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

Induced Distributions from Generalized Unfair Dice

In this paper we analyze the probability distributions associated with rolling (possibly unfair) dice infinitely often. Specifically, given a $q$-sided die, if $x_i\in\{0,\ldots,q-1\}$ denotes the outcome of the $i^{\text{th}}$ toss, then the distribution function is $F(x)=\mathbb{P}[X\leq x]$, where $X = \sum_{i=1}^\infty x_i q^{-i}$. We show that $F$ is singular and establish a piecewise linear, iterative construction for it. We investigate two ways of comparing $F$ to the fair distribution -- one using supremum norms and another using arclength. In the case of coin flips, we also address the case where each independent flip could come from a different distribution. In part, this work aims to address outstanding claims in the literature on Bernoulli schemes. The results herein are motivated by emerging needs, desires, and opportunities in computation to leverage physical stochasticity in microelectronic devices for random number generation.Comment: 18 pages, 1 figur

Diurnal water-pressure fluctuations: timing and pattern of termination below Bench Glacier, Alaska, USA

Observations from basal water-pressure sensors along the length of Bench Glacier, Alaska, USA, show that diurnal fluctuations of water pressure are seasonal and restricted to summer. Most notable about these fluctuations is their disappearance in the late summer and early autumn, long before the seasonal end of diurnal meltwater input. Here we present data documenting the end of diurnal water-pressure fluctuations during the 2002 and 2003 melt seasons. The end of diurnal fluctuations occurred abruptly in multiple boreholes spaced meters to kilometers apart. There was no obvious spatial progression of termination events, and a clear correlation with meteorological forcing or discharge in the outlet stream was not apparent. After diurnal pressure fluctuations ended, basal water pressure returned to a high, generally steady, value either in an irregular pattern or by a distinct increase. This high water pressure was interrupted by episodic, acyclic events throughout the autumn before becoming stable and high in winter

Identification of a new family of enzymes with potential O-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

Diurnal fluctuations in borehole water levels: configuration of the drainage system beneath Bench Glacier, Alaska, USA

Water levels were measured in boreholes spaced along the entire length of Bench Glacier, Alaska, USA, for a period in excess of 2 years. Instrumented boreholes were arranged as nine pairs along the center line of the glacier and an orthogonal grid of 16 boreholes in a 3600 m2 region at the center of the ablation area. Dirunal fluctuations of the water levels were found to be restricted to the late melt season. Pairs of boreholes spaced along the length of the ablation area often exhibited similar fluctuations and diurnal changes in water levels. Three distinct and independent types of diurnal fluctuations in water level were observed in cluster of boreholes within the grid of boreholes. Head gradients suggest water did not flow between clusters,and a single tunnel connecting the boreholes could not explain the observed pattern of diunal water-level fluctuations. Inter-borehole and borehole-cluster connectivity suggests the cross-glacier width of influence of a segment of the drainage system connected to a borehole was limited to tens of meters. A drainage configuration whereby boreholes are connected to a somewhat distant tunnel by drainage pipes of differing lengths, often hundreds of meters, is shown with a numerical test to be a plausible explanation for the observed borehole behavior

Incorporating a rule-based model of judgment into a wastewater treatment plant design optimization model

The use of a rule-based modeling technique for the formal consideration of poorly modeled issues in a water quality management problem is illustrated in the context of wastewater treatment plant design. Sludge bulking is a poorly understood problem in activated sludge wastewater treatment plants. An engineer must use judgement gained from experience when he designs an activated sludge plant to prevent bulking from causing the plant to fail. An attempt was made to use fuzzy logic in order to model that judgement. Results from research were taken from the literature and used independently as constraints to an activated sludge wastewater plant design optimization model to see their effect on the optimal design. Some of the research results were then formulated as rules in a rule-based system which relates design variable values to the likelihood of a design experiencing bulking problems. The weights of association of those rules to the conclusion that a given design would experience bulking problems and the logical interaction of those rules were calibrated using an experienced engineer's evaluation of a set of 15 plant designs. The consistency of the engineer's and the judgement model's evaluations were then checked with a second set of 15 designs. The model of judgement could be used to evaluate the bulking potential of any design. In the particular example developed, the judgement model was incorporated into a wastewater treatment plant design optimization model so that the cost effectiveness of constraint combinations could be examined. The tradeoff between cost and the likelihood of experiencing bulking problems was examined for a typical plant design problem.U.S. Department of the InteriorU.S. Geological SurveyOpe

Culture change in a professional sports team: Shaping environmental contexts and regulating power

Although high performing cultures are crucial for the enduring success of professional sport performance teams, theoretical and practical understanding of how they are established and sustained is lacking. To develop knowledge in this area, a case study was undertaken to examine the key mechanisms and processes of a successful culture change programme at English Rugby Union’s Leeds Carnegie. Exploring the change process from a 360 degree perspective, semi-structured interviews were conducted with team management, one specialist coach, six players, and the CEO. Analysed and explained through decentred theory, results revealed that culture change was effectively facilitated by team management: a) subtly and covertly shaping the physical, structural, and psychosocial context in which support staff and players made performance-impacting choices, and b) regulating the ‘to and fro’ of power which characterises professional sport performance teams. Decentred theory is also supported as an effective framework for culture change study

Evolution of subglacial water pressure along a glacier’s length

Observations from along the length of Bench Glacier, Alaska, USA, show that the subglacial water-pressure field undergoes a multiphase transition from a winter mode to a summer mode. Data were collected at the glacier surface, the outlet stream, and in a network of 47 boreholes spanning the length of the 7 km long glacier. The winter pressure field was near overburden, with low-magnitude (centimeter to meter scale) and long-period (days to weeks) variations. During a spring speed-up event, boreholes showed synchronous variations and a slight pressure drop from prior winter values. Diurnal pressure variations followed the speed-up, with their onset associated with a glacier-wide pressure drop and flood at the terminus stream. Diurnal variations with swings of up to 80% of overburden pressure were typical of mid-summer. Several characteristics of our observations contradict common conceptions about the seasonal development of the subglacial drainage system and the linkages between subglacial hydrology and basal sliding: (1) increased water pressure did not accompany high sliding rates; (2) the drainage system showed activity characteristic of the spring season long before abundant water was available on the glacier surface; (3) the onset of both spring activity and diurnal variations of the drainage system did not show a spatial progression along the length of the glacier

In situ stress tensor measured in an Alaskan glacier

An experimental program at Worthington Glacier, Alaska, U.S.A., has yielded the first in situ measurements of the full stress tensor in glacier ice. Measurements were made with an array of stiff (low-compliance) normal-force sensors frozen into a borehole at 120 m depth. Freezing in temperate ice was accomplished by a down-hole heat exchanger which extracted heat at the rate of 15 W. Under slowly varying stress conditions, relaxation of stress anomalies by viscous creep following drilling of the hole and installation of the sensors allows for equilibration of measured stresses with far-field stresses. Equilibration of local and far-field stresses was confirmed and pressure sensor calibrated in laboratory experiments prior to the field program. Results of the stress measurements show principal axes of the stress tensor oriented in directions consistent with the geometry of the glacier and broadly consistent with measured englacial strain rate. The magnitudes of stress-tensor components are more error-prone and more sensitive to uncertainty in sensor magnitude than uncertainty in sensor orientation. Mean stress determined by pressure measurements agrees with estimated lithostatic overburden with within approximately 15%. Unexpected results include a stress perturbation lasted about 5 days that caused a rotation of the orientations of the principal stress axes of approximately 5 degrees about an axis pointing in the down-flow direction

Effect of bulk inversion asymmetry on the Datta-Das transistor

A model of the Datta-Das spin field-effect transistor is presented which, in addition to the Rashba interaction, takes into account the influence of bulk inversion asymmetry of zinc-blende semiconductors. In the presence of bulk inversion asymmetry, the conductance is found to depend significantly on the crystallographic orientation of the channel. We determine the channel direction optimal for the observation of the Datta-Das effect in GaAs and InAs-based devices.Comment: 4 pages, Revtex4, 4 EPS figure