolution of the SN ejecta. We also construct a bolometric light curve and perform hydrodynamical calculations to model this light curve to constrain the synthesized radioactive nickel mass and the total ejecta mass of the SN. Late-time photometry is analyzed to constrain the amount of oxygen. Furthermore, image registration of pre- and post-explosion HST images is performed. Results. Our HST astrometry confirms the location of the progenitor candidate of iPTF13bvn, and follow-up spectra securely classify this as a SN Ib. We use our hydrodynamical model to fit the observed bolometric light curve, estimating the total ejecta mass to be 1.9 M⊙ and the radioactive nickel mass to be 0.05 M⊙. The model fit requires the nickel synthesized in the explosion to be highly mixed out in the ejecta. We also find that the late-time nebular r′-band luminosity is not consistent with predictions based on the expected oxygen nucleosynthesis in very massive stars. Conclusions. We find that our bolometric light curve of iPTF13bvn is not consistent with the previously proposed single massive WR-star progenitor scenario. The total ejecta mass and, in particular, the late-time oxygen emission are both significantly lower than what would be expected from a single WR progenitor with a main-sequence mass of at least 30 M⊙

Rectal Carriage of Extended-Spectrum Beta-Lactamase-Producing Gram-Negative Bacilli in Community Settings in Madagascar

BACKGROUND: Extended-spectrum ß-lactamase-producing Enterobacteria (ESBL-PE) emerged at the end of the 1980s, causing nosocomial outbreaks and/or hyperendemic situations in hospitals and long-term care facilities. In recent years, community-acquired infections due to ESBL-PE have spread worldwide, especially across developing countries including Madagascar. OBJECTIVES: This study aimed to determine the prevalence and risk factors of intestinal carriage of ESBL-PE in the community of Antananarivo. METHODS: Non-hospitalized patients were recruited in three health centers in different socio economic settings. Fresh stool collected were immediately plated on Drigalski agar containing 3 mg/liter of ceftriaxone. Gram-negative bacilli species were identified and ESBL production was tested by a double disk diffusion (cefotaxime and ceftazidime +/- clavulanate) assay. Characterization of ESBLs were perfomed by PCR and direct sequencing . Molecular epidemiology was analysed by Rep-PCR and ERIC-PCR. RESULTS: 484 patients were screened (sex ratio  = 1.03, median age 28 years). 53 ESBL-PE were isolated from 49 patients (carrier rate 10.1%). The isolates included Escherichia coli (31), Klebsiella pneumoniae (14), Enterobacter cloacae (3), Citrobacter freundii (3), Kluyvera spp. (1) and Pantoae sp.(1). In multivariate analysis, only the socioeconomic status of the head of household was independently associated with ESBL-PE carriage, poverty being the predominant risk factor. CONCLUSIONS: The prevalence of carriage of ESBL in the community of Antananarivo is one of the highest reported worldwide. This alarming spread of resistance genes should be stopped urgently by improving hygiene and streamlining the distribution and consumption of antibiotics

Estimation of the atmospheric flux of nutrients and trace metals to the Eastern Tropical North Atlantic Ocean

Atmospheric deposition contributes potentially significant amounts of the nutrients iron, nitrogen and phosphorus (via mineral dust and anthropogenic aerosols) to the oligotrophic tropical North Atlantic Ocean. Transport pathways, deposition processes and source strengths contributing to this atmospheric flux are all highly variable in space and time. Atmospheric sampling was conducted during 28 research cruises through the Eastern Tropical North Atlantic (ETNA) over a 12 year period and a substantial dataset of measured concentrations of nutrients and trace metals in aerosol and rainfall over the region was acquired. This database was used to quantify (on a spatial- and seasonal-basis) the atmospheric input of ammonium, nitrate, soluble phosphorus and soluble and total iron, aluminium and manganese to the ETNA. The magnitude of atmospheric input varies strongly across the region, with high rainfall rates associated with the Inter-tropical Convergence Zone contributing to high wet deposition fluxes in the south, particularly for soluble species. Dry deposition fluxes of species associated with mineral dust exhibited strong seasonality, with highest fluxes associated with winter-time low-level transport of Saharan dust. Overall (wet plus dry) atmospheric inputs of soluble and total trace metals were used to estimate their soluble fractions. These also varied with season and were generally lower in the dry north than in the wet south. The ratio of ammonium plus nitrate to soluble iron in deposition to the ETNA was lower than the N:Fe requirement for algal growth in all cases, indicating the importance of the atmosphere as a source of excess iron

iPTF16fnl: a faint and fast tidal disruption event in an E+A galaxy

We present ground-based and \textit{Swift} observations of iPTF16fnl, a likely tidal disruption event (TDE) discovered by the intermediate Palomar Transient Factory (iPTF) survey at 66.6 Mpc. The lightcurve of the object peaked at absolute $M_g=-17.2$ mag. The maximum bolometric luminosity (from optical and UV) was $L_p~\simeq~(1.0\,\pm\,0.15) \times 10^{43}$ erg/s, an order of magnitude fainter than any other optical TDE discovered so far. The luminosity in the first 60 days is consistent with an exponential decay, with $L \propto e^{-(t-t_0)/\tau}$, where $t_0$=~57631.0 (MJD) and $\tau\simeq 15$ days. The X-ray shows a marginal detection at $L_X=2.4^{1.9}_{-1.1}\times 10^{39}$ erg/s (\textit{Swift} X-ray Telescope). No radio counterpart was detected down to 3$\sigma$, providing upper limits for monochromatic radio luminosity of $\nu L_{\nu} < 2.3\times10^{36}$ erg/s and $\nu L_{\nu}<1.7\times 10^{37}$ erg/s (VLA, 6.1 and 22 GHz). The blackbody temperature, obtained from combined \textit{Swift} UV and optical photometry, shows a constant value of 19,000 K. The transient spectrum at peak is characterized by broad He II and H$\alpha$ emission lines, with an FWHM of about 14,000 km/s and 10,000 km/s respectively. He I lines are also detected at $\lambda\lambda$ 5875 and 6678. The spectrum of the host is dominated by strong Balmer absorption lines, which are consistent with a post-starburst (E+A) galaxy with an age of $\sim$650 Myr and solar metallicity. The characteristics of iPTF16fnl make it an outlier on both luminosity and decay timescales, as compared to other optically selected TDEs. The discovery of such a faint optical event suggests a higher rate of tidal disruptions, as low luminosity events may have gone unnoticed in previous searches.Comment: 14 pages, 11 figures, accepted for publication in Ap