Identification of a New Family of Enzymes with Potential \u3cem\u3eO\u3c/em\u3e-acetylpeptidoglycan esterase activity in both Gram-positive and Gram-negative bacteria

Background: The metabolism of the rigid bacterial cell wall heteropolymer peptidoglycan is a dynamic process requiring continuous biosynthesis and maintenance involving the coordination of both lytic and synthetic enzymes. The O-acetylation of peptidoglycan has been proposed to provide one level of control on these activities as this modification inhibits the action of the major endogenous lytic enzymes, the lytic transglycosylases. The O-acetylation of peptidoglycan also inhibits the activity of the lysozymes which serve as the first line of defense of host cells against the invasion of bacterial pathogens. Despite this central importance, there is a dearth of information regarding peptidoglycan O-acetylation and nothing has previously been reported on its de-acetylation. Results: Homology searches of the genome databases have permitted this first report on the identification of a potential family of O-Acetylpeptidoglycan esterases (Ape). These proteins encoded in the genomes of a variety of both Gram-negative and Gram-positive bacteria, including a number of important human pathogens such as species of Neisseria, Helicobacter, Campylobacter, and Bacillus anthracis, have been organized into three families based on amino acid sequence similarities with family 1 being further divided into three sub-families. The genes encoding these proteins are shown to be clustered with Peptidoglycan O-acetyltransferases (Pat) and in some cases, together with other genes involved in cell wall metabolism. Representative bacteria that encode the Ape proteins were experimentally shown to produce O-acetylated peptidoglycan. Conclusion: The hypothetical proteins encoded by the pat and ape genes have been organized into families based on sequence similarities. The Pat proteins have sequence similarity to Pseudomonas aeruginosa AlgI, an integral membrane protein known to participate in the O-acetylation of the exopolysaccaride, alginate. As none of the bacteria that harbor the pat genes produce alginate, we propose that the Pat proteins serve to O-acetylate peptidoglycan which is known to be a maturation event occurring in the periplasm. The Ape sequences have amino acid sequence similarity to the CAZy CE 3 carbohydrate esterases, a family previously known to be composed of only O-acetylxylan esterases. They are predicted to contain the α/β hydrolase fold associated with the GDSL and TesA hydrolases and they possess the signature motifs associated with the catalytic residues of the CE3 esterases. Specific signature sequence motifs were identified for the Ape proteins which led to their organization into distinct families. We propose that by expressing both Pat and Ape enzymes, bacteria would be able to obtain a high level of localized control over the degradation of peptidoglycan through the attachment and removal of O-linked acetate. This would facilitate the efficient insertion of pores and flagella, localize spore formation, and control the level of general peptidoglycan turnover

Iue observations of Neptune for H Lyman‐ α emission

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94965/1/grl3980.pd

Sounding Rocket

This project has resulted in 4 launches from the White Sands Missile Range of our payload in different stages of development, on: (1) 4 May 1991 Flight 36.062; (2) 16 June 1993 Flight 36.101; (3) 1 April 1995 Flight 36.104; and (5) 28 October 1996 Flight 36.149. For each flight, the following activities were accomplished: (1) prepare the experiment, including replacement and upgrading of critical components, at the University of Michigan; (2) integrate the payload either at the Wallops Flight Facility; (3) perform final far-UV calibration of instrument; (4) perform final alignment, integration, and electrical checks at WSMR (5) launch payload from WSMR (6) check condition of recovered payload (7) perform post-flight calibration, if necessary and applicable; and (8) reduce and analyze flight data. A description of the instrument is presented, along with overviews of the results of the four flights. We are presently preparing the payload for the next flight in 1998/99

SNIFFER WFD119: Enhancement of the River Invertebrate Classification Tool (RICT)

EXECUTIVE SUMMARY Project funders/partners: Environment Agency (EA), Northern Ireland Environment Agency (NIEA), Scotland & Northern Ireland Forum for Environmental Research (SNIFFER), Scottish Environment Protection Agency (SEPA) Background to research The Regulatory Agencies in the UK (the Environment Agency; Scottish Environment Protection Agency; and the Northern Ireland Environment Agency) now use the River Invertebrate Classification Tool (RICT) to classify the ecological quality of rivers for Water Framework Directive compliance monitoring. RICT incorporates RIVPACS IV predictive models and is a highly capable tool written in a modern software programming language. While RICT classifies waters for general degradation and organic pollution stress, producing assessments of status class and uncertainty, WFD compliance monitoring also requires the UK Agencies to assess the impacts of a wide range of pressures including hydromorphological and acidification stresses. Some of these pressures alter the predictor variables that current RIVPACS models use to derive predicted biotic indices. This project has sought to broaden the scope of RICT by developing one or more RIVPACS model(s) that do not use predictor variables that are affected by these stressors, but instead use alternative GIS based variables that are wholly independent of these pressures. This project has also included a review of the wide range of biotic indices now available in RICT, identifying published sources, examining index performance, and where necessary making recommendations on further needs for index testing and development. Objectives of research •To remove and derive alternative predictive variables that are not affected by stressors, with particular emphasis on hydrological/acidification metric predictors. •To construct one or more new RIVPACS model(s) using stressor independent variables. •Review WFD reporting indices notably AWIC(species), LIFE (species), PSI & WHPT. Key findings and recommendations : Predictor variables and intellectual property rights : An extensive suite of new variables have been derived by GIS for the RIVPACS reference sites that have been shown to act as stressor-independent predictor variables. These include measures of stream order, solid and drift geology, and a range of upstream catchment characteristics (e.g. catchment area, mean altitude of upstream catchment, and catchment aspect). It is recommended that decisions are reached on which of the newly derived model(s) are implemented in RICT so that IPR issues for the relevant datasets can be quickly resolved and the datasets licensed. It is also recommended that licensing is sought for a point and click system (where the dataset cannot be reverse engineered) that is capable of calculating any of the time-invariant RIVPACS environmental predictor variables used by any of the newly derived (and existing) RIVPACS models, and for any potential users. New stressor-independent RIVPACS models : Using the existing predictor variables, together with new ones derived for their properties of stressor-independence, initial step-wise forward selection discriminant models suggested a range of 36 possible models that merited further testing. Following further testing, the following models are recommended for assessing watercourses affected by flow/hydromorphological and/or acidity stress: • For flow/hydromorphological stressors that may have modified width, depth and/or substrate in GB, it is suggested that a new ‘RIVPACS IV – Hydromorphology Independent’ model (Model 24) is used (this does not use the predictor variables width, depth and substratum, but includes a suite of new stressor-independent variables). • For acidity related stressors in GB, it is suggested that a new ‘RIVPACS IV – Alkalinity Independent’ model (Model 35) is used (this does not use the predictor variable alkalinity, but includes new stressor-independent variables). • For flow/hydromorphological stressors and acidity related stressors in GB, it is suggested that a new ‘RIVPACS IV – Hydromorphology & Alkalinity Independent’ model (Model 13) is used (this does not use the predictor variables width, depth, substratum and alkalinity, but includes a suite of new stressor-independent variables). • Reduced availability of appropriate GIS tools at this time has meant that no new models have been developed for Northern Ireland. Discriminant functions and end group means have now been calculated to enable any of these models to be easily implemented in the RICT software. Biotic indices : The RIVPACS models in RICT can now produce expected values for a wide range of biotic indices addressing a variety of stressors. These indices will support the use of RICT as a primary tool for WFD classification and reporting of the quality of UK streams and rivers. There are however a number of outstanding issues with indices that need to be addressed: • There is a need to develop a biotic index for assessing metal pollution. • WFD EQR banding schemes are required for many of the indices to report what is considered an acceptable degree of stress (High-Good) and what is not (Moderate, Poor or Bad). • A comprehensive objective testing process needs to be undertaken on the indices in RICT using UK-wide, large-scale, independent test datasets to quantify their index-stressor relationships and their associated uncertainty, for example following the approach to acidity index testing in Murphy et al., (in review) or organic/general degradation indices in Banks & McFarland (2010). • Following objective testing, the UK Agencies should make efforts to address any index under-performance issues that have been identified, and where necessary new work should be commissioned to modify existing indices, or develop new ones where required so that indices for all stress types meet certain minimum performance criteria. • Testing needs to be done to examine index-stressor relationships with both observed index scores and RIVPACS observed/expected ratios. Work should also be done to compare the existing RIVPACS IV and the new stressor-independent models (developed in this project) as alternative sources of the expected index values for these tests. • Consideration should be given to assessing the extent to which chemical and biological monitoring points co-occur. Site-matched (rather than reach-matched) chemical and biological monitoring points would i) generate the substantial training datasets needed to refine or develop new indices and ii) generate the independent datasets for testing

The ability of typically developing 2–3 year olds to infer the control mechanism for eye-gaze technology and the impact of causal language instruction

Purpose: Little is known about how children learn to control eye-gaze technology, and clinicians lack information to guide decision-making. This paper examines whether typically developing 2–3 year olds can infer for themselves the causal mechanisms by which eye-gaze technology is controlled, whether a teaching intervention based on causal language improves performance and how their performance compares to the same task accessed via a touchscreen. Methods and materials: Typically developing children’s (n = 9, Mean Age 28.7 months) performance on a cause and effect game presented on eye-gaze and touchscreen devices was compared. The game was presented first with no specific instruction on how to control the devices. This was followed by a subsequent presentation with explicit instruction about how the access methods worked, using a causal language approach. A final presentation examined whether children had retained any learning. Results: Performance in the eye-gaze condition without instruction (42.5% successful trials) was significantly below performance in the corresponding touchscreen condition (75%). However, when causal language instruction was added, performance with both access methods rose to comparable levels (90.7% eye-gaze and 94.6% touchscreen success). Performance gains were not retained post-intervention. Conclusions: Although 2–3 years in the study could make use of eye-gaze technology with support, this study found no evidence that these children could infer the causal mechanisms of control independently or intuitively. The lack of spatial contiguity and the comparative lack of feedback from eye-gaze devices are discussed as possible contributory factors.</p

Flux Qubits and Readout Device with Two Independent Flux Lines

We report measurements on two superconducting flux qubits coupled to a readout Superconducting QUantum Interference Device (SQUID). Two on-chip flux bias lines allow independent flux control of any two of the three elements, as illustrated by a two-dimensional qubit flux map. The application of microwaves yields a frequency-flux dispersion curve for 1- and 2-photon driving of the single-qubit excited state, and coherent manipulation of the single-qubit state results in Rabi oscillations and Ramsey fringes. This architecture should be scalable to many qubits and SQUIDs on a single chip.Comment: 5 pages, 4 figures, higher quality figures available upon request. Submitted to PR

Entangling flux qubits with a bipolar dynamic inductance

We propose a scheme to implement variable coupling between two flux qubits using the screening current response of a dc Superconducting QUantum Interference Device (SQUID). The coupling strength is adjusted by the current bias applied to the SQUID and can be varied continuously from positive to negative values, allowing cancellation of the direct mutual inductance between the qubits. We show that this variable coupling scheme permits efficient realization of universal quantum logic. The same SQUID can be used to determine the flux states of the qubits.Comment: 4 pages, 4 figure

The excitation of the far ultraviolet electroglow emissions on Uranus, Saturn, and Jupiter

We propose that the diffuse FUV emissions of H and H_2 in excess of photoelectron excitation observed from the sunlit atmospheres of Uranus, Saturn, and Jupiter are produced by electric field acceleration of photoelectrons and ions locally in the upper atmospheres. This in situ acceleration is required to satisfy the many observational constraints on the altitude distribution, exciting particle energy, and total input energy requirements of the electroglow mechanism. We further suggest that a primary mechanism leading to this acceleration is an ionospheric dynamo, which is created in the same manner as the Earth's dynamo. The calculated altitude of charge separation by the neutral wind drag on ions across magnetic field lines is consistent with the observed peaks in electroglow emissions from the Voyager ultraviolet spectrometer limb scan data on both Saturn (near the homopause) and Uranus (just above the homopause). This dynamo action therefore appears to initiate the acceleration process, which must have the form of field-aligned potentials to accelerate the magnetized electrons. We propose that these field-aligned potentials are due to anomalous resistivity, which results from sufficiently high field-aligned currents in the ionosphere to generate plasma instabilities and therefore runaway electrons and ions above some critical lower initial energy. There are multiple candidate processes for inducing these currents, including polarization in the equivalent F regions and inner magnetospheric convection, and each of these processes should exhibit latitudinal structure. The acceleration of low-energy electrons in an H_2 atmosphere preferentially results in FUV radiation and further ionization, whereas electron acceleration in a nitrogen/oxygen atmosphere such as the Earth' is dominated by elastic scattering and thus results in electric currents. Individual electron and proton collisions with H_2 molecules will result in excitation, ionization, and heating, so that considerable enhancement of the ionospheric density and heating of the upper atmosphere will accompany the FUV emission