When and where? Pathogenic Escherichia coli differentially sense host D-serine using a universal transporter system to monitor their environment

Sensing environmental stimuli is critically important for bacteria when faced with the multitude of adversities presented within the host. Responding appropriately to these signals and in turn integrating these responses into the regulatory network of the cell allows bacteria to control precisely when and where they should establish colonization. D-serine is an abundant metabolite of the human urinary tract but is a toxic metabolite for Escherichia coli that lack a D-serine tolerance locus. Enterohaemorrhagic E. coli (EHEC) cannot catabolize D-serine for this reason and colonize the large intestine specifically, an environment low in D-serine. EHEC can however use D-serine sensing to repress colonization thus signaling the presence of an unfavorable environment. In our recent work (Connolly, et al. PLoS Pathogens (2016) 12(1): e1005359), we describe the discovery of a functional and previously uncharacterized D-serine uptake system in E. coli. The genes identified are highly conserved in all E. coli lineages but are regulated differentially in unique pathogenic backgrounds. The study identified that EHEC, counter-intuitively, increase D-serine uptake in its presence but that this is a tolerated process and is used to increase the transcriptional response to this signal. It was also found that the system has been integrated into the transcriptional network of EHEC-specific virulence genes, demonstrating an important pathotype-specific adaptation of core genome components

Towards More Precise Photometric Redshifts: Calibration Via CCD Photometry

We present the initial results from a deep, multi-band photometric survey of selected high Galactic latitude redshift fields. Previous work using the photographic data of Koo and Kron demonstrated that the distribution of galaxies in the multi-dimensional flux space U B R I is nearly planar. The position of a galaxy within this plane is determined by its redshift, luminosity and spectral type. Using recently acquired deep CCD photometry in existing, published redshift fields, we have redetermined the distribution of galaxies in this four-dimensional magnitude space. Furthermore, from our CCD photometry and the published redshifts, we have quantified the photometric-redshift relation within the standard AB magnitude system. This empirical relation has a measured dispersion of approximately 0.02 for z < 0.4. With this work we are reaching the asymptotic intrinsic dispersions that were predicted from simulated distributions of galaxy colors.Comment: submitted to the Astrophysical Journal Letter

Evolution in the Clustering of Galaxies for Z < 1

Measuring the evolution in the clustering of galaxies over a large redshift range is a challenging problem. For a two-dimensional galaxy catalog, however, we can measure the galaxy-galaxy angular correlation function which provides information on the density distribution of galaxies. By utilizing photometric redshifts, we can measure the angular correlation function in redshift shells (Brunner 1997, Connolly et al. 1998) which minimizes the galaxy projection effect, and allows for a measurement of the evolution in the correlation strength with redshift. In this proceedings, we present some preliminary results which extend our previous work using more accurate photometric redshifts, and also incorporate absolute magnitudes, so that we can measure the evolution of clustering with either redshift or intrinsic luminosity.Comment: 6 pages, 6 figures requires paspconf.sty. To be published in "Photometric Redshifts and High Redshift Galaxies", eds. R. Weymann, L. Storrie-Lombardi, M. Sawicki & R. Brunner, (San Francisco: ASP Conference Series

Tracking elusive cargo: Illuminating spatio-temporal type 3 effector protein dynamics using reporters

Type 3 secretion systems (T3SS) form an integral part of the arsenal of many pathogenic bacteria. These injection machines, together with their cargo of subversive effector proteins are capable of manipulating the cellular environment of the host in order to ensure persistence of the pathogen. In order to fully appreciate the functions of Type 3 effectors it is necessary to gain spatio-temporal knowledge of each effector during the process of infection. A number of genetic modifications have been exploited in order to reveal effector protein secretion, translocation and subsequent activity and localisation within host cells. In this review, we will discuss the many available approaches for tracking effector protein dynamics and discuss the challenges faced to improve the current technologies and gain a clearer picture of effector protein function

Inter-cluster filaments in a Λ\LambdaCDM Universe

The large--scale structure (LSS) in the Universe comprises a complicated filamentary network of matter. We study this network using a high--resolution simulation of structure formation of a $\Lambda$ Cold Dark Matter cosmology. We investigate the distribution of matter between neighbouring large haloes whose masses are comparable to massive clusters of galaxies. We identify a total of 228 filaments between neighbouring clusters. Roughly half of the filaments are either warped or lie off the cluster--cluster axis. We find that straight filaments on the average are shorter than warped ones. More massive clusters are connected to more filaments than less massive ones on average. This finding indicates that the most massive clusters form at the intersections of the filamentary backbone of LSS. For straight filaments, we compute mass profiles. Radial profiles show a fairly well--defined radius, $r_s$, beyond which the profiles follow an $r^{-2}$ power law fairly closely. For the majority of filaments, $r_s$ lies between 1.5 $h^{-1}$ Mpc and 2.0 $h^{-1}$ Mpc. The enclosed overdensity inside $r_s$ varies between a few times up to 25 times mean density, independent of the length of the filaments. Along the filaments' axes, material is not distributed uniformly. Towards the clusters, the density rises, indicating the presence of the cluster infall regions. In addition, we also find some sheet--like connections between clusters. In roughly a fifth of all cluster--cluster connections where we could not identify a filament or sheet, projection effects lead to filamentary structures in the projected mass distribution. (abridged)Comment: 10 pages, 18 figures; submitted to MNRAS; updated: final version, accepted for publicatio

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