Book reviews

Teaching/Communication/Extension/Profession,

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

Alien Registration- Clarke, John M. (Portland, Cumberland County)

https://digitalmaine.com/alien_docs/24547/thumbnail.jp

Binary Capture Rates for Massive Protostars

The high multiplicity of massive stars in dense, young clusters is established early in their evolution. The mechanism behind this remains unresolved. Recent results suggest that massive protostars may capture companions through disk interactions with much higher efficiency than their solar mass counterparts. However, this conclusion is based on analytic determinations of capture rates and estimates of the robustness of the resulting binaries. We present the results of coupled n-body and SPH simulations of star-disk encounters to further test the idea that disk-captured binaries contribute to the observed multiplicity of massive stars.Comment: 4 pages, 3 figures, accepted to ApJ

80 Gb/s optimised pulse source using a gain-switched laser diode in conjunction with a nonlinearly chirped grating

The authors demonstrate the generation of transforms limited short optical pulses, which display excellent spectral and temporal qualities by employing a novel technology, based on an externally injected gain-switched laser in conjunction with a non-linearly chirped grating. Using this technique, 3.5 ps optical pulses, exhibiting a time bandwidth product of 0.45, are generated, which are suitable for use in high-speed 80 Gb/s OTDM communications systems

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

Magnetism in SQUIDs at Millikelvin Temperatures

We have characterized the temperature dependence of the flux threading dc SQUIDs cooled to millikelvin temperatures. The flux increases as 1/T as temperature is lowered; moreover, the flux change is proportional to the density of trapped vortices. The data is compatible with the thermal polarization of surface spins in the trapped fields of the vortices. In the absence of trapped flux, we observe evidence of spin-glass freezing at low temperature. These results suggest an explanation for the "universal" 1/f flux noise in SQUIDs and superconducting qubits.Comment: 4 pages, 4 figure

System-performance analysis of optimized gain-switched pulse source employed in 40-and 80-Gb/s OTDM systems

The development of ultrashort optical pulse sources, exhibiting excellent temporal and spectral profiles, will play a crucial role in the performance of future optical time division multiplexed (OTDM) systems. In this paper, we demonstrate the difference in performance in 40- and 80-Gb/s OTDM systems between optical pulse sources based on a gain-switched laser whose pulses are compressed by a nonlinearly and linearly chirped fiber Bragg grating. The results achieved show that nonlinear chirp in the wings of the pulse leads to temporal pedestals formed on either side of the pulse when using the linearly chirped grating, whereas with the nonlinearly chirped grating, pedestals are essentially eliminated. In an OTDM system, these pedestals cause coherent interaction between neighboring channels, resulting in intensity fluctuations that lead to a power penalty of 1.5 dB (40 Gb/s) and 3.5 dB (80 Gb/s) in comparison to the case where the nonlinearly chirped grating is used. Simulations carried out with the aid of Virtual Photonics Inc. verify the results achieved

Stabilizing Superconductivity in Nanowires by Coupling to Dissipative Environments

We present a theory for a finite-length superconducting nanowire coupled to an environment. We show that in the absence of dissipation quantum phase slips always destroy superconductivity, even at zero temperature. Dissipation stabilizes the superconducting phase. We apply this theory to explain the "anti-proximity effect" recently seen by Tian et. al. in Zinc nanowires.Comment: 4 pages, 3 figure