bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of Ventricular Catheter Design Using High-Performance Computing
Authors: Weisenberg Sofy H. , TerMaath Stephanie C.
Published: December 2016

Cerebrospinal fluid (CSF) shunts are fully implantable medical devices that are used to treat patients suffering from conditions characterized by elevated intracranial pressure, such as hydrocephalus. One of the primary causes of CSF shunt failure is mechanical obstruction of the ventricular catheter, a component of the shunt system implanted directly into the brain’s ventricular system. This study aims to characterize the CSF flow through ventricular catheters via a 3-dimensional computational fluid dynamics (CFD) model. The fully-parametrized model has allowed for exploration of the catheter’s geometric design features, with the goal of reducing the incidence of catheter obstruction. As the first step towards this goal, a design optimization study was performed with the objective of achieving a uniform flow rate distribution among the catheter’s inlet holes. To perform this study, the CFD model was coupled with an optimization framework, and a large number of simulations were run on a high-performance computing system to determine the optimal design for target flow performance. This optimization study advances the field of CSF shunt design by providing systematically derived correlations between the catheter’s geometric parameters and CSF flow through the catheter’s inlet holes.
Direct Numerical Simulation of Nonlinear Secondary Instabilities on the Pressure Side of a Savonius Style Wind Turbine
Authors: Ducoin Antoine , Roy Sukanta , Safdari Shadloo Mostafa
Published: December 2016

Savonius-style wind turbines are a class of vertical axis wind turbine usually used for off-grid applications. It appears to be promising for energy conversion because of its better self-starting capability and flexible design promises. The blades are characterized by relatively large surface, which are thin circular shape to produce large drag, which is used for power generation. Typically, the suction side of the advancing blade is submitted to strong adverse pressure gradient, causing a well known vortex shedding process, which is responsible for the wake flow. This topic has been the subject of many researches in the past decades, as it obviously depends on tip speed ratio (TSR) and directly influences the turbine efficiency. The flow on the pressure side of the blade is generally considered as fully attached and is characterized by high pressure, low velocity level that produces most of the drag used in the energy conversion. However, because of the gap between the two blades, the flow is accelerated on the pressure side of the returning blade and a thicker boundary layer develops at this side. Because of the concave curvature of the blade and the small scale of the turbine, centrifugal instabilities may occurs, depending on the flow regime that can cause natural transition on the blade. Moreover, these vortices induce different mechanisms of ejections and sweeps, causing thereby strong transverse variations of the drag coefficient, which results in the formation of hot spots near solid walls. This can leads to a rapid degradation of mechanical structures and materials fatigue. In this paper, Direct Numerical Simulations (DNS) are carried out in order to capture the flow instabilities and transition to turbulence occurring on the pressure of a conventional design Savonius wind turbine blade. Simulations are conducted with the open source code Nek5000, solving the incompressible Navier-Stokes equations with a high order, spectral element method. Because of the relatively high Reynolds numbers considered (Reξ = 90,000), the computational domain of the Savonius blade is reduced to the pressure side, whereas no turbine rotation is considered, which avoid the large scale vortex shedding that occurs on the suction side. The results suggest that Gortler vortices can occurs and cause the flow to transit to turbulence, which modify the pressure distribution and the drag force significantly.
PIV Investigation of Turbulent Flow Over a Wavy-Wall in a Horizontal Channel
Authors: Martins Segunda Vinicius , Tachie Mark , Ormiston Scott
Published: December 2016

Experimental investigation of turbulent flow in a channel with flat upper wall and wavy lower wall using a particle image velocimetry technique is presented. The mean flow and turbulent characteristics in both the developing region and fully periodic region over the wavy wall were examined. It was observed that the flow characteristics become fully periodic after the eighth wave. The results also showed that the separation and reattachment points within the developing region and fully periodic region are similar. Detailed investigation of the flow field in the fully periodic region was examined using contour plots and one-dimensional profiles of the mean velocities, mean spanwise vorticity, streamwise and wall-normal turbulence intensities and Reynolds shear stress.
Flow Analysis of the Guide Vanes Region of Pump Turbine at the Slight Opening in the Pumping Startup Process
Authors: Fan Honggang , Ji Qingfeng , Liao Weili , Yang Haixia
Published: December 2016

The unit of a Pumped Storage Power Station experienced abnormal noise and vibration in the guide vanes at the slight opening when the pump turbine was in the process of startup in the pumping mode. Based on this phenomena, the three dimensional model of the pump turbine was established, RNG k-epsilon two equations turbulence model was selected for the flow numerical simulation in the pump turbine because this model can simulate both the flow separation and vortex dynamics, and it is more accurate in the near wall areas. The governing equations were discretized with the finite volume method. The computation was carried out with three steps, 1.steady calculation, 2.unsteady calculation with constant guide vane opening, 3.unsteady calculations with the increase of the opening of guide vanes, by using the results of the last step as the initial condition. According to the three dimensional simulation results, the main flow between the guide vanes was deflected from attaching to the one vane to the other vane with the opening of the guide vanes. The calculation of complete 3D flow indicated that the deflections of the flows between the different adjacent guide vanes were basically the same, however, the deflections starting times had a few differences. The variation of the torque on the guide vane was also investigated, and the results shown the abrupt changes occurred during the deflection process of the main flow. When the torque produced by the servomotor cannot adapt quickly enough to the abrupt changes, the vibration and loud scrape noise might occur.
Enhancement of Turbulent Shear Stress and Mass Transfer in Wall Turbulence Accompanied With Wall Blowing
Authors: Okamura Yushi , Sugioka Hideaki , Kawaguchi Yasuo
Published: December 2016

Spatial distribution of velocity and mass concentration fluctuation in turbulent channel flow with wall blowing were simultaneously measured by PIV/PLIF. The recorded pictures were analyzed to clarify the turbulent momentum and mass transfer from statistical view point and from spatial evolution of coherent eddy structure.

Experimental result revealed that the Reynold shear stress and turbulent intensity are enhanced as the blowing rate increasing. On the other hand, structural parameters based on local turbulence such as turbulent Schmidt number and a degree of turbulent anisotropy is not affected by wall blowing. In comparison without wall blowing, we found that the turbulent eddy structure locates apart from the wall. Besides, energy spectrum and swirling strength is also enhanced by wall blowing. It is associated with increase of resistance by wall blowing. Generally in wall turbulence, fluctuation motions are restricted by the presence of solid wall. But for the blowing from the wall relaxes this restriction and Reynolds shear stress is enhanced, which leads to enhancement of turbulent mass flux. Moreover, from results of spatial distribution of instantaneous fields, wall-blowing helps development of hairpin vortexes. It is concluded that development of hairpins leads to enhancement of turbulent mass transfer.
A Turbulent Boundary Layer Flow Over an Open Shallow Cavity
Authors: Hammad Khaled J.
Published: December 2016

Particle Image Velocimetry (PIV) was used to study the flow structure and turbulence, upstream, over, and downstream a shallow open cavity. Three sets of PIV measurements, corresponding to a turbulent incoming boundary layer and a cavity length-to-depth ratio of four, are reported. The cavity depth based Reynolds numbers were 21,000; 42,000; and 54,000. The selected flow configuration and well characterized inflow conditions allow for straightforward assessment of turbulence models and numerical schemes. All mean flow field measurements display a large flow recirculation region, spanning most of the cavity and a smaller, counter-rotating, secondary vortex, immediately downstream of the cavity leading edge. The Galilean decomposed instantaneous velocity vector fields, clearly demonstrate two distinct modes of interaction between the free shear and the cavity trailing edge. The first corresponds to a cascade of vortical structures emanating from the tip of the leading edge of the cavity that grow in size as they travel downstream and directly interact with the trailing edge, i.e., impinging vortices. The second represents vortices that travel above the trailing edge of the cavity, i.e., non-impinging vortices. In the case of impinging vortices, a strong, large scale region of recirculation forms inside the cavity and carries the flow disturbances, arising from the impingement of vortices on the trailing edge of the cavity, upstream in a manner that interacts with and influences the flow as it separates from the cavity leading edge.
Aerodynamic and Performance Behavior of a Radial Turbine at Design and Off-Design Conditions
Authors: Zhu Cheng , Zhuge Weilin , Zhang Yangjun , Peng Jie
Published: December 2016

When a turbocharged engine which was designed to work at sea level works at high altitude area, its power will decrease because of the decrease of the air density. And the expansion ratio of the turbine will increase a lot because of the decrease of the out pressure, leading to a bad efficiency of the turbine. In order to recover the power of the turbocharged engine when it worked at the high altitude area, the efficiency of the turbine should be increased when it worked at high expansion ratio condition.

This paper shows a numerical investigation of the flow fields in a radial inflow turbine at design and off design condition. The comparison of the flow characteristics between the design and off design conditions is researched. When the turbine work at a high expansion ratio, there will occur a supersonic zone at the leading edge on the suction side and a shock wave will occur at the trailing edge, causing a flow separation and making a lot of losses, leading the decrease of the turbine efficiency.
Modelling and Design of Thermoelectric Generator for Waste Heat Recovery
Authors: Ji Dongxu , Romagnoli Alessandro
Published: December 2016

In order to design an effective thermoelectric generator (TEG) heat exchanger for waste heat recovery, an accurate model is required for system design and performance predicting. In this paper, 1-D model is developed in MATLAB, taking into consideration of the multi-physics phenomena within TEG. The proposed model is different from existing thermoelectric models which mainly focus on the thermoelectric couple or device level without providing any guidance for designing an optimal system. When optimizing some TEG parameters, the optimal value found in a device level model might not be suitable when put into a waste heat recovery system. Therefore, in order to develop an optimized TEG system with optimum output power performance, a more comprehensive thermoelectric model integrated with the other components is needed. The current model integrates the thermoelectric module with the heat exchangers. Through this study, we found that the heat exchanger and module design have an impact on the total TEG output power in waste heat recovery system and a systematic design approach is needed.
Numerical Study of Gravity Effects on Phase Separation in a Swirl Chamber
Authors: Hsiao Chao-Tsung , Ma Jingsen , Chahine Georges L.
Published: December 2016

The effects of gravity on a phase separator are studied numerically using an Eulerian/Lagrangian two-phase flow approach. The separator utilizes high intensity swirl to separate bubbles from the liquid. The two-phase flow enters tangentially a cylindrical swirl chamber and rotate around the cylinder axis. On earth, as the bubbles are captured by the vortex formed inside the swirl chamber due to the centripetal force, they also experience the buoyancy force due to gravity. In a reduced or zero gravity environment buoyancy is reduced or inexistent and capture of the bubbles by the vortex is modified. The present numerical simulations enable study of the relative importance of the acceleration of gravity on the bubble capture by the swirl flow in the separator. In absence of gravity, the bubbles get stratified depending on their sizes, with the larger bubbles entering the core region earlier than the smaller ones. However in presence of gravity, stratification is more complex as the two acceleration fields — due to gravity and to rotation — compete or combine during the bubble capture.
Computational Model of Human Capillary Hydrodynamics
Authors: Windes Peter W. , Tafti Danesh K. , Behkam Bahareh
Published: December 2016

The present work lays out an accurate, three-dimensional computational fluid dynamics (CFD) model of a human blood capillary. This model is composed of red blood cells and blood plasma inside a cylindrical section of a capillary. The plasma flow is resolved using an incompressible Navier-Stokes solver. At the level of capillaries, red blood cells must be individually handled to correctly resolve the hydrodynamics in the system. They cannot be lumped in with the plasma and considered as a non-Newtonian suspension because of the relative scale of the capillaries and the blood cells. Red blood cells act as highly deformable, fluid filled vesicles which readily deform from their typical biconcave shape when passing through narrow capillaries. In the present model, the deformed shape of red blood cells is predicted using a combination of analytical models and experimental data on cell deformation. The cell volume, cell surface area, and plasma layer thickness are found to be the key parameters which define red blood cell deformation in capillaries. The red blood cells are imposed in the flow using the immersed boundary method (IBM). To save computational resources while still yielding an accurate model, the deformed shape of each red blood cell is calculated once prior to running the simulation and then held constant throughout the run. In order to validate the model, two parameters — apparent relative viscosity and hematocrit ratio — were examined. The present model shows good comparison to experimental values for both these parameters.
Theoretical Analysis of a Cyclic Pitch Turbine
Authors: Prasad Rao Jubilee , Villegas Arturo , Diez F. Javier
Published: December 2016

Theoretical analysis of a drag based vertical axis wind turbine is presented. This builds on previous work where we introduced a novel turbine (Cyclic pitch turbine, CPT) with a tilting mechanism. It allows for cyclic pitch variations of the blades while they rotate about an axis perpendicular to the fluid flow direction. The pitching mechanism changes the angle of attack of the blades from 90 degrees while in the drive stroke to 0 degrees while in the recovery stroke and then back to 90 degrees so that the blades are active during the drive stroke and passive during the recovery stroke. The tilting of the blades takes place while the blades are transitioning from one stroke to the other stroke. In this configuration, the blades present maximum frontal area during the drive stroke and minimum frontal area during the recovery stroke. The drag force on a simple shaped bodies is directly proportional to the effective frontal area with respect to the flow direction of the fluid and hence it is expected that the drag force is maximum during the drive stroke while the blades are perpendicular to the flow and that it is minimum during the recovery stroke as the blades are parallel to the fluid flow direction. Comparison of static torque coefficients of a flat plate to that of a bucket blade typical in a Savonius turbine is performed. It is shown that this new turbine has higher and more consistent starting torque. It is also shown that the positive difference in the torque coefficient would only increase as the turbine starts to rotate and increase in rpm. As a consequence, the relative velocity between the blades and the fluid flow negatively affects the Savonius configuration more than a CPT turbine. As a result, this turbine is expected to be more efficient than the Savonius turbine. Optimization has been performed for this formulation for tip speed ratio (TSR) and active blade angle. To perform the tilting motion of the blades, the turbine uses a novel hybrid mechanism combining the workings of cams and swashplates. A prototype has been developed which integrates ball bearings into the mechanism instead of sliding components used in our first generation turbine that change sliding motion into lower friction rolling motion. This increased the efficiency of the turbine. The mathematical formulations developed compares the static characteristics of the developed CPT turbine to Savonius turbines and help understand its dynamic characteristics.
Flow Over a Sudden Expansion in an Annular Pipe: Steady Axisymmetric Flow and its Stability
Authors: Beladi Behnaz , Kuhlmann Hendrik C.
Published: December 2016

The stability of the axisymmetric incompressible Newtonian flow in an annular pipe suddenly expanding radially inward is investigated. The axisymmetric steady basic flow is discretized using primitive variables and second-order finite volumes on a staggered grid. The resulting algebraic equations are solved by Newton–Raphson iteration. A three-dimensional global linear stability analysis is performed. The solutions to the linear stability problem are represented by normal modes. The generalized eigenvalue problem is solved using an implicitly restarted Arnoldi algorithm which is provided by the ARPACK library and a Cayley transformation. Stability boundaries have been computed for a range of parameters varying the outlet radius ratio. The physical instability mechanisms are studied by a an posteriori analysis of the kinetic energy transferred between the basic state and the critical mode. Neutral curves and critical modes are presented and the instability mechanisms are discussed.
Numerical Analysis of Flow and Heat Transfer at a Backward-Facing Step With an Obstacle Based on Lattice Boltzmann Method
Authors: Mehrez Insaf , Gheith Ramla , Aloui Fethi , Ben Nasrallah Sassi
Published: December 2016

The Lattice Boltzmann method is actually considered as one of the simplest approach. The flow and heat transfer distribution in a duct containing a backward and an obstacle are studied for different geometric and physical parameters.

The LBM is applied to solve the backward-facing step flow problems for an expansion ratio H/h = 2 in rectangular duct and to determine the effect of the obstacle on flow and heat transfer distribution. The obstacle is situated in the bottom wall of the duct. The effect of various obstacle lengths (0.5<h/S<1.5) will be also considered. All this results were observed for a Prandtl number of 0.71 and different range of Reynolds number (1–200).

This study showed the instabilities of velocity, recirculation length, temperature and Nusselt number with the obstacle downstream the step. These results were compared to with published experimental.
Discretization Error Estimation in Transient Flow Simulations
Authors: Celik Ismail B. , Ma Zhiyuan , Benyahia Sofiane
Published: December 2016

Most methods presented in the literature for estimation of discretization errors focus primarily on steady flows. The transport of error in strongly transient flow has not been adequately addressed. Issues related to transient error calculations are discussed and some methods that are viable for such applications are proposed. Examples are presented on simple flows such as transient Burgers equation followed by applications to more complex flows, e.g. two-phase gas-solid flow relevant fluidized beds. It is demonstrated that error estimation can be made with reasonable accuracy using a combination of various methods.
Low-carbon steel ultra-high-vacuum Schottky emitter electron gun with double O-rings for axis adjustment
Authors: Park In-Yong , Cho Boklae
Published: December 2016

With the aim to create a simpler structure and reduce the production cost of an existing Schottky emitter-scanning electron microscope (SE-SEM), the authors have built and tested a double-O-ring electron gun which is also compatible with ultrahigh vacuum (UHV). Specifically, the gun and column of the SEM consist of low-carbon steel, of which the magnetic shielding effect is greater than that of stainless steel, allowing magnification of ×200 000 in the adapted SEM base without additional magnetic shielding material, such as permalloy or mu-metal. The position of the electron gun can be adjusted along the horizontal axis while maintaining the UHV condition. Excellent beam current stability with less than 1% variation for more than 1 h was noted. Therefore, the authors anticipate that the double-O-ring electron gun and column of low-carbon steel together represent an inexpensive and uncomplicated SE-SEM compared to existing types.
Representing the intelligibility advantage of ideal binary masking with the most energetic channels
Authors: Chen Fei
Published: December 2016

This study investigates how the intelligibility advantage of ideal binary mask (IBM) processing in synthesizing speech is affected by the use of a small number of the most energetic channels. In experiment 1, IBM-processed Mandarin speech that had been corrupted by speech spectrum-shaped noise or two-talker babble was synthesized by using as few as four of the most energetic target-dominated channels at each frame. This approach provided intelligibility comparable to that of speech synthesized with all of the target-dominated channels. Experiments 2, 3, and 4 examined how the intelligibility advantage of IBM processing from experiment 1 was affected by the local SNR threshold, low-frequency region (LFR) cut-off frequency, and vowel-based segmentation, respectively. Experiments 2 and 3 showed that a threshold of 0 dB for local SNR and a cutoff of 3000 Hz for LFR were optimal choices for improving the intelligibility of IBM processing based on the most energetic channels. Experiment 4 found that the intelligibility advantage of IBM processing with the most energetic channels was preserved at the segmental level of vowel-only IBM-processed speech. Taken together, the results suggest that compared to IBM-processed speech synthesized with all of the target-dominated channels, Mandarin speech synthesized by selecting a small number of the most energetic target-dominated channels can achieve similar levels of intelligibility.
Soft robotics: Technologies and systems pushing the boundaries of robot abilities
Authors: Laschi Cecilia , Mazzolai Barbara , Cianchetti Matteo
Published: December 2016

Soft materials and deformable structures have given robots the ability to stretch, squash, climb, and morph, with potential for biodegradability and self-healing.
Motor learning affects car-to-driver handover in automated vehicles
Authors: Russell Holly E. B. , Harbott Lene K. , Nisky Ilana , Pan Selina , Okamura Allison M. , Gerdes J. Christian
Published: December 2016

A human driver requires a period of motor adaptation to resume normal steering after taking control of an automated vehicle.
Bacteria stop fermentation with lactic acid
Authors: Mushegian Alexandra A.
Published: December 2016

Bacteria release lactic acid, inducing a prion-based metabolic switch in yeast.
SUMO versus ubiquitin in Hedgehog signaling
Authors: Gough Nancy R.
Published: December 2016

SUMOylation of Smoothened promotes deubiquitylation, stabilizing Smoothened at the membrane.
Circadian effects on immunization responses
Authors: Foley John F.
Published: December 2016

Diurnal control of lymphocyte trafficking by adrenergic signaling determines the timing of effective immunization.
Genetic Environment of the
bla
KPC-2
Gene in a Klebsiella pneumoniae Isolate That May Have Been Imported to Russia from Southeast Asia
Authors: Ageevets Vladimir , Sopova Julia , Lazareva Irina , Malakhova Maya , Ilina Elena , Kostryukova Elena , Babenko Vladislav , Carattoli Alessandra , Lobzin Yuri , Uskov Alexander , Sidorenko Sergey
Published: December 2016

The nucleotide sequence of a
bla
KPC-2
-harboring plasmid (pKPCAPSS) from
Klebsiella pneumoniae
ST273 isolated in Saint Petersburg, Russia, from a patient with history of recent travel to Vietnam is presented. This 127,970-bp plasmid possessed both IncFII and IncR replicons.
bla
KPC-2
was localized on a hypothetical mobile element. This element was flanked by 38-bp inverted Tn
3
repeats and included a Tn
3
-specific transposase gene, macrolide resistance operon (
mphA-mrx-mphR
), and a fragment of
bla
TEM
with unique polymorphisms.
Genetic Evidence for Cytochrome
b
Q
i
Site Inhibition by 4(1
H
)-Quinolone-3-Diarylethers and Antimycin in Toxoplasma gondii
Authors: Alday P. Holland , Bruzual Igor , Nilsen Aaron , Pou Sovitj , Winter Rolf , Ben Mamoun Choukri , Riscoe Michael K. , Doggett J. Stone
Published: December 2016

Toxoplasma gondii
is an apicomplexan parasite that causes fatal and debilitating brain and eye disease. Endochinlike quinolones (ELQs) are preclinical compounds that are efficacious against apicomplexan-caused diseases, including toxoplasmosis, malaria, and babesiosis. Of the ELQs, ELQ-316 has demonstrated the greatest efficacy against acute and chronic experimental toxoplasmosis. Although genetic analyses in other organisms have highlighted the importance of the cytochrome
bc
1
complex Q
i
site for ELQ sensitivity, the mechanism of action of ELQs against
T. gondii
and the specific mechanism of ELQ-316 remain unknown. Here, we describe the selection and genetic characterization of
T. gondii
clones resistant to ELQ-316. A
T. gondii
strain selected under ELQ-316 drug pressure was found to possess a Thr222-Pro amino acid substitution that confers 49-fold resistance to ELQ-316 and 19-fold resistance to antimycin, a well-characterized Q
i
site inhibitor. These findings provide further evidence for ELQ Q
i
site inhibition in
T. gondii
and greater insight into the interactions of Q
i
site inhibitors with the apicomplexan cytochrome
bc
1
complex.
Intracellular Staphylococcus aureus Control by Virulent Bacteriophages within MAC-T Bovine Mammary Epithelial Cells
Authors: Zhang Lili , Sun Lichang , Wei Ruicheng , Gao Qiang , He Tao , Xu Cunfa , Liu Xianjin , Wang Ran
Published: December 2016

Bacteriophages (phages) are known to effectively kill extracellular multiplying bacteria. The present study demonstrated that phages penetrated bovine mammary epithelial cells and cleared intracellular
Staphylococcus aureus
in a time-dependent manner. In particular, phage vB_SauM_JS25 reached the nucleus within 3 h postincubation. The phages had an endocytotic efficiency of 12%. This ability to kill intracellular host bacteria suggests the utility of phage-based therapies and may protect patients from recurrent infection and treatment failure.
N
-Acetyl-
l
-Cysteine and Cysteamine as New Strategies against Mixed Biofilms of Nonencapsulated Streptococcus pneumoniae and Nontypeable Haemophilus influenzae
Authors: Domenech Mirian , García Ernesto
Published: December 2016

Acute otitis media, a polymicrobial disease of the middle ear cavity of children, is a significant public health problem worldwide. It is most frequently caused by encapsulated
Streptococcus pneumoniae
and nontypeable
Haemophilus influenzae
, although the widespread use of pneumococcal conjugate vaccines is apparently producing an increase in the carriage of nonencapsulated
S. pneumoniae
. Frequently, pneumococci and
H. influenzae
live together in the human nasopharynx, forming a self-produced biofilm. Biofilms present a global medical challenge since the inherent antibiotic resistance of their producers demands the use of large doses of antibiotics over prolonged periods. Frequently, these therapeutic measures fail, contributing to bacterial persistence. Here, we describe the development of an
in vitro
nonencapsulated
S. pneumoniae
-nontypeable
H. influenzae
biofilm system with polystyrene or glass-bottom plates. Confocal laser scanning microscopy and specific fluorescent labeling of pneumococcal cells with
Helix
pomatia
agglutinin revealed an even distribution of both species within the biofilm. This simple and robust protocol of mixed biofilms was used to test the antimicrobial properties of two well-known antioxidants that are widely used in the clinical setting, i.e.,
N
-acetyl-
l
-cysteine and cysteamine. This repurposing approach showed the high potency of
N
-acetyl-
l
-cysteine and cysteamine against mixed biofilms of nonencapsulated
S. pneumoniae
and nontypeable
H. influenzae
. Decades of clinical use mean that these compounds are safe to use, which may accelerate their evaluation in humans.
Cephalosporin-3′-Diazeniumdiolate NO Donor Prodrug PYRRO-C3D Enhances Azithromycin Susceptibility of Nontypeable Haemophilus influenzae Biofilms
Authors: Collins Samuel A. , Kelso Michael J. , Rineh Ardeshir , Yepuri Nageshwar R. , Coles Janice , Jackson Claire L. , Halladay Georgia D. , Walker Woolf T. , Webb Jeremy S. , Hall-Stoodley Luanne , Connett Gary J. , Feelisch Martin , Faust Saul N. , Lucas Jane S. A. , Allan Raymond N.
Published: December 2016

PYRRO-C3D is a cephalosporin-3-diazeniumdiolate nitric oxide (NO) donor prodrug designed to selectively deliver NO to bacterial infection sites. The objective of this study was to assess the activity of PYRRO-C3D against nontypeable
Haemophilus influenzae
(NTHi) biofilms and examine the role of NO in reducing biofilm-associated antibiotic tolerance. The activity of PYRRO-C3D on
in vitro
NTHi biofilms was assessed through CFU enumeration and confocal microscopy. NO release measurements were performed using an ISO-NO probe. NTHi biofilms grown on primary ciliated respiratory epithelia at an air-liquid interface were used to investigate the effects of PYRRO-C3D in the presence of host tissue. Label-free liquid chromatography-mass spectrometry (LC/MS) proteomic analyses were performed to identify differentially expressed proteins following NO treatment. PYRRO-C3D specifically released NO in the presence of NTHi, while no evidence of spontaneous NO release was observed when the compound was exposed to primary epithelial cells. NTHi lacking β-lactamase activity failed to trigger NO release. Treatment significantly increased the susceptibility of
in vitro
NTHi biofilms to azithromycin, causing a log fold reduction (10-fold reduction or 1-log-unit reduction) in viability (
P
< 0.05) relative to azithromycin alone. The response was more pronounced for biofilms grown on primary respiratory epithelia, where a 2-log-unit reduction was observed (
P
< 0.01). Label-free proteomics showed that NO increased expression of 16 proteins involved in metabolic and transcriptional/translational functions. NO release from PYRRO-C3D enhances the efficacy of azithromycin against NTHi biofilms, putatively via modulation of NTHi metabolic activity. Adjunctive therapy with NO mediated through PYRRO-C3D represents a promising approach for reducing biofilm-associated antibiotic tolerance.
Plazomicin Activity against 346 Extended-Spectrum-β-Lactamase/AmpC-Producing Escherichia coli Urinary Isolates in Relation to Aminoglycoside-Modifying Enzymes
Authors: López-Diaz Maria del Carmen , Culebras Esther , Rodríguez-Avial Iciar , Rios Esther , Viñuela-Prieto José Manuel , Picazo Juan J. , Rodríguez-Avial Carmen
Published: December 2016

The activity of plazomicin and clinically relevant aminoglycosides was tested against 346 extended-spectrum-β-lactamase/AmpC-producing
Escherichia coli
urinary isolates, and the results were correlated with the presence of aminoglycoside-modifying enzymes (AMEs). Data showed that plazomicin was very active against all ESBL/AmpC-producing
E. coli
urinary isolates. Its activity was not related to the AME genes studied.
The Type III Secretion System Effector SptP of Salmonella enterica Serovar Typhi
Authors: Johnson Rebecca , Byrne Alexander , Berger Cedric N. , Klemm Elizabeth , Crepin Valerie F. , Dougan Gordon , Frankel Gad
Published: December 2016

Strains of the various
Salmonella enterica
serovars cause gastroenteritis or typhoid fever in humans, with virulence depending on the action of two type III secretion systems (
Salmonella
pathogenicity island 1 [SPI-1] and SPI-2). SptP is a
Salmonella
SPI-1 effector, involved in mediating recovery of the host cytoskeleton postinfection. SptP requires a chaperone, SicP, for stability and secretion. SptP has 94% identity between
S. enterica
serovar Typhimurium and
S
. Typhi; direct comparison of the protein sequences revealed that
S
. Typhi SptP has numerous amino acid changes within its chaperone-binding domain. Subsequent comparison of Δ
sptP S
. Typhi and
S.
Typhimurium strains demonstrated that, unlike SptP in
S.
Typhimurium, SptP in
S
. Typhi was not involved in invasion or cytoskeletal recovery postinfection. Investigation of whether the observed amino acid changes within SptP of
S
. Typhi affected its function revealed that
S
. Typhi SptP was unable to complement
S.
Typhimurium Δ
sptP
due to an absence of secretion. We further demonstrated that while
S.
Typhimurium SptP is stable intracellularly within
S
. Typhi,
S
. Typhi SptP is unstable, although stability could be recovered following replacement of the chaperone-binding domain with that of
S.
Typhimurium. Direct assessment of the strength of the interaction between SptP and SicP of both serovars via bacterial two-hybrid analysis demonstrated that
S
. Typhi SptP has a significantly weaker interaction with SicP than the equivalent proteins in
S.
Typhimurium. Taken together, our results suggest that changes within the chaperone-binding domain of SptP in
S
. Typhi hinder binding to its chaperone, resulting in instability, preventing translocation, and therefore restricting the intracellular activity of this effector.

IMPORTANCE
Studies investigating
Salmonella
pathogenesis typically rely on
Salmonella
Typhimurium, even though
Salmonella
Typhi causes the more severe disease in humans. As such, an understanding of
S.
Typhi pathogenesis is lacking. Differences within the type III secretion system effector SptP between typhoidal and nontyphoidal serovars led us to characterize this effector within
S
. Typhi. Our results suggest that SptP is not translocated from typhoidal serovars, even though the loss of
sptP
results in virulence defects in
S.
Typhimurium. Although SptP is just one effector, our results exemplify that the behavior of these serovars is significantly different and genes identified to be important for
S.
Typhimurium virulence may not translate to
S
. Typhi.
Malate Synthase and β-Methylmalyl Coenzyme A Lyase Reactions in the Methylaspartate Cycle in Haloarcula hispanica
Authors: Borjian Farshad , Han Jing , Hou Jing , Xiang Hua , Zarzycki Jan , Berg Ivan A.
Published: December 2016

Haloarchaea are extremely halophilic heterotrophic microorganisms belonging to the class
Halobacteria
(
Euryarchaeota
). Almost half of the haloarchaea possesses the genes coding for enzymes of the methylaspartate cycle, a recently discovered anaplerotic acetate assimilation pathway. In this cycle, the enzymes of the tricarboxylic acid cycle together with the dedicated enzymes of the methylaspartate cycle convert two acetyl coenzyme A (acetyl-CoA) molecules to malate. The methylaspartate cycle involves two reactions catalyzed by homologous enzymes belonging to the CitE-like enzyme superfamily, malyl-CoA lyase/thioesterase (haloarchaeal malate synthase [hMS]; Hah_2476 in
Haloarcula hispanica
) and β-methylmalyl-CoA lyase (haloarchaeal β-methylmalyl-CoA lyase [hMCL]; Hah_1341). Although both enzymes catalyze the same reactions, hMS was previously proposed to preferentially catalyze the formation of malate from acetyl-CoA and glyoxylate (malate synthase activity) and hMCL was proposed to primarily cleave β-methylmalyl-CoA to propionyl-CoA and glyoxylate. Here we studied the physiological functions of these enzymes during acetate assimilation in
H. hispanica
by using biochemical assays of the wild type and deletion mutants. Our results reveal that the main physiological function of hMS is malyl-CoA (not malate) formation and that hMCL catalyzes a β-methylmalyl-CoA lyase reaction
in vivo
. The malyl-CoA thioesterase activities of both enzymes appear to be not essential for growth on acetate. Interestingly, despite the different physiological functions of hMS and hMCL, structural comparisons predict that these two proteins have virtually identical active sites, thus highlighting the need for experimental validation of their catalytic functions. Our results provide further proof of the operation of the methylaspartate cycle and indicate the existence of a distinct, yet-to-be-discovered malyl-CoA thioesterase in haloarchaea.

IMPORTANCE
Acetate is one of the most important substances in natural environments. The activated form of acetate, acetyl coenzyme A (acetyl-CoA), is the high-energy intermediate at the crossroads of central metabolism: its oxidation generates energy for the cell, and about a third of all biosynthetic fluxes start directly from acetyl-CoA. Many organic compounds enter the central carbon metabolism via this key molecule. To sustain growth on acetyl-CoA-generating compounds, a dedicated assimilation (anaplerotic) pathway is required. The presence of an anaplerotic pathway is a prerequisite for growth in many environments, being important for environmentally, industrially, and clinically important microorganisms. Here we studied specific reactions of a recently discovered acetate assimilation pathway, the methylaspartate cycle, functioning in extremely halophilic archaea.
Role of the
nifB1
and
nifB2
Promoters in Cell-Type-Specific Expression of Two Mo Nitrogenases in the Cyanobacterium Anabaena variabilis ATCC 29413
Authors: Vernon Susan A. , Pratte Brenda S. , Thiel Teresa
Published: December 2016

Anabaena variabilis
ATCC 29413 has one Mo nitrogenase that is made under oxic growth conditions in specialized cells called heterocysts and a second Mo nitrogenase that is made only under anoxic conditions in vegetative cells. The two large
nif
gene clusters responsible for these two nitrogenases are under the control of the promoter of the first gene in the operon,
nifB1
or
nifB2
. Despite differences in the expression patterns of
nifB1
and
nifB2
, related to oxygen and cell type, the regions upstream of their transcription start sites (tss) show striking homology, including three highly conserved sequences (CS). CS1, CS2, and the region just upstream from the tss were required for optimal expression from the
nifB1
promoter, but CS3 and the 5′ untranslated region (UTR) were not. Hybrid fusions of the
nifB1
and
nifB2
upstream regions revealed that the region including CS1, CS2, and CS3 of
nifB2
could substitute for the similar region of
nifB1
; however, the converse was not true. Expression from the
nifB2
promoter region required the CS1, CS2, and CS3 regions of
nifB2
and also required the
nifB2
5′ UTR. A hybrid promoter that was mostly
nifB2
but that had the region from about position −40 to the tss of
nifB1
was expressed in heterocysts and in anoxic vegetative cells. Thus, addition of the
nifB1
promoter region (from about position −40 to the tss of
nifB1
) in the
nifB
hybrid promoter supported expression in heterocysts but did not prevent the mostly
nifB2
promoter from also functioning in anoxic vegetative cells.

IMPORTANCE
In the filamentous cyanobacterium
Anabaena variabilis
, two Mo nitrogenase gene clusters,
nif1
and
nif2
, function under different environmental conditions in different cell types. Little is known about the regulation of transcription from the promoter upstream of the first gene of the cluster, which drives transcription of each of these two large operons. The similarity in the sequences upstream of the primary promoters for the two
nif
gene clusters belies the differences in their expression patterns. Analysis of these
nif
promoters in strains with mutations in the conserved sequences and in strains with hybrid promoters, comprising parts from
nif1
and
nif2
, provides strong evidence that each promoter has key elements required for cell-type-specific expression of the
nif1
and
nif2
gene clusters.
A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea
Authors: Rodionov Dmitry A. , Leyn Semen A. , Li Xiaoqing , Rodionova Irina A.
Published: December 2016

Thiamine (vitamin B
1
) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamine biosynthesis and salvage genes are controlled at the RNA level by TPP-responsive riboswitches. In
Archaea
, TPP riboswitches are restricted to the
Thermoplasmatales
order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages in the
Crenarchaeota
phylum as well as in the
Halobacteria
and
Thermococci
classes of the
Euryarchaeota
. ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain, which is similar to the archaeal thiamine phosphate synthase ThiN. By using comparative genomics, we predicted ThiR-binding DNA motifs and reconstructed ThiR regulons in 67 genomes representing all above-mentioned lineages. The predicted ThiR-binding motifs are characterized by palindromic symmetry with several distinct lineage-specific consensus sequences. In addition to thiamine biosynthesis genes, the reconstructed ThiR regulons include various transporters for thiamine and its precursors. Bioinformatics predictions were experimentally validated by
in vitro
DNA-binding assays with the recombinant ThiR protein from the hyperthermophilic archaeon
Metallosphaera yellowstonensis
MK1. Thiamine phosphate and, to some extent, TPP and hydroxyethylthiazole phosphate were required for the binding of ThiR to its DNA targets, suggesting that ThiR is derepressed by limitation of thiamine phosphates. The thiamine phosphate-binding residues previously identified in ThiN are highly conserved in ThiR regulators, suggesting a conserved mechanism for effector recognition.

IMPORTANCE
Thiamine pyrophosphate is a cofactor for many essential enzymes for glucose and energy metabolism. Thiamine or vitamin B
1
biosynthesis and its transcriptional regulation in
Archaea
are poorly understood. We applied the comparative genomics approach to identify a novel family of regulators for the transcriptional control of thiamine metabolism genes in
Archaea
and reconstructed the respective regulons. The predicted ThiR regulons in archaeal genomes control the majority of thiamine biosynthesis genes. The reconstructed regulon content suggests that numerous uptake transporters for thiamine and/or its precursors are encoded in archaeal genomes. The ThiR regulon was experimentally validated by DNA-binding assays with
Metallosphaera
spp. These discoveries contribute to our understanding of metabolic and regulatory networks involved in vitamin homeostasis in diverse lineages of
Archaea
.
Contrasting magmatic cannibalism forms evolved phonolitic magmas in the Canary Islands
Authors: Turner S. , Kokfelt T. , Hoernle K. , Johansen T.S. , Hauff F. , Lundstrom C. , van den Bogaard P. , Klügel A.
Published: December 2016

Volcanic sequences on ocean islands record the temporal evolution of underlying magmatic systems and provide insights into how silicic crust is produced away from convergent margins. Assimilation has often been suspected to contribute, but the detection of such a process and its evolving maturity during migration across a mantle plume is less well documented. Here we present new major and trace element and Sr-Nd-Pb-U-Th-Ra-Pa isotope data that facilitate comparison of basanite to phonolite evolution on Tenerife (Canary Islands) with that shown by published data from La Palma. On both islands, (230Th/238U) ratios decrease with differentiation from parental magmas with 230Th excess toward different, silicic contaminants in secular equilibrium. On La Palma, this is inferred to reflect assimilation of small amounts of mafic wall rock. On Tenerife, both (230Th/238U) and (231Pa/235U) ratios decrease toward 1 with increasing differentiation, and this is accompanied by a subtle increase in Pb isotope ratios. At the same time, (226Ra/230Th) ratios change from >1 to <1 (a hitherto unreported magnitude). The Tenerife assimilant is thus constrained to be a partial melt of syenite formed in equilibrium with residual feldspar. The differences reflect a primarily deeper, more mafic magma system beneath La Palma during its late shield-building stage, whereas recent magmatic evolution at Tenerife occurs primarily at lower temperatures in small, shallower magma systems formed during its post–basaltic shield stage. Differentiation takes millennia or less.
Tracing crustal evolution by U-Th-Pb, Sm-Nd, and Lu-Hf isotopes in detrital monazite and zircon from modern rivers
Authors: Liu Xiao-Chi , Wu Yuan-Bao , Fisher Christopher M. , Hanchar John M. , Beranek Luke , Gao Shan , Wang Hao
Published: December 2016

Detrital zircon U-Pb age and Hf isotope studies are useful for identifying the chemical evolution of the continental crust. Zircon, however, is typically a magmatic mineral and thus often fails to document the timing of low-grade metamorphism, and its survival through multiple sedimentary cycles potentially biases the crustal evolution record toward older events. In contrast, monazite typically records metamorphic events and is less likely to survive sedimentary recycling processes, thus providing information not available by zircon. Here, we demonstrate that monazite apparently faithfully records the Sm-Nd isotope composition of the bulk rock and can therefore track the record of crustal evolution and growth, similar to Hf isotopes in zircon. We examine the utility of detrital zircon and monazite for studies of crustal evolution through a comparison of age and tracer isotope information using sediments from two large rivers draining the South China block (SCB). Monazite and zircon grains yield mostly Mesozoic and Paleozoic U-Pb ages and depleted mantle model age peaks at ca. 1900–1300 Ma, indicating that both minerals preserve similar, yet critical, information on the crustal evolution of the catchment area. In contrast, zircon yields abundant Neoproterozoic and older U-Pb ages with a very large spread of model ages, preserving a history strongly skewed to older ages. Based on the lack of known rocks of this age in the catchments, ancient zircon was likely sourced from sedimentary rocks within the catchment area. This combined data set presents a more complete history of crustal evolution and growth in the SCB and demonstrates the advantages of an integrated approach that includes both detrital monazite and zircon.