On the calculation of UNil

Cappell's codimension 1 splitting obstruction surgery group UNil_n(R;R,R) of a ring with involution R is a direct summand of the Wall surgery obstruction group L_n(R[D_{\infty}]) of the amalgamated free product R[D_{\infty}] = R[Z_2]*_RR[Z_2], with D_{\infty}=Z_2*Z_2 the infinite dihedral group. We use the quadratic Poincar\'e cobordism formulation of the L-groups to prove that L_n(R[x]) = L_n(R)\oplus UNil_n(R;R,R), with \bar{x} = x . We combine this with M. Weiss' universal chain bundle theory to produce almost complete calculations of UNil_*(Z;Z,Z) and L_*(Z[D_{\infty}]).Comment: 48 pages, LATEX. Final version, to appear in Advances in Mathematic

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

Pseudomonas aeruginosa can be detected in a polymicrobial competition model using impedance spectroscopy with a novel biosensor

Electrochemical Impedance Spectroscopy (EIS) is a powerful technique that can be used to elicit information about an electrode interface. In this article, we highlight six principal processes by which the presence of microorganisms can affect impedance and show how one of these - the production of electroactive metabolites - changes the impedance signature of culture media containing Pseudomonas aeruginosa. EIS, was used in conjunction with a low cost screen printed carbon sensor to detect the presence of P. aeruginosa when grown in isolation or as part of a polymicrobial infection with Staphylococcus aureus. By comparing the electrode to a starting measurement, we were able to identify an impedance signature characteristic of P. aeruginosa. Furthermore, we are able to show that one of the changes in the impedance signature is due to pyocyanin and associated phenazine compounds. The findings of this study indicate that it might be possible to develop a low cost sensor for the detection of P. aeruginosa in important point of care diagnostic applications. In particular, we suggest that a development of the device described here could be used in a polymicrobial clinical sample such as sputum from a CF patient to detect P. aeruginosa

Efficient Iterative Processing in the SciDB Parallel Array Engine

Many scientific data-intensive applications perform iterative computations on array data. There exist multiple engines specialized for array processing. These engines efficiently support various types of operations, but none includes native support for iterative processing. In this paper, we develop a model for iterative array computations and a series of optimizations. We evaluate the benefits of an optimized, native support for iterative array processing on the SciDB engine and real workloads from the astronomy domain

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

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