bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural Dynamics Testing and Analysis for Design Evaluation and Monitoring of Heliostats
Authors: Todd Griffith D. , Moya Adam C. , Ho Clifford K. , Hunter Patrick S.
Published: September 2014

Heliostat vibrations due to wind loading can degrade optical pointing accuracy while fatiguing the structural components. This paper reports the use of structural dynamic measurements for design evaluation and monitoring of heliostat vibrations. A heliostat located at the national solar thermal testing facility (NSTTF) at Sandia National Laboratories in Albuquerque, New Mexico, has been instrumented to measure its modes of vibration, strain and displacements under wind loading. The information gained from these tests will be used to evaluate and improve structural models that predict the motions/deformations of the heliostat due to gravitational and dynamic wind loadings. These deformations can cause optical errors and motions that degrade the performance of the heliostat. The main contributions of this work include: (1) demonstration of the role of structural dynamic tests (also known as modal tests) to provide a characterization of the important dynamics of the heliostat structure as they relate to durability and optical accuracy, (2) the use of structural dynamic tests to provide data to evaluate and improve the accuracy of computer-based design models, and (3) the selection of sensors and data-processing techniques that are appropriate for long-term monitoring of heliostat motions. This work also demonstrates the first measurements of rigid body modes of vibration associated with heliostat drive (azimuth and elevation) mechanisms, which are important structural dynamic response characteristics in dynamic design of heliostats.
Improvement of Radiative Performances of High Temperature Solar Particle Receivers Using Coated Particles and Mixtures
Authors: Ordóñez Freddy , Caliot Cyril , Bataille Françoise , Lauriat Guy
Published: September 2014

The use of HfB2, ZrB2, HfC, ZrC, W, and SiC particles in a high temperature solar particle receiver (SPR) is analyzed. The SPR is modeled as a 1D slab of spherical particles dispersion, submitted to a concentrated and collimated solar flux (q0 = 1500 kW/m2). The temperature inside the SPR is taken constant (T = 1300 K), as for a well-stirred receiver. For the W and SiC, the refractive indexes reported in the literature are retained while the real and imaginary parts of the refractive indexes of the others materials are obtained from available reflectance data, using the Kramers–Kronig (KK) relationships. Three SPR configurations are considered: a homogeneous medium with only one kind of particles, a medium with a mixture of two materials and a medium with coated particles. The three configuration results are compared with those obtained using particles made with an ideal material. For the first configuration, the lowest radiative losses are found using small particles of sizes close to d = 2 μm. For the second configuration, non-noticeable improvements are found by the use of mixtures of the studied materials. For the third configuration, when the SiC is used as mantle, the radiative losses decrease to approach the ideal minimum. The best combination corresponds to a particle with a core of W coated by SiC. Improvements of 2.6% and 2.8% may be achieved using coating thickness of 50 nm with particles of d = 2 μm and d = 100 μm, respectively. The use of coated particles may thus lead to significant improvements in the radiative performances of a SPR working at high temperature.
Analysis of Fully Developed Opposing Mixed Convection Flow in an Inclined Channel Filled by a Nanofluid
Authors: You Xiang-Cheng , Xu Hang , Pop Ioan
Published: September 2014

In this paper, an analysis is made on the convective heat transfer of a nanofluid between two inclined parallel plates with a uniform heat flux boundary condition. The analytical solutions are obtained explicitly for the velocity, temperature, and pressure distributions, which are dependent on two parameters P1 and P2. By alerting their values, four different regimes for flow reversal are found. On the other hand, it is found that the nanoparticle volume fraction φ has a significant influence on the flow reversal. Physically important quantities such as wall friction and Nusselt number are in detail discussed for the TiO2-water nanofluid.
Liquid Jets in Subsonic Air Crossflow at Elevated Pressure
Authors: Song Jinkwan , Cary Cain Charles , Guen Lee Jong
Published: September 2014

The breakup, penetration, droplet size, and size distribution of a Jet A-1 fuel in air crossflow has been investigated with focus given to the impact of surrounding air pressure. Data have been collected by particle Doppler phased analyzer (PDPA), Mie-scattering with high speed photography augmented by laser sheet, and Mie-scattering with intensified charge-coupled device (ICCD) camera augmented by nanopulse lamp. Nozzle orifice diameter, do, was 0.508 mm and nozzle orifice length to diameter ratio, lo/do, was 5.5. Air crossflow velocities ranged from 29.57 to 137.15 m/s, air pressures from 2.07 to 9.65 bar, and temperature held constant at 294.26 K. Fuel flow provides a range of fuel/air momentum flux ratio (q) from 5 to 25 and Weber number from 250 to 1000. From the results, adjusted correlation of the mean drop size has been proposed using drop size data measured by PDPA as follows: (D0/D32)=0.267Wea0.44q0.08(ρl/ρa)0.30(μl/μa)-0.16. This correlation agrees well and shows roles of aerodynamic Weber number, Wea, momentum flux ratio, q, and density ratio, ρl/ρa. Change of the breakup regime map with respect to surrounding air pressure has been observed and revealed that the boundary between each breakup modes can be predicted by a transformed correlation obtained from above correlation. In addition, the spray trajectory for the maximum Mie-scattering intensity at each axial location downstream of injector is extracted from averaged Mie-scattering images. From these results, correlations with the relevant parameters including q, x/do, density ratio, viscosity ratio, and Weber number are made over a range of conditions. According to spray trajectory at the maximum Mie-scattering intensity, the effect of surrounding air pressure becomes more important in the farfield. On the other hand, effect of aerodynamic Weber number is more important in the nearfield.
Turbofan Engine Health Assessment From Flight Data
Authors: Aretakis N. , Roumeliotis I. , Alexiou A. , Romesis C. , Mathioudakis K.
Published: September 2014

The paper presents the use of different approaches to engine health assessment using on-wing data obtained over a year from an engine of a commercial short-range aircraft. The on-wing measurements are analyzed with three different approaches, two of which employ two models of different quality. Initially, the measurements are used as the sole source of information and are postprocessed utilizing a simple “model” (a table of corrected parameter values at different engine power levels) to obtain diagnostic information. Next, suitable engine models are built utilizing a semi-automated method which allows for quick and efficient creation of engine models adapted to specific data. Two engine models are created, one based on publicly available data and one adapted to engine specific on-wing “healthy” data. These models of different details are used in a specific diagnostic process employing model-based diagnostic methods, namely the probabilistic neural network (PNN) method and the deterioration tracking method. The results demonstrate the level of diagnostic information that can be obtained for this set of data from each approach (raw data, generic engine model or adapted to measurements engine model). A subsystem fault is correctly identified utilizing the diagnostic process combined with the engine specific model while the deterioration tracking method provides additional information about engine deterioration.
Flat-Plate Solar Collector in Transient Operation: Modeling and Measurements
Authors: Saleh Ahmad M. , Mueller Donald W. , Abu-Mulaweh Hosni I.
Published: September 2014

This paper describes a mathematical model for simulating the transient processes which occur in liquid flat-plate solar collectors. A discrete nodal model that represents the flat-plate solar collector's layers and the storage tank is employed. The model is based on solving a system of coupled differential equations which describe the energy conservation for the glass cover, air gap, absorber, fluid, insulation, and the storage tank. Inputs to the model include the time-varying liquid flow rate, incident solar radiation, and the ambient air temperature, as well as the volume of liquid in the storage tank and initial temperature of the system. The system of differential equations is solved iteratively using an implicit, finite-difference formulation executed with Matlab software. In order to verify the proposed method, an experiment was designed and conducted on different days with variable ambient conditions and flow rates. The comparison between the computed and measured results of the transient fluid temperature at the collector outlet shows good agreement. The proposed method is extremely general and flexible accounting for variable ambient conditions and flow rates and allowing for a geometrical and thermophysical description of all major components of the solar collector system, including the storage tank. The validated, general model is suitable to investigate the effectiveness of various components without the necessity of carrying out experimental work, and the flexible computational scheme is useful for transient simulations of energy systems.
Modeling Transmission Effects on Multilayer Insulation
Authors: Youngquist Robert C. , Nurge Mark A. , Johnson Wesley L. , Starr Stanley O.
Published: September 2014

Multilayer insulation (MLI), commonly used in cryogenics, is typically composed of many layers of thin polymer sheets each coated with a thin film of highly reflective metal. The primary purpose of this insulation is to block radiative energy transfer. However, at very low temperatures where blackbody radiation occurs at long wavelengths, some energy may be transmitted through these layers, degrading the performance of the insulation. Traditional modeling techniques assume that the films are opaque and are not easily extended to include radiative transmission through the layers. In order to model the effect of wavelength dependent transmission on the thermal performance of MLI, an L1-norm energy vector is defined and combined with a square energy distribution matrix. The key here is that the energy distribution matrix describes one time step of the radiation—one set of reflections, transmissions, and absorptions—and since this matrix is square, it can be easily raised to a large power, describing the final state of the system quickly. This approach removes the need to track every reflected and transmitted radiation element, but instead determines the eventual location where the thermal radiation energy is deposited. This method can be generalized to model dependence of the reflection and transmission of the radiation on wavelength or angle of propagation, to include thermal conduction effects, and to model transient behavior. The results of this work predict the degree of transmission dependent degradation expected to be seen when using state-of-the-art MLI in low temperature cryogenic systems.
Computational Fluid Dynamics Modeling of Two-Phase Flow in an Adiabatic Capillary Tube
Authors: Prajapati Yogesh K. , Pathak Manabendra , Kaleem Khan Mohd.
Published: September 2014

In this work computational fluid dynamics (CFD) technique has been used to analyze the detailed flow structures of refrigerant R-134a in an adiabatic capillary tube using volume of fluid based finite volume method. Also, an attempt has been made to understand the flashing phenomenon within the adiabatic capillary tube. A source term has been incorporated in the governing equations to model the mass transfer rate from liquid phase to vapor phase during the flashing process. The developed numerical model has been validated with the available experimental data. The unsteady variations of flow properties such as velocity, void fraction distributions, and flow turbulence across the cross section and at different axial length of the tube have been presented. It has been observed that flashing initiates from the wall of the tube. With the inception of vapor, the flow properties change drastically with very short transient period. As far as flow turbulence is concerned, the role of flashing parameter seems to be stronger than internal tube wall roughness.
Natural Frequency Computation of Parallel Robots
Authors: Germain Coralie , Briot Sébastien , Caro Stéphane , Wenger Philippe
Published: September 2014

The characterization of the elastodynamic behavior and natural frequencies of parallel robots is a crucial point. Accurate elastodynamic models of parallel robots are useful at both their design and control stages in order to define their optimal dimensions and shapes while improving their vibratory behavior. Several methods exist to write the elastodynamic model of manipulators. However, those methods do not provide a straightforward way to write the Jacobian matrices related to the kinematic constraints of parallel manipulators. Therefore, the subject of this paper is about a systematic method for the determination of the mass and stiffness matrices of any parallel robot in stationary configurations. The proposed method is used to express the mass and stiffness matrices of the Nantes Variable Actuation Robot (NaVARo), a three-degree-of-freedom (3DOF) planar parallel robot with variable actuation schemes, developed at IRCCyN. Then, its natural frequencies are evaluated and compared with those obtained from both Cast3m software and experimentally.
Design and Analysis of a Unique Energy Storage Flywheel System—An Integrated Flywheel, Motor/Generator, and Magnetic Bearing Configuration
Authors: Kailasan Arunvel , Dimond Tim , Allaire Paul , Sheffler David
Published: September 2014

Energy storage is becoming increasingly important with the rising need to accommodate the energy needs of a greater population. Energy storage is especially important with intermittent sources such as solar and wind. Flywheel energy storage systems store kinetic energy by constantly spinning a compact rotor in a low-friction environment. When short-term back-up power is required as a result of utility power loss or fluctuations, the rotor’s inertia allows it to continue spinning and the resulting kinetic energy is converted to electricity. Unlike fossil-fuel power plants and batteries, the flywheel based energy storage systems do not emit any harmful byproducts during their operation and have attracted interest recently. A typical flywheel system is comprised of an energy storage rotor, a motor-generator system, bearings, power electronics, controls, and a containment housing. Conventional outer flywheel designs have a large diameter energy storage rotor attached to a smaller diameter section which is used as a motor/generator. The cost to build and maintain such a system can be substantial. This paper presents a unique concept design for a 1 kW-h inside-out integrated flywheel energy storage system. The flywheel operates at a nominal speed of 40,000 rpm. This design can potentially scale up for higher energy storage capacity. It uses a single composite rotor to perform the functions of energy storage. The flywheel design incorporates a five-axis active magnetic bearing system. The flywheel is also encased in a double layered housing to ensure safe operation. Insulated-gate bipolar transistor (IBGT) based power electronics are adopted as well. The design targets cost savings from reduced material and manufacturing costs. This paper focuses on the rotor design, the active magnetic bearing design, the associated rotordynamics, and a preliminary closed-loop controller.
Application of Boil Off Gas Compressors in Liquefied Natural Gas Plants
Authors: Chaker Mustapha , Meher-Homji Cyrus B. , Pillai Pradeep , Bhattacharya Dipanjan , Messersmith David
Published: September 2014

This paper discusses complexities and challenges of managing boil off gas (BOG) in liquefied natural gas (LNG) liquefaction plants. Most publications in the past have focused on regasification terminals and have not addressed the area of liquefaction plants. The paper discusses the generation and management of BOG and the associated networks and machinery to manage it. BOG options available for both Greenfield plants and in debottlenecking situations are covered. The advantages and disadvantages of different options and compressor systems are covered and the concept of dynamic simulation as an analysis tool is addressed.
Modeling, Analysis, and Simulation of Paste Freezing in Freeze-Form Extrusion Fabrication of Thin-Wall Parts
Authors: Li Mingyang , Landers Robert G. , Leu Ming C.
Published: September 2014

During the freeze-form extrusion fabrication (FEF) process for aqueous-based pastes, the subzero temperature (in Celsius) environment aids the part in maintaining its shape by freezing the water present in the paste. The first few layers of paste freeze very quickly when deposited; however, as the part's height increases, the freezing time increases as the rate of heat conduction to the substrate decreases rapidly. The freezing time can substantially exceed the time required to deposit one layer of paste due to water's high latent heat, leaving the extruded paste in its semiliquid state, and causing the part to deform or even collapse. Therefore, dwell time may be required between layers. A method is needed to predict paste freezing time in order to fabricate a part successfully while minimize the part build time. In this paper, a simplified one-dimensional (1D) heat transfer model was introduced for fabricating thin-wall parts by the FEF process. The simplified model, which could reduce computation times from days to minutes, was validated by the commercial finite element software Fluent. The paste temperature and paste freezing time for various process parameters were computed via numerical simulation using this model. As the layer number increases, the paste freezing time reaches a steady state. The relationship between the steady-state freezing time and the total time, which is the sum of the deposition time for the current layer and the dwell time between the current and next layers, was studied for various convection coefficients, paste materials, paste solids loadings, initial paste temperatures, ambient temperatures, and layer thicknesses.
Freeform Vertical and Horizontal Fabrication of Alginate-Based Vascular-Like Tubular Constructs Using Inkjetting
Authors: Xu Changxue , Zhang Zhengyi , Christensen Kyle , Huang Yong , Fu Jianzhong , Markwald Roger R.
Published: September 2014

Organ printing, among different tissue engineering innovations, is a freeform fabrication approach for making three-dimensional (3D) tissue and organ constructs using cellular spheroids or bioinks as building blocks. The capability to fabricate vascular-like tubular constructs is an important indicator of the overall feasibility of envisioned organ printing technology. In this study, vascular-like alginate tubes, which mimic typical vascular constructs, are fabricated both vertically and horizontally using drop-on-demand (DOD) inkjetting. Manufacturing-related challenges are different for the vertical and horizontal printing configurations. In general, the vertical printing configuration has instability or collapse/buckling problems and may experience some difficulty in fabricating complex constructs such as Y- or K-shaped constructs if there is no supporting material. The horizontal printing configuration may easily result in a deformed hollow cross section and may require extra effort to mitigate the undesired deformation. It is envisioned that the combination of vertical and horizontal printing provides an efficient and effective way to fabricate complex tubular constructs with both vertical and horizontal branching features.
Adaptive Slicing in Additive Manufacturing Process Using a Modified Boundary Octree Data Structure
Authors: Siraskar Nandkumar , Paul Ratnadeep , Anand Sam
Published: September 2014

In additive manufacturing (AM) processes, the layer-by-layer fabrication leads to a staircase error resulting in dimensional inaccuracies in the part surface. Using thinner slices reduces the staircase error and improves part accuracy but also increases the number of layers and the build time for manufacturing the part. Another approach called adaptive slicing uses slices of varying thicknesses based on the part geometry to build the part. A new algorithm to compute adaptive slice thicknesses using octree data structure is presented in this study. This method, termed as modified boundary octree data structure (MBODS) algorithm, is used to convert the stereolithography (STL) file of an object to an octree data structure based on the part's geometry, the machine parameters, and a user defined tolerance value. A subsequent algorithm computes the variable slice thicknesses using the MBODS representation of the part and virtually manufactures the part using these calculated slice thicknesses. Points sampled from the virtually manufactured part are inspected to evaluate the volumetric, profile, and cylindricity part errors. The MBODS based slicing algorithm is validated by comparing it with the uniform slicing approach using various slice thicknesses for different parts. The developed MBODS algorithm is observed to be more effective in improving the part quality while using lesser number of slices.
An Integrated Approach to Additive Manufacturing Simulations Using Physics Based, Coupled Multiscale Process Modeling
Authors: Pal Deepankar , Patil Nachiket , Zeng Kai , Stucker Brent
Published: September 2014

The complexity of local and dynamic thermal transformations in additive manufacturing (AM) processes makes it difficult to track in situ thermomechanical changes at different length scales within a part using experimental process monitoring equipment. In addition, in situ process monitoring is limited to providing information only at the exposed surface of a layer being built. As a result, an understanding of the bulk microstructural transformations and the resulting behavior of a part requires rigorous postprocess microscopy and mechanical testing. In order to circumvent the limited feedback obtained from in situ experiments and to better understand material response, a novel 3D dislocation density based thermomechanical finite element framework has been developed. This framework solves for the in situ response much faster than currently used state-of-the-art modeling software since it has been specifically designed for AM platforms. This modeling infrastructure can predict the anisotropic performance of AM-produced components before they are built, can serve as a method to enable in situ closed-loop process control and as a method to predict residual stress and distortion in parts and thus enable support structure optimization. This manuscript provides an overview of these software modules which together form a robust and reliable AM software suite to address future needs for machine development, material development, and geometric optimization.
Breast tissue decomposition with spectral distortion correction: A postmortem study
Authors: Ding Huanjun , Zhao Bo , Baturin Pavlo , Behroozi Farnaz , Molloi Sabee
Published: September 2014

Purpose:

To investigate the feasibility of an accurate measurement of water, lipid, and protein composition of breast tissue using a photon‐counting spectral computed tomography (CT) with spectral distortion corrections.

Methods:

Thirty‐eight postmortem breasts were imaged with a cadmium‐zinc‐telluride‐based photon‐counting spectral CT system at 100 kV. The energy‐resolving capability of the photon‐counting detector was used to separate photons into low and high energy bins with a splitting energy of 42 keV. The estimated mean glandular dose for each breast ranged from 1.8 to 2.2 mGy. Two spectral distortion correction techniques were implemented, respectively, on the raw images to correct the nonlinear detector response due to pulse pileup and charge‐sharing artifacts. Dual energy decomposition was then used to characterize each breast in terms of water, lipid, and protein content. In the meantime, the breasts were chemically decomposed into their respective water, lipid, and protein components to provide a gold standard for comparison with dual energy decomposition results.

Results:

The accuracy of the tissue compositional measurement with spectral CT was determined by comparing to the reference standard from chemical analysis. The averaged root‐mean‐square error in percentage composition was reduced from 15.5% to 2.8% after spectral distortion corrections.

Conclusions:

The results indicate that spectral CT can be used to quantify the water, lipid, and protein content in breast tissue. The accuracy of the compositional analysis depends on the applied spectral distortion correction technique.
Investigation of sagittal image acquisition for 4D‐MRI with body area as respiratory surrogate
Authors: Liu Yilin , Yin Fang‐Fang , Chang Zheng , Czito Brian G. , Palta Manisha , Bashir Mustafa R. , Qin Yujiao , Cai Jing
Published: September 2014

Purpose:

The authors have recently developed a novel 4D‐MRI technique for imaging organ respiratory motion employing cine acquisition in the axial plane and using body area (BA) as a respiratory surrogate. A potential disadvantage associated with axial image acquisition is the space‐dependent phase shift in the superior–inferior (SI) direction, i.e., different axial slice positions reach the respiratory peak at different respiratory phases. Since respiratory motion occurs mostly in the SI and anterior–posterior (AP) directions, sagittal image acquisition, which embeds motion information in these two directions, is expected to be more robust and less affected by phase‐shift than axial image acquisition. This study aims to develop and evaluate a 4D‐MRI technique using sagittal image acquisition.

Methods:

The authors evaluated axial BA and sagittal BA using both 4D‐CT images (11 cancer patients) and cine MR images (6 healthy volunteers and 1 cancer patient) by comparing their corresponding space‐dependent phase‐shift in the SI direction and in the lateral direction , respectively. To evaluate sagittal BA 4D‐MRI method, a motion phantom study and a digital phantom study were performed. Additionally, six patients who had cancer(s) in the liver were prospectively enrolled in this study. For each patient, multislice sagittal MR images were acquired for 4D‐MRI reconstruction. 4D retrospective sorting was performed based on respiratory phases. Single‐slice cine MRI was also acquired in the axial, coronal, and sagittal planes across the tumor center from which tumor motion trajectories in the SI, AP, and medial–lateral (ML) directions were extracted and used as references from comparison. All MR images were acquired in a 1.5 T scanner using a steady‐state precession sequence (frame rate ∼ 3 frames/s).

Results:

4D‐CT scans showed that was significantly greater than (p‐value: 0.012); the median phase‐shift was 16.9% and 7.7%, respectively. Body surface motion measurement from axial and sagittal MR cines also showed was significantly greater than . The median and was 11.0% and 9.2% (p‐value = 0.008), respectively. Tumor motion trajectories from 4D‐MRI matched with those from single‐slice cine MRI: the mean (±SD) absolute differences in tumor motion amplitude between the two were 1.5 ± 1.6 mm, 2.1 ± 1.9 mm, and 1.1 ± 1.0 mm in the SI, ML, and AP directions from this patient study.

Conclusions:

Space‐dependent phase shift is less problematic for sagittal acquisition than for axial acquisition. 4D‐MRI using sagittal acquisition was successfully carried out in patients with hepatic tumors.
Free-Living and Particle-Associated Bacterioplankton in Large Rivers of the Mississippi River Basin Demonstrate Biogeographic Patterns
Authors: Jackson Colin R. , Millar Justin J. , Payne Jason T. , Ochs Clifford A.
Published: September 2014

The different drainage basins of large rivers such as the Mississippi River represent interesting systems in which to study patterns in freshwater microbial biogeography. Spatial variability in bacterioplankton communities in six major rivers (the Upper Mississippi, Missouri, Illinois, Ohio, Tennessee, and Arkansas) of the Mississippi River Basin was characterized using Ion Torrent 16S rRNA amplicon sequencing. When all systems were combined, particle-associated (>3 μm) bacterial assemblages were found to be different from free-living bacterioplankton in terms of overall community structure, partly because of differences in the proportional abundance of sequences affiliated with major bacterial lineages (
Alphaproteobacteria
,
Cyanobacteria
, and
Planctomycetes
). Both particle-associated and free-living communities ordinated by river system, a pattern that was apparent even after rare sequences or those affiliated with
Cyanobacteria
were removed from the analyses. Ordination of samples by river system correlated with environmental characteristics of each river, such as nutrient status and turbidity. Communities in the Upper Mississippi and the Missouri and in the Ohio and the Tennessee, pairs of rivers that join each other, contained similar taxa in terms of presence-absence data but differed in the proportional abundance of major lineages. The most common sequence types detected in particle-associated communities were picocyanobacteria in the
Synechococcus
/
Prochlorococcus
/
Cyanobium
(Syn/Pro) clade, while free-living communities also contained a high proportion of LD12 (SAR11/
Pelagibacter
)-like
Alphaproteobacteria
. This research shows that while different tributaries of large river systems such as the Mississippi River harbor distinct bacterioplankton communities, there is also microhabitat variation such as that between free-living and particle-associated assemblages.
Major Role of NAD-Dependent Lactate Dehydrogenases in the Production of
l
-Lactic Acid with High Optical Purity by the Thermophile Bacillus coagulans
Authors: Wang Limin , Cai Yumeng , Zhu Lingfeng , Guo Honglian , Yu Bo
Published: September 2014

Bacillus coagulans
2-6 is an excellent producer of optically pure
l
-lactic acid. However, little is known about the mechanism of synthesis of the highly optically pure
l
-lactic acid produced by this strain. Three enzymes responsible for lactic acid production—NAD-dependent
l
-lactate dehydrogenase (
l
-nLDH; encoded by
ldhL
), NAD-dependent
d
-lactate dehydrogenase (
d
-nLDH; encoded by
ldhD
), and glycolate oxidase (GOX)—were systematically investigated in order to study the relationship between these enzymes and the optical purity of lactic acid.
Lactobacillus delbrueckii
subsp.
bulgaricus
DSM 20081 (a
d
-lactic acid producer) and
Lactobacillus plantarum
subsp.
plantarum
DSM 20174 (a
dl
-lactic acid producer) were also examined in this study as comparative strains, in addition to
B. coagulans
. The specific activities of key enzymes for lactic acid production in the three strains were characterized
in vivo
and
in vitro
, and the levels of transcription of the
ldhL
,
ldhD
, and GOX genes during fermentation were also analyzed. The catalytic activities of
l
-nLDH and
d
-nLDH were different in
l
-,
d
-, and
dl
-lactic acid producers. Only
l
-nLDH activity was detected in
B. coagulans
2-6 under native conditions, and the level of transcription of
ldhL
in
B. coagulans
2-6 was much higher than that of
ldhD
or the GOX gene at all growth phases. However, for the two
Lactobacillus
strains used in this study,
ldhD
transcription levels were higher than those of
ldhL
. The high catalytic efficiency of
l
-nLDH toward pyruvate and the high transcription ratios of
ldhL
to
ldhD
and
ldhL
to the GOX gene provide the key explanations for the high optical purity of
l
-lactic acid produced by
B. coagulans
2-6.
Calcium-Enhanced Twitching Motility in Xylella fastidiosa Is Linked to a Single PilY1 Homolog
Authors: Cruz Luisa F. , Parker Jennifer K. , Cobine Paul A. , De La Fuente Leonardo
Published: September 2014

The plant-pathogenic bacterium
Xylella fastidiosa
is restricted to the xylem vessel environment, where mineral nutrients are transported through the plant host; therefore, changes in the concentrations of these elements likely impact the growth and virulence of this bacterium. Twitching motility, dependent on type IV pili (TFP), is required for movement against the transpiration stream that results in basipetal colonization. We previously demonstrated that calcium (Ca) increases the motility of
X. fastidiosa
, although the mechanism was unknown. PilY1 is a TFP structural protein recently shown to bind Ca and to regulate twitching and adhesion in bacterial pathogens of humans. Sequence analysis identified three
pilY1
homologs in
X. fastidiosa
(PD0023, PD0502, and PD1611), one of which (PD1611) contains a Ca-binding motif. Separate deletions of PD0023 and PD1611 resulted in mutants that still showed twitching motility and were not impaired in attachment or biofilm formation. However, the response of increased twitching at higher Ca concentrations was lost in the
pilY1
-1611 mutant. Ca does not modulate the expression of any of the
X. fastidiosa
PilY1 homologs, although it increases the expression of the retraction ATPase
pilT
during active movement. The evidence presented here suggests functional differences between the PilY1 homologs, which may provide
X. fastidiosa
with an adaptive advantage in environments with high Ca concentrations, such as xylem sap.
A Highly Stable
d
-Amino Acid Oxidase of the Thermophilic Bacterium Rubrobacter xylanophilus
Authors: Takahashi Shouji , Furukawara Makoto , Omae Keishi , Tadokoro Namiho , Saito Yayoi , Abe Katsumasa , Kera Yoshio
Published: September 2014

d
-Amino acid oxidase (DAO) is a biotechnologically attractive enzyme that can be used in a variety of applications, but its utility is limited by its relatively poor stability. A search of a bacterial genome database revealed a gene encoding a protein homologous to DAO in the thermophilic bacterium
Rubrobacter xylanophilus
(RxDAO). The recombinant protein expressed in
Escherichia coli
was a monomeric protein containing noncovalently bound flavin adenine dinucleotide as a cofactor. This protein exhibited oxidase activity against neutral and basic
d
-amino acids and was significantly inhibited by a DAO inhibitor, benzoate, but not by any of the tested
d
-aspartate oxidase (DDO) inhibitors, thus indicating that the protein is DAO. RxDAO exhibited higher activities and affinities toward branched-chain
d
-amino acids, with the highest specific activity toward
d
-valine and catalytic efficiency (
k
cat
/

K
m

) toward
d
-leucine. Substrate inhibition was observed in the case of
d
-tyrosine. The enzyme had an optimum pH range and temperature of pH 7.5 to 10 and 65°C, respectively, and was stable between pH 5.0 and pH 8.0, with a
T
50
(the temperature at which 50% of the initial enzymatic activity is lost) of 64°C. No loss of enzyme activity was observed after a 1-week incubation period at 30°C. This enzyme was markedly inactivated by phenylmethylsulfonyl fluoride but not by thiol-modifying reagents and diethyl pyrocarbonate, which are known to inhibit certain DAOs. These results demonstrated that RxDAO is a highly stable DAO and suggested that this enzyme may be valuable for practical applications, such as the determination and quantification of branched-chain
d
-amino acids, and as a scaffold to generate a novel DAO via protein engineering.
Sensitive, Efficient Quantitation of
13
C-Enriched Nucleic Acids via Ultrahigh-Performance Liquid Chromatography–Tandem Mass Spectrometry for Applications in Stable Isotope Probing
Authors: Wilhelm Roland , Szeitz András , Klassen Tara L. , Mohn William W.
Published: September 2014

Stable isotope probing (SIP) of nucleic acids is a powerful tool for studying the functional traits of microbial populations within complex communities, but SIP involves a number of technical challenges. Many of the difficulties in DNA-SIP and RNA-SIP experiments can be effectively overcome with an efficient, sensitive method for quantitating the isotopic enrichment of nucleic acids. Here, we present a sensitive method for quantitating
13
C enrichment of nucleic acids, requiring a few nanograms of sample, and we demonstrate its utility in typical DNA-SIP and RNA-SIP experiments. All five nucleobases (adenine, guanine, cytosine, thymine, and uracil) were separated and detected by using ultrahigh-performance liquid chromatography–tandem mass spectrometry. We detected all isotopic species in samples with as low as 1.5 atom%
13
C above natural abundance, using 1-ng loadings. Quantitation was used to characterize the isotopic enrichment kinetics of cellulose- and lignin-based microcosm experiments and to optimize the recovery of enriched nucleic acids. Application of our method will minimize the quantity of expensive isotopically labeled substrates required and reduce the risk of failed experiments due to insufficient recovery of labeled nucleic acids for sequencing library preparation.
Effects of Nicotine on Streptococcus gordonii Growth, Biofilm Formation, and Cell Aggregation
Authors: Huang R. , Li M. , Ye M. , Yang K. , Xu X. , Gregory R. L.
Published: September 2014

Streptococcus gordonii
is a commensal species of human oral flora. It initiates dental biofilm formation and provides binding sites for later colonizers to attach to and generate mature biofilm. Smoking is the second highest risk factor for periodontal disease, and cigarette smoke extract has been reported to facilitate
Porphyromonas gingivalis
-
S. gordonii
dual-species biofilm formation. Our hypothesis is that nicotine, one of the most important and active components of tobacco, stimulates
S. gordonii
multiplication and aggregation. In the present study,
S. gordonii
planktonic cell growth (kinetic absorbance and CFU), biofilm formation (crystal violet stain and confocal laser scanning microscopy [CLSM]), aggregation with/without sucrose, and 11 genes that encode binding proteins or regulators of gene expression were investigated. Results demonstrated planktonic cell growth was stimulated by 1 to 4 mg/ml nicotine treatment. Biofilm formation was increased at 0.5 to 4 mg/ml nicotine. CLSM indicated bacterial cell mass was increased by 2 and 4 mg/ml nicotine, but biofilm extracellular polysaccharide was not significantly affected by nicotine. Cell aggregation was upregulated by 4, 8, and 16 mg/ml nicotine with sucrose and by 16 mg/ml nicotine without sucrose. Quantitative reverse transcriptase PCR indicated
S. gordonii
abpA
,
scaA
,
ccpA
, and
srtA
were upregulated in planktonic cells by 2 mg/ml nicotine. In conclusion, nicotine stimulates
S. gordonii
planktonic cell growth, biofilm formation, aggregation, and gene expression of binding proteins. Those effects may promote later pathogen attachment to tooth surfaces, the accumulation of tooth calculus, and the development of periodontal disease in cigarette smokers.
High-Level Production of Plasmid DNA by Escherichia coli DH5α Ω
sacB
by Introducing
inc
Mutations
Authors: Trivedi Ram Narayan , Akhtar Parvez , Meade Jonathan , Bartlow Patrick , Ataai Mohammad M. , Khan Saleem A. , Domach Michael M.
Published: September 2014

For small-copy-number pUC-type plasmids, the
inc1
and
inc2
mutations, which deregulate replication, were previously found to increase the plasmid copy number 6- to 7-fold. Because plasmids can exert a growth burden, it was not clear if further amplification of copy number would occur due to
inc
mutations when the starting point for plasmid copy number was orders of magnitude higher. To investigate further the effects of the
inc
mutations and the possible limits of plasmid synthesis, the parent plasmid pNTC8485 was used as a starting point. It lacks an antibiotic resistance gene and has a copy number of ∼1,200 per chromosome. During early stationary-phase growth in LB broth at 37°C,
inc2
mutants of pNTC8485 exhibited a copy number of ∼7,000 per chromosome. In minimal medium at late log growth, the copy number was found to be significantly increased, to approximately 15,000. In an attempt to further increase the plasmid titer (plasmid mass/culture volume), enzymatic hydrolysis of the selection agent, sucrose, at late log growth extended growth and tripled the total plasmid amount such that an approximately 80-fold gain in total plasmid was obtained compared to the value for typical pUC-type vectors. Finally, when grown in minimal medium, no detectable impact on the exponential growth rate or the fidelity of genomic or plasmid DNA replication was found in cells with deregulated plasmid replication. The use of
inc
mutations and the sucrose degradation method presents a simplified way for attaining high titers of plasmid DNA for various applications.
The Facultative Symbiont Rickettsia Protects an Invasive Whitefly against Entomopathogenic Pseudomonas syringae Strains
Authors: Hendry Tory A. , Hunter Martha S. , Baltrus David A.
Published: September 2014

Facultative endosymbionts can benefit insect hosts in a variety of ways, including context-dependent roles, such as providing defense against pathogens. The role of some symbionts in defense may be overlooked, however, when pathogen infection is transient, sporadic, or asymptomatic. The facultative endosymbiont
Rickettsia
increases the fitness of the sweet potato whitefly (
Bemisia tabaci
) in some populations through mechanisms that are not yet understood. In this study, we investigated the role of
Rickettsia
in mediating the interaction between the sweet potato whitefly and
Pseudomonas syringae
, a common environmental bacterium, some strains of which are pathogenic to aphids. Our results show that
P. syringae
multiplies within whiteflies, leading to host death, and that whiteflies infected with
Rickettsia
show a decreased rate of death due to
P. syringae
. Experiments using plants coated with
P. syringae
confirmed that whiteflies can acquire the bacteria at a low rate while feeding, leading to increased mortality, particularly when the whiteflies are not infected with
Rickettsia
. These results suggest that
P. syringae
may affect whitefly populations in nature and that
Rickettsia
can ameliorate this effect. This study highlights the possible importance of interactions among opportunistic environmental pathogens and endosymbionts of insects.
Exposing the Secrets of Two Well-Known Lactobacillus casei Phages, J-1 and PL-1, by Genomic and Structural Analysis
Authors: Dieterle Maria Eugenia , Bowman Charles , Batthyany Carlos , Lanzarotti Esteban , Turjanski Adrián , Hatfull Graham , Piuri Mariana
Published: September 2014

Bacteriophage J-1 was isolated in 1965 from an abnormal fermentation of Yakult using
Lactobacillus casei
strain Shirota, and a related phage, PL-1, was subsequently recovered from a strain resistant to J-1. Complete genome sequencing shows that J-1 and PL-1 are almost identical, but PL-1 has a deletion of 1.9 kbp relative to J-1, resulting in the loss of four predicted gene products involved in immunity regulation. The structural proteins were identified by mass spectrometry analysis. Similarly to phage A2, two capsid proteins are generated by a translational frameshift and undergo proteolytic processing. The structure of gene product 16 (gp16), a putative tail protein, was modeled based on the crystal structure of baseplate distal tail proteins (Dit) that form the baseplate hub in other
Siphoviridae
. However, two regions of the C terminus of gp16 could not be modeled using this template. The first region accounts for the differences between J-1 and PL-1 gp16 and showed sequence similarity to carbohydrate-binding modules (CBMs). J-1 and PL-1 GFP-gp16 fusions bind specifically to
Lactobacillus casei/paracasei
cells, and the addition of
l
-rhamnose inhibits binding. J-1 gp16 exhibited a higher affinity than PL-1 gp16 for cell walls of
L. casei
ATCC 27139 in phage adsorption inhibition assays, in agreement with differential adsorption kinetics observed for both phages in this strain. The data presented here provide insights into how
Lactobacillus
phages interact with their hosts at the first steps of infection.
Mutational Analysis of Essential Septins Reveals a Role for Septin-Mediated Signaling in Filamentation
Authors: Blankenship Jill R. , Cheng Shaoji , Woolford Carol A. , Xu Wenjie , Johnson Tanner M. , Rogers P. David , Fanning Saranna , Nguyen M. Hong , Clancy Cornelius J. , Mitchell Aaron P.
Published: September 2014

Septin proteins are conserved structural proteins that often demarcate regions of cell division. The essential nature of the septin ring, composed of several septin proteins, complicates investigation of the functions of the ring, although careful analysis in the model yeast
Saccharomyces cerevisiae
has elucidated the role that septins play in the cell cycle. Mutation analysis of nonessential septins in the pathogenic fungus
Candida albicans
has shown that septins also have vital roles in
c
ell
w
all
r
egulation (CWR), hyphal formation, and pathogenesis. While mutations in nonessential septins have been useful in establishing phenotypes, the septin defect is so slight that identifying causative associations between septins and downstream effectors has been difficult. In this work, we describe decreased abundance by mRNA perturbation (DAmP) alleles of essential septins, which display a septin defect more severe than the defect observed in deletions of nonessential septins. The septin DAmP alleles have allowed us to genetically separate the roles of septins in hyphal growth and CWR and to identify the cyclic AMP pathway as a pathway that likely acts in a parallel manner with septins in hyphal morphogenesis.
Isoprenoid Biosynthesis in Plasmodium falciparum
Authors: Guggisberg Ann M. , Amthor Rachel E. , Odom Audrey R.
Published: September 2014

Malaria kills nearly 1 million people each year, and the protozoan parasite
Plasmodium falciparum
has become increasingly resistant to current therapies. Isoprenoid synthesis via the methylerythritol phosphate (MEP) pathway represents an attractive target for the development of new antimalarials. The phosphonic acid antibiotic fosmidomycin is a specific inhibitor of isoprenoid synthesis and has been a helpful tool to outline the essential functions of isoprenoid biosynthesis in
P. falciparum
. Isoprenoids are a large, diverse class of hydrocarbons that function in a variety of essential cellular processes in eukaryotes. In
P. falciparum
, isoprenoids are used for tRNA isopentenylation and protein prenylation, as well as the synthesis of vitamin E, carotenoids, ubiquinone, and dolichols. Recently, isoprenoid synthesis in
P. falciparum
has been shown to be regulated by a sugar phosphatase. We outline what is known about isoprenoid function and the regulation of isoprenoid synthesis in
P. falciparum
, in order to identify valuable directions for future research.