Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids

<p>Abstract</p> <p>Background</p> <p>Many microbes possess restriction-modification systems that protect them from parasitic DNA molecules. Unfortunately, the presence of a restriction-modification system in a given microbe also hampers genetic analysis. Although plasmids can be successfully conjugated into the enteropathogenic <it>Escherichia coli </it>strain E2348/69 and optimized protocols for competent cell preparation have been developed, we found that a large, low copy (~15) bioluminescent reporter plasmid, pJW15, that we modified for use in EPEC, was exceedingly difficult to transform into E2348/69. We reasoned that a restriction-modification system could be responsible for the low transformation efficiency of E2348/69 and sought to identify and inactivate the responsible gene(s), with the goal of creating an easily transformable strain of EPEC that could complement existing protocols for genetic manipulation of this important pathogen.</p> <p>Results</p> <p>Using bioinformatics, we identified genes in the unfinished enteropathogenic <it>Escherichia coli </it>(EPEC) strain E2348/69 genome whose predicted products bear homology to the HsdM methyltransferases, HsdS specificity subunits, and HsdR restriction endonucleases of type I restriction-modification systems. We constructed a strain carrying a deletion of the conserved enzymatic domain of the EPEC HsdR homologue, NH4, and showed that its transformation efficiency was up to four orders of magnitude higher than that of the parent strain. Further, the modification capacity of NH4 remained intact, since plasmids that were normally recalcitrant to transformation into E2348/69 could be transformed upon passage through NH4. NH4 was unaffected in virulence factor production, since bundle forming pilus (BFP) subunits and type III secreted (T3S) proteins were present at equivalent levels to those seen in E2348/69. Further, NH4 was indistinguishable from E2348/69 in tissue culture infection model assays of localized adherence and T3S.</p> <p>Conclusion</p> <p>We have shown that EPEC strain E2348/69 utilizes a type I restriction-modification system to limit entry of new DNA. This restriction-modification system does not appear to be involved in virulence determinant expression or infection phenotypes. The <it>hsdR </it>mutant strain should prove useful in genetic analysis of the important diarrheal pathogen EPEC.</p

The physical significance of the Babak-Grishchuk gravitational energy-momentum tensor

We examine the claim of Babak and Grishchuk [1] to have solved the problem of localising the energy and momentum of the gravitational field. After summarising Grishchuk's flat-space formulation of gravity, we demonstrate its equivalence to General Relativity at the level of the action. Two important transformations are described (diffeomorphisms applied to all fields, and diffeomorphisms applied to the flat-space metric alone) and we argue that both should be considered gauge transformations: they alter the mathematical representation of a physical system, but not the system itself. By examining the transformation properties of the Babak-Grishchuk gravitational energy-momentum tensor under these gauge transformations (infinitesimal and finite) we conclude that this object has no physical significance.Comment: 10 pages. Submitted to Phys. Rev. D; acknowledgements adjuste

Limits on Arcminute Scale Cosmic Microwave Background Anisotropy with the BIMA Array

We have used the Berkeley-Illinois-Maryland-Association (BIMA) millimeter array outfitted with sensitive cm-wave receivers to search for Cosmic Microwave Background (CMB) anisotropies on arcminute scales. The interferometer was placed in a compact configuration which produces high brightness sensitivity, while providing discrimination against point sources. Operating at a frequency of 28.5 GHz, the FWHM primary beam of the instrument is 6.6 arcminutes. We have made sensitive images of seven fields, five of which where chosen specifically to have low IR dust contrast and be free of bright radio sources. Additional observations with the Owens Valley Radio Observatory (OVRO) millimeter array were used to assist in the location and removal of radio point sources. Applying a Bayesian analysis to the raw visibility data, we place limits on CMB anisotropy flat-band power Q_flat = 5.6 (+3.0 -5.6) uK and Q_flat < 14.1 uK at 68% and 95% confidence. The sensitivity of this experiment to flat band power peaks at a multipole of l = 5470, which corresponds to an angular scale of approximately 2 arcminutes. The most likely value of Q_flat is similar to the level of the expected secondary anisotropies.Comment: 15 pages, 5 figures, LaTex, aas2pp4.sty, ApJ submitte

Scalability tests of R-GMA-based grid job monitoring system for CMS Monte Carlo data production

Copyright @ 2004 IEEEHigh-energy physics experiments, such as the compact muon solenoid (CMS) at the large hadron collider (LHC), have large-scale data processing computing requirements. The grid has been chosen as the solution. One important challenge when using the grid for large-scale data processing is the ability to monitor the large numbers of jobs that are being executed simultaneously at multiple remote sites. The relational grid monitoring architecture (R-GMA) is a monitoring and information management service for distributed resources based on the GMA of the Global Grid Forum. We report on the first measurements of R-GMA as part of a monitoring architecture to be used for batch submission of multiple Monte Carlo simulation jobs running on a CMS-specific LHC computing grid test bed. Monitoring information was transferred in real time from remote execution nodes back to the submitting host and stored in a database. In scalability tests, the job submission rates supported by successive releases of R-GMA improved significantly, approaching that expected in full-scale production

Filtering techniques for the detection of Sunyaev-Zel'dovich clusters in multifrequency CMB maps

The problem of detecting Sunyaev-Zel'dovich (SZ) clusters in multifrequency CMB observations is investigated using a number of filtering techniques. A multifilter approach is introduced, which optimizes the detection of SZ clusters on microwave maps. An alternative method is also investigated, in which maps at different frequencies are combined in an optimal manner so that existing filtering techniques can be applied to the single combined map. The SZ profiles are approximated by the circularly-symmetric template $\tau (x) = [1 +(x/r_c)^2]^{-\lambda}$, with $\lambda \simeq \tfrac{1}{2}$ and $x\equiv |\vec{x}|$, where the core radius $r_c$ and the overall amplitude of the effect are not fixed a priori, but are determined from the data. The background emission is modelled by a homogeneous and isotropic random field, characterized by a cross-power spectrum $P_{\nu_1 \nu_2}(q)$ with $q\equiv |\vec{q}|$. The filtering methods are illustrated by application to simulated Planck observations of a $12.8^\circ \times 12.8^\circ$ patch of sky in 10 frequency channels. Our simulations suggest that the Planck instrument should detect $\approx 10000$ SZ clusters in 2/3 of the sky. Moreover, we find the catalogue to be complete for fluxes $S > 170$ mJy at 300 GHz.Comment: 12 pages, 7 figures; Corrected figures. Submitted to MNRA

Cosmological applications of a wavelet analysis on the sphere

The cosmic microwave background (CMB) is a relic radiation of the Big Bang and as such it contains a wealth of cosmological information. Statistical analyses of the CMB, in conjunction with other cosmological observables, represent some of the most powerful techniques available to cosmologists for placing strong constraints on the cosmological parameters that describe the origin, content and evolution of the Universe. The last decade has witnessed the introduction of wavelet analyses in cosmology and, in particular, their application to the CMB. We review here spherical wavelet analyses of the CMB that test the standard cosmological concordance model. The assumption that the temperature anisotropies of the CMB are a realisation of a statistically isotropic Gaussian random field on the sphere is questioned. Deviations from both statistical isotropy and Gaussianity are detected in the reviewed works, suggesting more exotic cosmological models may be required to explain our Universe. We also review spherical wavelet analyses that independently provide evidence for dark energy, an exotic component of our Universe of which we know very little currently. The effectiveness of accounting correctly for the geometry of the sphere in the wavelet analysis of full-sky CMB data is demonstrated by the highly significant detections of physical processes and effects that are made in these reviewed works.Comment: 17 pages, 8 figures; JFAA invited review, in pres

Neural networks and separation of Cosmic Microwave Background and astrophysical signals in sky maps

The Independent Component Analysis (ICA) algorithm is implemented as a neural network for separating signals of different origin in astrophysical sky maps. Due to its self-organizing capability, it works without prior assumptions on the signals, neither on their frequency scaling, nor on the signal maps themselves; instead, it learns directly from the input data how to separate the physical components, making use of their statistical independence. To test the capabilities of this approach, we apply the ICA algorithm on sky patches, taken from simulations and observations, at the microwave frequencies, that are going to be deeply explored in a few years on the whole sky, by the Microwave Anisotropy Probe (MAP) and by the {\sc Planck} Surveyor Satellite. The maps are at the frequencies of the Low Frequency Instrument (LFI) aboard the {\sc Planck} satellite (30, 44, 70 and 100 GHz), and contain simulated astrophysical radio sources, Cosmic Microwave Background (CMB) radiation, and Galactic diffuse emissions from thermal dust and synchrotron. We show that the ICA algorithm is able to recover each signal, with precision going from 10% for the Galactic components to percent for CMB; radio sources are almost completely recovered down to a flux limit corresponding to $0.7\sigma_{CMB}$, where $\sigma_{CMB}$ is the rms level of CMB fluctuations. The signal recovering possesses equal quality on all the scales larger then the pixel size. In addition, we show that the frequency scalings of the input signals can be partially inferred from the ICA outputs, at the percent precision for the dominant components, radio sources and CMB.Comment: 15 pages; 6 jpg and 1 ps figures. Final version to be published in MNRA

The estimation of the SZ effects with unbiased multifilters

In this work we study the performance of linear multifilters for the estimation of the amplitudes of the thermal and kinematic Sunyaev-Zel'dovich effects. We show that when both effects are present, estimation of these effects with standard matched multifilters is intrinsically biased. This bias is due to the fact that both signals have basically the same spatial profile. We find a new family of multifilters related to the matched multifilters that cancel this systematic bias, hence we call them Unbiased Matched Multifilters. We test the unbiased matched multifilters and compare them with the standard matched multifilters using simulations that reproduce the future Planck mission's observations. We find that in the case of the standard matched multifilters the systematic bias in the estimation of the kinematic Sunyaev-Zel'dovich effect can be very large, even greater than the statistical error bars. Unbiased matched multifilters cancel effectively this kind of bias. In concordance with other works in the literature, our results indicate that the sensitivity and resolution of Planck will not be enough to give reliable estimations of the kinematic Sunyaev-Zel'dovich of individual clusters. However, since the estimation with the unbiased matched multifilters is not intrinsically biased, it can be possible to use them to statistically study peculiar velocities in large scales using large sets of clusters.Comment: 12 pages, 6 figures, submitted to MNRA

Bayesian modelling of clusters of galaxies from multi-frequency pointed Sunyaev--Zel'dovich observations

We present a Bayesian approach to modelling galaxy clusters using multi-frequency pointed observations from telescopes that exploit the Sunyaev--Zel'dovich effect. We use the recently developed MultiNest technique (Feroz, Hobson & Bridges, 2008) to explore the high-dimensional parameter spaces and also to calculate the Bayesian evidence. This permits robust parameter estimation as well as model comparison. Tests on simulated Arcminute Microkelvin Imager observations of a cluster, in the presence of primary CMB signal, radio point sources (detected as well as an unresolved background) and receiver noise, show that our algorithm is able to analyse jointly the data from six frequency channels, sample the posterior space of the model and calculate the Bayesian evidence very efficiently on a single processor. We also illustrate the robustness of our detection process by applying it to a field with radio sources and primordial CMB but no cluster, and show that indeed no cluster is identified. The extension of our methodology to the detection and modelling of multiple clusters in multi-frequency SZ survey data will be described in a future work.Comment: 12 pages, 7 figures, submitted to MNRA

Do measures of memory, language, and attention predict eyewitness memory in children with and without autism?

Background & aims. There are few investigations of the relationship between cognitive abilities (memory, language and attention) and children’s eyewitness performance in typically developing children (TD), and even fewer in children on the autism spectrum. Such investigations are important to identify key cognitive processes underlying eyewitness recall, and assess how predictive such measures are compared to non-verbal IQ, diagnostic group status (autism or TD) and age. Methods. A total of 272 children (162 boys; 110 girls) of age 76 months to 142 months (M = 105 months) took part in this investigation: 71 children with autism and 201 TD children. The children saw a staged event involving a minor mock crime and were asked about what they had witnessed in an immediate Brief Interview. This focused on free recall, included a small number of open-ended questions, and was designed to resemble an initial evidence gathering statement taken by police officers arriving at a crime scene. Children were also given standardised tests of intelligence, memory, language and attention. Results & conclusions. Despite the autism group recalling significantly fewer items of correct information than the TD group at Brief Interview, both groups were equally accurate in their recall: 89% of details recalled by the TD group and 87% of the details recalled by the autism group were correct. To explore the relationship between Brief Interview performance and the cognitive variables, alongside age, diagnostic group status and non-verbal IQ, multiple hierarchical regression analyses were conducted, with Brief Interview performance as the dependant variable. Age and diagnostic group status were significant predictors of correct recall, whereas non-verbal IQ was less important. After age, non-verbal IQ and diagnostic group status had been accounted for, the only cognitive variables that were significant predictors of Brief Interview performance were measures of memory (specifically, memory for faces and memory for stories). There was little evidence of there being differences between the autism and TD groups in the way the cognitive variables predicted the Brief Interview. Implications. The findings provide reassurance that age – the most straightforward information to which all relevant criminal justice professionals have access – provides a helpful indication of eyewitness performance. The accuracy of prediction can be improved by knowing the child’s diagnostic status (i.e., whether the child is on the autism spectrum), and further still by using more specific assessments (namely memory for faces and memory for stories), possibly via the input of a trained professional. Importantly, the findings also confirm that whilst children with autism may recall less information than TD children, the information they do recall is just as accurate