On the spectroastrometric separation of binary point-source fluxes

Spectroastrometry is a technique which has the potential to resolve flux distributions on scales of milliarcseconds. In this study, we examine the application of spectroastrometry to binary point sources which are spatially unresolved due to the observational point spread function convolution. The technique uses measurements with sub-pixel accuracy of the position centroid of high signal-to-noise long-slit spectrum observations. With the objects in the binary contributing fractionally more or less at different wavelengths (particularly across spectral lines), the variation of the position centroid with wavelength provides some information on the spatial distribution of the flux. We examine the width of the flux distribution in the spatial direction, and present its relation to the ratio of the fluxes of the two components of the binary. Measurement of three observables (total flux, position centroid and flux distribution width) at each wavelength allows a unique separation of the total flux into its component parts even though the angular separation of the binary is smaller than the observations' point-spread function. This is because we have three relevant observables for three unknowns (the two fluxes, and the angular separation of the binary), which therefore generates a closed problem. This is a wholly different technique than conventional deconvolution methods, which produce information on angular sizes of the sampling scale. Spectroastrometry can produce information on smaller scales than conventional deconvolution, and is successful in separating fluxes in a binary object with a separation of less than one pixel. We present an analysis of the errors involved in making binary object spectroastrometric measurements and the separation method, and highlight necessary observing methodology.Comment: 11 pages, 8 figures, accepted for publication in Astronomy and Astrophysic

Development and validation of a chemostat gut model to study both planktonic and biofilm modes of growth of Clostridium difficile and human microbiota

Copyright: 2014 Crowther et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The human gastrointestinal tract harbours a complex microbial community which exist in planktonic and sessile form. The degree to which composition and function of faecal and mucosal microbiota differ remains unclear. We describe the development and characterisation of an in vitro human gut model, which can be used to facilitate the formation and longitudinal analysis of mature mixed species biofilms. This enables the investigation of the role of biofilms in Clostridium difficile infection (CDI). A well established and validated human gut model of simulated CDI was adapted to incorporate glass rods that create a solid-gaseous-liquid interface for biofilm formation. The continuous chemostat model was inoculated with a pooled human faecal emulsion and controlled to mimic colonic conditions in vivo. Planktonic and sessile bacterial populations were enumerated for up to 46 days. Biofilm consistently formed macroscopic structures on all glass rods over extended periods of time, providing a framework to sample and analyse biofilm structures independently. Whilst variation in biofilm biomass is evident between rods, populations of sessile bacterial groups (log10 cfu/g of biofilm) remain relatively consistent between rods at each sampling point. All bacterial groups enumerated within the planktonic communities were also present within biofilm structures. The planktonic mode of growth of C. difficile and gut microbiota closely reflected observations within the original gut model. However, distinct differences were observed in the behaviour of sessile and planktonic C. difficile populations, with C. difficile spores preferentially persisting within biofilm structures. The redesigned biofilm chemostat model has been validated for reproducible and consistent formation of mixed species intestinal biofilms. This model can be utilised for the analysis of sessile mixed species communities longitudinally, potentially providing information of the role of biofilms in CDI.Peer reviewe

Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria

Clostridium difficile is a Gram-positive spore-forming anaerobe and a major cause of antibiotic-associated diarrhoea. Disruption of the commensal microbiota, such as through treatment with broad-spectrum antibiotics, is a critical precursor for colonisation by C. difficile and subsequent disease. Furthermore, failure of the gut microbiota to recover colonisation resistance can result in recurrence of infection. An unusual characteristic of C. difficile among gut bacteria is its ability to produce the bacteriostatic compound para-cresol (p-cresol) through fermentation of tyrosine. Here, we demonstrate that the ability of C. difficile to produce p-cresol in vitro provides a competitive advantage over gut bacteria including Escherichia coli, Klebsiella oxytoca and Bacteroides thetaiotaomicron. Metabolic profiling of competitive co-cultures revealed that acetate, alanine, butyrate, isobutyrate, p-cresol and p-hydroxyphenylacetate were the main metabolites responsible for differentiating the parent strain C. difficile (630Δerm) from a defined mutant deficient in p-cresol production. Moreover, we show that the p-cresol mutant displays a fitness defect in a mouse relapse model of C. difficile infection (CDI). Analysis of the microbiome from this mouse model of CDI demonstrates that colonisation by the p-cresol mutant results in a distinctly altered intestinal microbiota, and metabolic profile, with a greater representation of Gammaproteobacteria, including the Pseudomonales and Enterobacteriales. We demonstrate that Gammaproteobacteria are susceptible to exogenous p-cresol in vitro and that there is a clear divide between bacterial Phyla and their susceptibility to p-cresol. In general, Gram-negative species were relatively sensitive to p-cresol, whereas Gram-positive species were more tolerant. This study demonstrates that production of p-cresol by C. difficile has an effect on the viability of intestinal bacteria as well as the major metabolites produced in vitro. These observations are upheld in a mouse model of CDI, in which p-cresol production affects the biodiversity of gut microbiota and faecal metabolite profiles, suggesting that p-cresol production contributes to C. difficile survival and pathogenesis.Peer reviewedFinal Published versio

Short-term genome stability of serial Clostridium difficile ribotype 027 isolates in an experimental gut model and recurrent human disease

Copyright: © 2013 Eyre et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedClostridium difficile whole genome sequencing has the potential to identify related isolates, even among otherwise indistinguishable strains, but interpretation depends on understanding genomic variation within isolates and individuals.Serial isolates from two scenarios were whole genome sequenced. Firstly, 62 isolates from 29 timepoints from three in vitro gut models, inoculated with a NAP1/027 strain. Secondly, 122 isolates from 44 patients (2–8 samples/patient) with mostly recurrent/on-going symptomatic NAP-1/027 C. difficile infection. Reference-based mapping was used to identify single nucleotide variants (SNVs).Across three gut model inductions, two with antibiotic treatment, total 137 days, only two new SNVs became established. Pre-existing minority SNVs became dominant in two models. Several SNVs were detected, only present in the minority of colonies at one/two timepoints. The median (inter-quartile range) [range] time between patients’ first and last samples was 60 (29.5–118.5) [0–561] days. Within-patient C. difficile evolution was 0.45 SNVs/called genome/year (95%CI 0.00–1.28) and within-host diversity was 0.28 SNVs/called genome (0.05–0.53). 26/28 gut model and patient SNVs were non-synonymous, affecting a range of gene targets.The consistency of whole genome sequencing data from gut model C. difficile isolates, and the high stability of genomic sequences in isolates from patients, supports the use of whole genome sequencing in detailed transmission investigations.Peer reviewe

Chromosphere of K giant stars Geometrical extent and spatial structure detection

We aim to constrain the geometrical extent of the chromosphere of non-binary K giant stars and detect any spatial structures in the chromosphere. We performed observations with the CHARA interferometer and the VEGA beam combiner at optical wavelengths. We observed seven non-binary K giant stars. We measured the ratio of the radii of the photosphere to the chromosphere using the interferometric measurements in the Halpha and the Ca II infrared triplet line cores. For beta Ceti, spectro-interferometric observations are compared to an non-local thermal equilibrium (NLTE) semi-empirical model atmosphere including a chromosphere. The NLTE computations provide line intensities and contribution functions that indicate the relative locations where the line cores are formed and can constrain the size of the limb-darkened disk of the stars with chromospheres. We measured the angular diameter of seven K giant stars and deduced their fundamental parameters: effective temperatures, radii, luminosities, and masses. We determined the geometrical extent of the chromosphere for four giant stars. The chromosphere extents obtained range between 16% to 47% of the stellar radius. The NLTE computations confirm that the Ca II/849 nm line core is deeper in the chromosphere of ? Cet than either of the Ca II/854 nm and Ca II/866 nm line cores. We present a modified version of a semi-empirical model atmosphere derived by fitting the Ca II triplet line cores of this star. In four of our targets, we also detect the signature of a differential signal showing the presence of asymmetries in the chromospheres. Conclusions. It is the first time that geometrical extents and structure in the chromospheres of non-binary K giant stars are determined by interferometry. These observations provide strong constrains on stellar atmosphere models.Comment: 10 pages, 12 figure

Close binary companions of the HAeBe stars LkHa 198, Elias 1, HK Ori and V380 Ori

We present diffraction-limited bispectrum speckle interferometry observations of four well-known Herbig Ae/Be (HAeBe) stars, LkHa 198, Elias 1, HK Ori and V380 Ori. For two of these, LkHa 198 and Elias 1, we present the first unambiguous detection of close companions. The plane of the orbit of the new LkHa 198 companion appears to be significantly inclined to the plane of the circumprimary disk, as inferred from the orientation of the outflow. We show that the Elias 1 companion may be a convective star, and suggest that it could therefore be the true origin of the X-ray emission from this object. In the cases of HK Ori and V380 Ori, we present new measurements of the relative positions of already-known companions, indicating orbital motion. For HK Ori, photometric measurements of the brightness of the individual components in four bands allowed us to decompose the system spectral energy distribution (SED) into the two separate component SEDs. The primary exhibits a strong infrared excess which suggests the presence of circumstellar material, whereas the companion can be modelled as a naked photosphere. The infrared excess of HK Ori A was found to contribute around two thirds of the total emission from this component, suggesting that accretion power contributes significantly to the flux. Submillimetre constraints mean that the circumstellar disk cannot be particularly massive, whilst the near-infrared data indicates a high accretion rate. Either the disk lifetime is very short, or the disk must be seen in an outburst phase.Comment: 14 pages, 10 figures, 22 separate figure file

Randomized clinical trial to evaluate the effect of fecal microbiota transplant for initial Clostridium difficile infection in intestinal microbiome

Objective The aim of this study was to evaluate the impact of fecal donor-unrelated donor mix (FMT-FURM) transplantation as first-line therapy for C. difficile infection (CDI) in intestinal microbiome. Methods We designed an open, two-arm pilot study with oral vancomycin (250mg every 6 h for 10–14 days) or FMT-FURM as treatments for the first CDI episode in hospitalized adult patients in Hospital Universitario “Dr. Jose Eleuterio Gonzalez”. Patients were randomized by a closed envelope method in a 1: 1 ratio to either oral vancomycin or FMT-FURM. CDI resolution was considered when there was a reduction on the Bristol scale of at least 2 points, a reduction of at least 50% in the number of bowel movements, absence of fever, and resolution of abdominal pain (at least two criteria). From each patient, a fecal sample was obtained at days 0, 3, and 7 after treatment. Specimens were cultured to isolate C. difficile, and isolates were characterized by PCR. Susceptibility testing of isolates was performed using the agar dilution method. Fecal samples and FMT-FURM were analyzed by 16S rRNA sequencing. Results We included 19 patients; 10 in the vancomycin arm and 9 in the FMT-FURM arm. However, one of the patients in the vancomycin arm and two patients in the FMT-FURM arm were eliminated. Symptoms resolved in 8/9 patients (88.9%) in the vancomycin group, while symptoms resolved in 4/7 patients (57.1%) after the first FMT-FURM dose (P = 0.26) and in 5/7 patients (71.4%) after the second dose (P = 0.55). During the study, no adverse effects attributable to FMT-FURM were observed in patients. Twelve isolates were recovered, most isolates carried tcdB, tcdA, cdtA, and cdtB, with an 18-bp deletion in tcdC. All isolates were resistant to ciprofloxacin and moxifloxacin but susceptible to metronidazole, linezolid, fidaxomicin, and tetracycline. In the FMT-FURM group, the bacterial composition was dominated by Firmicutes, Bacteroidetes, and Proteobacteria at all-time points and the microbiota were remarkably stable over time. The vancomycin group showed a very different pattern of the microbial composition when comparing to the FMT-FURM group over time. Conclusion The results of this preliminary study showed that FMT-FURM for initial CDI is associated with specific bacterial communities that do not resemble the donors’ sample.Peer reviewedFinal Published versio

Equatorial winds on Saturn and the stratospheric oscillation

The zonal jets on the giant planets have been thought to be stable in time. A decline in the velocity of Saturn’s equatorial jet has been identified, on the basis of a comparison of cloud-tracking data across two decades, but the differences in cloud speeds have since been suggested to stem from changes in cloud altitude in combination with vertical wind shear, rather than from temporal changes in wind strength at a given height. Here, we combine observations of cloud tracks and of atmospheric temperatures taken by two instruments on the Cassini spacecraft to reveal a significant temporal variation in the strength of the high-altitude equatorial jet on Saturn. Specifically, we find that wind speeds at atmospheric pressure levels of 60 mbar, corresponding to Saturn’s tropopause, increased by about 20 m s^(−1) between 2004 and 2008, whereas the wind speed has been essentially constant over time in the southern equatorial troposphere. The observations further reveal that the equatorial jet intensified by about 60 m s^(−1) between 2005 and 2008 in the stratosphere, that is, at pressure levels of 1–5 mbar. Because the wind acceleration is weaker near the tropopause than higher up, in the stratosphere, we conclude that the semi-annual equatorial oscillation of Saturn’s middle atmosphere is also damped as it propagates downwards

Strong Temporal Variation Over One Saturnian Year: From Voyager to Cassini

Here we report the combined spacecraft observations of Saturn acquired over one Saturnian year (~29.5 Earth years), from the Voyager encounters (1980–81) to the new Cassini reconnaissance (2009–10). The combined observations reveal a strong temporal increase of tropic temperature (~10 Kelvins) around the tropopause of Saturn (i.e., 50 mbar), which is stronger than the seasonal variability (~a few Kelvins). We also provide the first estimate of the zonal winds at 750 mbar, which is close to the zonal winds at 2000 mbar. The quasi-consistency of zonal winds between these two levels provides observational support to a numerical suggestion inferring that the zonal winds at pressures greater than 500 mbar do not vary significantly with depth. Furthermore, the temporal variation of zonal winds decreases its magnitude with depth, implying that the relatively deep zonal winds are stable with time

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as ‘accidental cell death’ (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. ‘Regulated cell death’ (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death