bluuebunny/crossref_metadata_2025 huggingface dataset:
Presynaptic and postsynaptic effects of local cathodal DC polarization within the spinal cord in anaesthetized animal preparations
Authors: Bolzoni F. , Jankowska E.
Published: November 2014

Key points

Trans‐spinal DC stimulation affects both postsynaptic neurons and the presynaptic axons providing input to these neurons. In the present study, we show that intraspinally applied cathodal current replicates the effects of trans‐spinal direct current stimulation in deeply anaesthetized animals and affects spinal neurons both during the actual current application and during a post‐polarization period.

Presynaptic effects of local cathodal polarization were expressed in an increase in the excitability of skin afferents (in the dorsal horn) and group Ia afferents (in motor nuclei), both during and at least 30 min after DC application. However, although the postsynaptic facilitation (i.e. more effective) activation of motoneurons by stimuli applied in a motor nucleus was very potent during local DC application, it was only negligible once DC was discontinued.

The results suggest that the prolonged effects of cathodal polarization are primarily associated with changes in synaptic transmission.

The present study aimed to compare presynaptic and postsynaptic actions of direct current polarization in the spinal cord, focusing on DC effects on primary afferents and motoneurons. To reduce the directly affected spinal cord region, a weak polarizing direct current (0.1–0.3 μA) was applied locally in deeply anaesthetized cats and rats; within the hindlimb motor nuclei in the caudal lumbar segments, or in the dorsal horn within the terminal projection area of low threshold skin afferents. Changes in the excitability of primary afferents activated by intraspinal stimuli (20–50 μA) were estimated using increases or decreases in compound action potentials recorded from the dorsal roots or peripheral nerves as their measure. Changes in the postsynaptic actions of the afferents were assessed from intracellularly recorded monosynaptic EPSPs in hindlimb motoneurons and monosynaptic extracellular field potentials (evoked by group Ia afferents in motor nuclei, or by low threshold cutaneous afferents in the dorsal horn). The excitability of motoneurons activated by intraspinal stimuli was assessed using intracellular records or motoneuronal discharges recorded from a ventral root or a muscle nerve. Cathodal polarization was found to affect motoneurons and afferents providing input to them to a different extent. The excitability of both was markedly increased during DC application, although post‐polarization facilitation was found to involve presynaptic afferents and some of their postsynaptic actions, but only negligibly motoneurons themselves. Taken together, these results indicate that long‐lasting post‐polarization facilitation of spinal activity induced by locally applied cathodal current primarily reflects the facilitation of synaptic transmission.
Effect of Cetane Improver on Combustion and Emission Characteristics of Coal-Derived Sasol Isomerized Paraffinic Kerosene in a Single Cylinder Diesel Engine
Authors: Zheng Ziliang , Joshi Umashankar , Henein Naeim , Sattler Eric
Published: November 2014

Sasol isomerized paraffinic kerosene (IPK) is a coal-derived synthetic fuel under consideration as a blending stock with JP-8 for use in military ground vehicles. Since Sasol IPK is a low ignition quality fuel with derived cetane number (DCN) of 31, there is a need to improve its ignition quality. This paper investigates the effect of adding different amounts of Lubrizol 8090 cetane improver to Sasol IPK on increasing its DCN. The experimental investigation was conducted in a single cylinder research type diesel engine. The engine is equipped with a common rail injection system and an open engine control unit. Experiments covered different injection pressures and intake air temperatures. Analysis of test results was made to determine the effect of cetane improver percentage in the coal-derived Sasol IPK blend on auto-ignition, combustion and emissions of carbon monoxide (CO), total unburned hydrocarbon (HC), oxides of nitrogen (NOx), and particulate matter (PM). In addition, the effect of cetane improver on the apparent activation energy of the global auto-ignition reactions was determined.
The Interactions of In-Cylinder Flow and Fuel Spray in a Gasoline Direct Injection Engine With Variable Tumble
Authors: Zhang Xianhui , Wang Tianyou , Jia Ming , Li Wei , Cui Lei , Zhang Xigang
Published: November 2014

Particle image velocimetry (PIV) system was used to measure the tumble structure of the in-cylinder airflow in a four-valve optical gasoline direct injection (GDI) engine. The tumble ratio was controlled by a flap in the manifold and a baffle in the intake port. With proper orthogonal decomposition (POD) method, the velocity field was decomposed into four parts, i.e., the mean, coherent, transitional, and turbulent. The effect of tumble motion on the cycle-to-cycle variation (CCV) of airflow and spray was investigated by calculating the shear strain vorticity. The results indicate that the flow structure can be effectively changed through the combination of flap and baffle by forming a single large-scale tumble flow with the tumble ratio three times higher than the original one. According to POD analysis, it is revealed that the large-scale strong tumble motion leads to the energy occupation ratio of the mean part greatly increase by up to 30%, while the energy transferred to the coherent part is reduced. The above process also decreases the CCV of the coherent part by 50%; thus, the CCV of the whole airflow in the cylinder can be suppressed. A single large-scale tumble increases the maximum shear strain rate up to 2400 s−1. Meanwhile, the maximum vorticity increases to about 6000 s−1 by rolling up of the airflow. The contact area between spray droplets and air becomes larger, and the momentum exchanges between them contribute to wider sprays cone angle and shorter penetration distance when the flap is closed. The statistics of the measurements illustrate that a single large-scale tumble can promote the formation of homogeneous mixture and reduce the fluctuation between multicycles.
Numerical Simulation of an Industrial Fluid Catalytic Cracking Regenerator
Authors: Tang Guangwu , Silaen Armin K. , Wu Bin , Zhou Chenn Q. , Agnello-Dean Dwight , Wilson Joseph , Meng Qingjun , Khanna Samir
Published: November 2014

Fluid catalytic cracking (FCC) is one of the most important conversion processes in petroleum refineries, and the FCC regenerator is a key part of an FCC unit utilized in the recovery of solid catalyst reactivity by burning off the deposited coke on the catalyst surface. A three-dimensional multiphase, multispecies reacting flow computational fluid dynamics (CFD) model was established to simulate the flow and reactions inside an FCC regenerator. The Euler–Euler approach, where the two phases (gas and solid) are considered to be continuous and fully interpenetrating, is employed. The model includes gas–solid momentum exchange, gas–solid heat exchange, gas–solid mass exchange, and chemical reactions. Chemical reactions incorporated into the model simulate the combustion of coke which is present on the catalyst surface. The simulation results were validated by plant data.
Measurement Systems for Cell Adhesive Forces
Authors: Zhou Dennis W. , García Andrés J.
Published: November 2014

Cell adhesion to the extracellular matrix (ECM) involves integrin receptor–ligand binding and clustering to form focal adhesion (FA) complexes, which mechanically link the cell’s cytoskeleton to the ECM and regulate fundamental cell signaling pathways. Although elucidation of the biochemical events in cell-matrix adhesive interactions is rapidly advancing, recent studies show that the forces underlying cell-matrix adhesive interactions are also critical to cell responses. Therefore, multiple measurement systems have been developed to quantify the spatial and temporal dynamics of cell adhesive forces, and these systems have identified how mechanical events influence cell phenotype and FA structure–function relationships under physiological and pathological settings. This review focuses on the development, methodology, and applications of measurement systems for probing (a) cell adhesion strength and (b) 2D and 3D cell traction forces.
Vibration and Acoustic Analysis of Trussed Railroad Bridge Under Moving Loads
Authors: Daniel Costley R. , Diaz-Alvarez Henry , McKenna Mihan H. , Jordan Anna M.
Published: November 2014

A finite element (FE) model was developed for a Pratt truss railroad bridge located at Ft. Leonard Wood, MO. This model was used to investigate the vibration responses of a bridge under vehicle loading. Modeling results were obtained for a single axle with two wheels traversing the bridge at different speeds. The current model does not include the effects of vehicle suspension. Superposition of multiple axles was used to represent a locomotive transiting the bridge. The output of the vibration response was used as an input to an acoustic FE model to determine which vibrational modes radiate infrasound. The vibration and acoustic models of the railroad bridge will be reviewed, and results from the analysis will be presented. Measurements from an accelerometer mounted on the bridge agree reasonably well with model results. Infrasound could potentially be used to remotely provide information on the capacity and number of vehicles traversing the bridge and to monitor the bridge for significant structural damage.
Assessing the Effects of Impedance Modifications Using the Moebius Transformation
Authors: Zhang Y. , Herrin D. W.
Published: November 2014

The Moebius transformation maps straight lines or circles in one complex domain into straight lines or circles in another. It has been observed that the equations relating acoustic or mechanical impedance modifications to responses under harmonic excitation are in the form of the Moebius transformation. Using the properties of the Moebius transformation, the impedance modification that will minimize the response at a particular frequency can be predicted provided that the modification is between two positions. To prove the utility of this method for acoustic and mechanical systems, it is demonstrated that the equations for calculation of transmission and insertion loss of mufflers, insertion loss of enclosures, and insertion loss of mounts are in the form of the Moebius transformation for impedance modifications. The method is demonstrated for enclosure insertion loss by adding a short duct in a partition introduced to an enclosure. In a similar manner, it is shown that the length or area of a bypass duct in a muffler can be tuned to maximize the transmission loss. In the final example, the insertion loss of an isolator system is improved at a particular frequency by adding mass to one side of the isolator.
Comparison Between Healthy and Reduced Hand Function Using Ranges of Motion and a Weighted Fingertip Space Model
Authors: Leitkam Samuel T. , Reid Bush Tamara
Published: November 2014

Detection and quantification of changes in hand function are important for patients with loss of function and clinicians who are treating them. A recently developed model, the weighted fingertip space (WFS) quantifies the hand function of individuals in three-dimensional space and applies kinematic weighting parameters to identify regions of reachable space with high and low hand function. The goal of this research was to use the WFS model to compare and contrast the functional abilities of healthy individuals with the abilities of individuals with reduced functionality due to arthritis (RFA). Twenty two individuals with no reported issues with hand function and 21 individuals with arthritis affecting the hand were included in the research. Functional models were calculated from the ranges of motion and hand dimension data for each individual. Each model showed the volume of reachable space for each fingertip of each hand, the number of ways to reach a point in space, the range of fingertip orientations possible at each point, and the range of possible force application directions (FADs) at each point. In addition, two group models were developed that showed how many individuals in both the healthy and RFA groups were able to reach the same points in space. The results showed differences between the two groups for the range of motion (ROM) measurements, the individual model calculations, and the group models. The ROM measurements showed significant differences for the joints of the thumb, extension of the nonthumb metacarpophalangeal (MCP) joints, and flexion of the distal interphalangeal (DIP) joints. Comparing the models, the two groups qualitatively showed similar patterns of functional measures in space, but with the RFA group able to reach a smaller volume of space. Quantitatively, the RFA group showed trends of smaller values for all of the calculated functional weighting parameters and significantly smaller reachable volume for all of the fingers. The group models showed that all healthy individuals were able to reach an overlapping space, while 18 of 21 RFA individuals were able to reach similar spaces. Combined, the results showed that the WFS model presents the abilities of the hand in ways that can be quantitatively and qualitatively compared. Thus, the potential of this hand model is that it could be used to assess and document the changes that occur in hand function due to rehabilitation or surgery, or as a guide to determine areas most accessible by various populations.
Formal Language for GeoSpelling
Authors: Ballu Alex , Mathieu Luc , Dantan Jean-Yves
Published: November 2014

In order to tackle the ambiguities of geometrical product specification (GPS), GeoSpelling language has been developed to express the semantics of specifications. A detailed syntax of GeoSpelling is proposed in this paper. A specification is defined as a sequence of operations on the skin model. The syntax is based on instructions used in computer programming language: call to functions and flow control by condition and loop. In GeoSpelling, the call to functions corresponds to the declaration of operations; loops make it possible to manage a set of features with rigor and conditions to select features from a set.
Real-Time Visualization of Finite Element Models Using Surrogate Modeling Methods
Authors: Heap Ryan C. , Hepworth Ammon I. , Greg Jensen C.
Published: November 2014

Parametric finite element analysis (FEA) models are commonly used in iterative design processes to obtain an optimum model given a set of loads, constraints, objectives, and design parameters to vary. In some instances, it is desirable for a designer to obtain some intuition about how changes in design parameters can affect the FEA solution of interest, before simply sending the model through the optimization loop. For example, designers who wish to explore the design space and understand how each variable changes the output in a visual way, looking at the whole model and not just numbers or a response surface of a single FEA node. This could be accomplished by running the FEA on the parametric model for a set of part family members, but this can be very time consuming and only gives snapshots of the model's real behavior. This paper presents a method of visualizing the FEA solution of the parametric model as design parameters are changed in real-time by approximating the FEA solution using parametric FEA modeling, surrogate modeling methods, and visualization methods. The implementation develops a parametric FEA mode that includes mesh morphing algorithms that allow the mesh to change parametrically along with the model geometry. This allows the surrogate models assigned to each individual node to use the nodal solution of multiple finite element analyses as regression points to approximate the FEA solution. The surrogate models can then be mapped to their respective geometric locations in real-time. The results of the FEA calculations are updated in real-time as the parameters of the design model change allowing real-time visualization.
A New Method for Making Design Decisions: Decision Topologies
Authors: Pandey Vijitashwa , Mourelatos Zissimos P.
Published: November 2014

This paper shows how reliability block diagrams can be used as a decision making tool. The premise behind the idea is that classical decision analysis (DA), while very powerful, does not provide much tractability in assessing utility functions and their use in making decisions. Our recent work has shown that a reliability block diagram which is a visual representation of systems, can be used to describe a decision situation. In decision making, we called these block diagrams decision topologies (DTs). We show that DTs can be used to make engineering decisions just as DA. The paper also proves that in the limit, using DTs is entirely consistent with DA for both single attribute and multi-attribute cases. The main advantages of the proposed method are that (1) it provides a visual representation of a decision situation, and (2) accommodates continuous and binary attributes together, as well as the tradeoff between them. The paper details the theoretical basis of the proposed method and highlights its benefits. An example is used to demonstrate how DTs can be used in practice.
Trust Region Based Mode Pursuing Sampling Method for Global Optimization of High Dimensional Design Problems
Authors: Cheng George H. , Younis Adel , Haji Hajikolaei Kambiz , Gary Wang G.
Published: November 2014

Mode pursuing sampling (MPS) was developed as a global optimization algorithm for design optimization problems involving expensive black box functions. MPS has been found to be effective and efficient for design problems of low dimensionality, i.e., the number of design variables is less than 10. This work integrates the concept of trust regions into the MPS framework to create a new algorithm, trust region based mode pursuing sampling (TRMPS2), with the aim of dramatically improving performance and efficiency for high dimensional problems. TRMPS2 is benchmarked against genetic algorithm (GA), dividing rectangles (DIRECT), efficient global optimization (EGO), and MPS using a suite of standard test problems and an engineering design problem. The results show that TRMPS2 performs better on average than GA, DIRECT, EGO, and MPS for high dimensional, expensive, and black box (HEB) problems.
Stochastic Multidisciplinary Analysis Under Epistemic Uncertainty
Authors: Liang Chen , Mahadevan Sankaran , Sankararaman Shankar
Published: November 2014

This paper presents a probabilistic framework to include the effects of both aleatory and epistemic uncertainty sources in coupled multidisciplinary analysis (MDA). A likelihood-based decoupling approach has been previously developed for probabilistic analysis of multidisciplinary systems, but only with aleatory uncertainty in the inputs. This paper extends this approach to incorporate the effects of epistemic uncertainty arising from data uncertainty and model errors. Data uncertainty regarding input variables (due to sparse and interval data) is included through parametric or nonparametric distributions using the principle of likelihood. Model error is included in MDA through an auxiliary variable approach based on the probability integral transform. In the presence of natural variability, data uncertainty, and model uncertainty, the proposed methodology is employed to estimate the probability density functions (PDFs) of coupling variables as well as the subsystem and system level outputs that satisfy interdisciplinary compatibility. Global sensitivity analysis (GSA), which has previously considered only aleatory inputs and feedforward or monolithic problems, is extended in this paper to quantify the contribution of model uncertainty in feedback-coupled MDA by exploiting the auxiliary variable approach. The proposed methodology is demonstrated using a mathematical MDA problem and an electronic packaging application example featuring coupled thermal and electrical subsystem analyses. The results indicate that the proposed methodology can effectively quantify the uncertainty in MDA while maintaining computational efficiency.
An Integrated Performance Measure Approach for System Reliability Analysis
Authors: Wang Zequn , Wang Pingfeng
Published: November 2014

This paper presents a new adaptive sampling approach based on a novel integrated performance measure approach, referred to as “iPMA,” for system reliability assessment with multiple dependent failure events. The developed approach employs Gaussian process (GP) regression to construct surrogate models for each component failure event, thereby enables system reliability estimations directly using Monte Carlo simulation (MCS) based on surrogate models. To adaptively improve the accuracy of the surrogate models for approximating system reliability, an iPM, which envelopes all component level failure events, is developed to identify the most useful sample points iteratively. The developed iPM possesses three important properties. First, it represents exact system level joint failure events. Second, the iPM is mathematically a smooth function “almost everywhere.” Third, weights used to reflect the importance of multiple component failure modes can be adaptively learned in the iPM. With the weights updating process, priorities can be adaptively placed on critical failure events during the updating process of surrogate models. Based on the developed iPM with these three properties, the maximum confidence enhancement (MCE) based sequential sampling rule can be adopted to identify the most useful sample points and improve the accuracy of surrogate models iteratively for system reliability approximation. Two case studies are used to demonstrate the effectiveness of system reliability assessment using the developed iPMA methodology.
Sub-20 nm silicon patterning and metal lift-off using thermal scanning probe lithography
Authors: Wolf Heiko , Rawlings Colin , Mensch Philipp , Hedrick James L. , Coady Daniel J. , Duerig Urs , Knoll Armin W.
Published: November 2014

The most direct definition of a patterning process' resolution is the smallest half-pitch feature that is capable of transferring onto the substrate. Here, the authors demonstrate that thermal scanning probe lithography (t-SPL) is capable of fabricating dense line patterns in silicon and metal lift-off features at sub-20 nm feature size. The dense silicon lines were written at a half pitch of 18.3 nm to a depth of 5 nm into a 9 nm polyphthalaldehyde thermal imaging layer by t-SPL. For processing, the authors used a three-layer stack comprising an evaporated SiO2 hardmask, which is just 2–3 nm thick. The hardmask is used to amplify the pattern into a 50 nm thick polymeric transfer layer. The transfer layer subsequently serves as an etch mask for transfer into silicon to a depth of ≈65 nm. The line edge roughness (3σ) was evaluated to be less than 3 nm both in the transfer layer and in silicon. The authors also demonstrate that a similar three-layer stack can be used for metal lift-off of high resolution patterns. A device application is demonstrated by fabricating 50 nm half pitch dense nickel contacts to an InAs nanowire.
Optimized MEMS Pirani sensor with increased pressure measurement sensitivity in the fine and rough vacuum regimes
Authors: Grau Mario , Völklein Friedemann , Meier Andreas , Kunz Christina , Kaufmann Ilia , Woias Peter
Published: November 2014

A new microelectromechanical systems (MEMS) Pirani sensor with a working range from 10−3 to 7.6 × 102 Torr and an increased sensitivity in the rough vacuum regime is presented. The sensor design, fabrication technologies, and voltage–pressure responses of the measurements and analytical simulations are described and shown. A future perspective is given, which describes the combination of this sensor with the high vacuum sensor of our previous work to form a MEMS Pirani gauge for the high, fine, and rough vacuum ranges.
Determination of the intrinsic energy dependence of LiF:Mg,Ti thermoluminescent dosimeters for 125I and 103Pd brachytherapy sources relative to 60Co
Authors: Reed J. L. , Rasmussen B. E. , Davis S. D. , Micka J. A. , Culberson W. S. , DeWerd L. A.
Published: November 2014

Purpose:

To determine the intrinsic energy dependence of LiF:Mg,Ti thermoluminescent dosimeters (TLD‐100) for 125I and 103Pd brachytherapy sources relative to 60Co.

Methods:

LiF:Mg,Ti TLDs were irradiated with low‐energy brachytherapy sources and with a 60Co teletherapy source. The brachytherapy sources measured were the Best 2301 125I seed, the OncoSeed 6711 125I seed, and the Best 2335 103Pd seed. The TLD light output per measured air‐kerma strength was determined for the brachytherapy source irradiations, and the TLD light output per air kerma was determined for the 60Co irradiations. Monte Carlo (MC) simulations were used to calculate the dose‐to‐TLD rate per air‐kerma strength for the brachytherapy source irradiations and the dose to TLD per air kerma for the 60Co irradiations. The measured and MC‐calculated results for all irradiations were used to determine the TLD intrinsic energy dependence for 125I and 103Pd relative to 60Co.

Results:

The relative TLD intrinsic energy dependences (relative to 60Co) and associated uncertainties (k = 1) were determined to be 0.883 ± 1.3%, 0.870 ± 1.4%, and 0.871 ± 1.5% for the Best 2301 seed, OncoSeed 6711 seed, and Best 2335 seed, respectively.

Conclusions:

The intrinsic energy dependence of TLD‐100 is dependent on photon energy, exhibiting changes of 13%–15% for 125I and 103Pd sources relative to 60Co. TLD measurements of absolute dose around 125I and 103Pd brachytherapy sources should explicitly account for the relative TLD intrinsic energy dependence in order to improve dosimetric accuracy.
Phage-Encoded Colanic Acid-Degrading Enzyme Permits Lytic Phage Infection of a Capsule-Forming Resistant Mutant Escherichia coli Strain
Authors: Kim Min Soo , Kim Young Deuk , Hong Sung Sik , Park Kwangseo , Ko Kwan Soo , Myung Heejoon
Published: November 2014

In this study, we isolated a bacteriophage T7-resistant mutant strain of
Escherichia coli
(named S3) and then proceeded to characterize it. The mutant bacterial colonies appeared to be mucoid. Microarray analysis revealed that genes related to colanic acid production were upregulated in the mutant. Increases in colanic acid production by the mutant bacteria were observed when
l
-fucose was measured biochemically, and protective capsule formation was observed under an electron microscope. We found a point mutation in the
lon
gene promoter in S3, the mutant bacterium. Overproduction of colanic acid was observed in some phage-resistant mutant bacteria after infection with other bacteriophages, T4 and lambda. Colanic acid overproduction was also observed in clinical isolates of
E. coli
upon phage infection. The overproduction of colanic acid resulted in the inhibition of bacteriophage adsorption to the host. Biofilm formation initially decreased shortly after infection but eventually increased after 48 h of incubation due to the emergence of the mutant bacteria. Bacteriophage PBECO4 was shown to infect the colanic acid-overproducing mutant strains of
E. coli
. We confirmed that the gene product of open reading frame 547 (ORF547) of PBECO4 harbored colanic acid-degrading enzymatic (CAE) activity. Treatment of the T7-resistant bacteria with both T7 and PBECO4 or its purified enzyme (CAE) led to successful T7 infection. Biofilm formation decreased with the mixed infection, too. This procedure, using a phage cocktail different from those exploiting solely receptor differences, represents a novel strategy for overcoming phage resistance in mutant bacteria.
Adaptation Genomics of a Small-Colony Variant in a Pseudomonas chlororaphis 30-84 Biofilm
Authors: Wang Dongping , Dorosky Robert J. , Han Cliff S. , Lo Chien-chi , Dichosa Armand E. K. , Chain Patrick S. , Yu Jun Myoung , Pierson Leland S. , Pierson Elizabeth A.
Published: November 2014

The rhizosphere-colonizing bacterium
Pseudomonas chlororaphis
30-84 is an effective biological control agent against take-all disease of wheat. In this study, we characterize a small-colony variant (SCV) isolated from a
P. chlororaphis
30-84 biofilm. The SCV exhibited pleiotropic phenotypes, including small cell size, slow growth and motility, low levels of phenazine production, and increased biofilm formation and resistance to antimicrobials. To better understand the genetic alterations underlying these phenotypes, RNA and whole-genome sequencing analyses were conducted comparing an SCV to the wild-type strain. Of the genome's 5,971 genes, transcriptomic profiling indicated that 1,098 (18.4%) have undergone substantial reprograming of gene expression in the SCV. Whole-genome sequence analysis revealed multiple alterations in the SCV, including mutations in
yfiR
(cyclic-di-GMP production),
fusA
(elongation factor), and
cyoE
(heme synthesis) and a 70-kb deletion. Genetic analysis revealed that the
yfiR
locus plays a major role in controlling SCV phenotypes, including colony size, growth, motility, and biofilm formation. Moreover, a point mutation in the
fusA
gene contributed to kanamycin resistance. Interestingly, the SCV can partially switch back to wild-type morphologies under specific conditions. Our data also support the idea that phenotypic switching in
P. chlororaphis
is not due to simple genetic reversions but may involve multiple secondary mutations. The emergence of these highly adherent and antibiotic-resistant SCVs within the biofilm might play key roles in
P. chlororaphis
natural persistence.
Alternative Fecal Indicators and Their Empirical Relationships with Enteric Viruses, Salmonella enterica, and Pseudomonas aeruginosa in Surface Waters of a Tropical Urban Catchment
Authors: Liang L. , Goh S. G. , Vergara G. G. R. V. , Fang H. M. , Rezaeinejad S. , Chang S. Y. , Bayen S. , Lee W. A. , Sobsey M. D. , Rose J. B. , Gin K. Y. H.
Published: November 2014

The suitability of traditional microbial indicators (i.e.,
Escherichia coli
and enterococci) has been challenged due to the lack of correlation with pathogens and evidence of possible regrowth in the natural environment. In this study, the relationships between alternative microbial indicators of potential human fecal contamination (
Bacteroides thetaiotaomicron
,
Methanobrevibacter smithii
, human polyomaviruses [HPyVs], and F+ and somatic coliphages) and pathogens (
Salmonella
spp.,
Pseudomonas aeruginosa
, rotavirus, astrovirus, norovirus GI, norovirus GII, and adenovirus) were compared with those of traditional microbial indicators, as well as environmental parameters (temperature, conductivity, salinity, pH, dissolved oxygen, total organic carbon, total suspended solids, turbidity, total nitrogen, and total phosphorus). Water samples were collected from surface waters of urban catchments in Singapore.
Salmonella
and
P. aeruginosa
had significant positive correlations with most of the microbial indicators, especially
E. coli
and enterococci. Norovirus GII showed moderately strong positive correlations with most of the microbial indicators, except for HPyVs and coliphages. In general, high geometric means and significant correlations between human-specific markers and pathogens suggest the possibility of sewage contamination in some areas. The simultaneous detection of human-specific markers (i.e.,
B. thetaiotaomicron
,
M. smithii
, and HPyVs) with
E. coli
and enterococcus supports the likelihood of recent fecal contamination, since the human-specific markers are unable to regrow in natural surface waters. Multiple-linear-regression results further confirm that the inclusion of
M. smithii
and HPyVs, together with traditional indicators, would better predict the occurrence of pathogens. Further study is needed to determine the applicability of such models to different geographical locations and environmental conditions.
Rapid Redox Signal Transmission by “Cable Bacteria” beneath a Photosynthetic Biofilm
Authors: Malkin S. Y. , Meysman F. J. R.
Published: November 2014

Recently, long filamentous bacteria, belonging to the family
Desulfobulbaceae
, were shown to induce electrical currents over long distances in the surface layer of marine sediments. These “cable bacteria” are capable of harvesting electrons from free sulfide in deeper sediment horizons and transferring these electrons along their longitudinal axes to oxygen present near the sediment-water interface. In the present work, we investigated the relationship between cable bacteria and a photosynthetic algal biofilm. In a first experiment, we investigated sediment that hosted both cable bacteria and a photosynthetic biofilm and tested the effect of an imposed diel light-dark cycle by continuously monitoring sulfide at depth. Changes in photosynthesis at the sediment surface had an immediate and repeatable effect on sulfide concentrations at depth, indicating that cable bacteria can rapidly transmit a geochemical effect to centimeters of depth in response to changing conditions at the sediment surface. We also observed a secondary response of the free sulfide at depth manifest on the time scale of hours, suggesting that cable bacteria adjust to a moving oxygen front with a regulatory or a behavioral response, such as motility. Finally, we show that on the time scale of days, the presence of an oxygenic biofilm results in a deeper and more acidic suboxic zone, indicating that a greater oxygen supply can enable cable bacteria to harvest a greater quantity of electrons from marine sediments. Rapid acclimation strategies and highly efficient electron harvesting are likely key advantages of cable bacteria, enabling their success in high sulfide generating coastal sediments.
Temporal and Vertical Distributions of Bacterioplankton at the Gray's Reef National Marine Sanctuary
Authors: Lu Xinxin , Sun Shulei , Zhang Yu-Qin , Hollibaugh James T. , Mou Xiaozhen
Published: November 2014

Large spatial scales and long-term shifts of bacterial community composition (BCC) in the open ocean can often be reliably predicted based on the dynamics of physical-chemical variables. The power of abiotic factors in shaping BCC on shorter time scales in shallow estuarine mixing zones is less clear. We examined the diurnal variation in BCC at different water depths in the spring and fall of 2011 at a station in the Gray's Reef National Marine Sanctuary (GRNMS). This site is located in the transition zone between the estuarine plume and continental shelf waters of the South Atlantic Bight. A total of 234,516 pyrotag sequences of bacterial 16S rRNA genes were recovered; they were taxonomically affiliated with >200 families of 23 bacterial phyla. Nonmetric multidimensional scaling analysis revealed significant differences in BCC between spring and fall samples, likely due to seasonality in the concentrations of dissolved organic carbon and nitrate plus nitrite. Within each diurnal sampling, BCC differed significantly by depth only in the spring and differed significantly between day and night only in the fall. The former variation largely tracked changes in light availability, while the latter was most correlated with concentrations of polyamines and chlorophyll
a
. Our results suggest that at the GRNMS, a coastal mixing zone, diurnal variation in BCC is attributable to the mixing of local and imported bacterioplankton rather than to bacterial growth in response to environmental changes. Our results also indicate that, like members of the
Roseobacter
clade, SAR11 bacteria may play an important role in processing dissolved organic material in coastal oceans.
Population Genetic Analysis of Streptomyces albidoflavus Reveals Habitat Barriers to Homologous Recombination in the Diversification of Streptomycetes
Authors: Cheng Kun , Rong Xiaoying , Pinto-Tomás Adrián A. , Fernández-Villalobos Marcela , Murillo-Cruz Catalina , Huang Ying
Published: November 2014

Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of
Streptomyces albidoflavus
derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in
S. albidoflavus
, supported by multiple lines of evidence from the pairwise homoplasy index (Φ

w

) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within
Streptomyces
species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for
S. albidoflavus
, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes.
Novel Variant Serotype of Streptococcus suis Isolated from Piglets with Meningitis
Authors: Pan Zihao , Ma Jiale , Dong Wenyang , Song Wenchao , Wang Kaicheng , Lu Chengping , Yao Huochun
Published: November 2014

Streptococcus suisis an emerging zoonotic pathogen causing severe infections in pigs and humans. In previous studies, 33 serotypes ofS. suishave been identified using serum agglutination. Here, we describe a novelS. suisstrain, CZ130302, isolated from an outbreak of acute piglet meningitis in eastern China. Strong pathogenicity of meningitis caused by strain CZ130302 was reproduced in the BALB/c mouse model. The strain showed a high fatality rate (8/10), higher than those for known virulent serotype 2 strains P1/7 (1/10) and 9801 (2/10). Cell adhesion assay results with bEnd.3 and HEp2 cells showed that CZ130302 was significantly close to P1/7 and 9801. Both the agglutination test and its complementary test showed that strain CZ130302 had no strong cross-reaction with the other 33S. suisserotypes. The multiplex PCR assays revealed no specified bands for all four sets used to detect the other 33 serotypes. In addition, genetic analysis of the wholecpsgene clusters of all serotypes was performed in this study. The results of comparative genomics showed that thecpsgene cluster of CZ130302, which was not previously reported, showed no homology to the gene sequences of the other strains. Especially, thewzy,wzx, and acetyltransferase genes of strain CZ130302 are phylogenetically distinct from strains of the other 33 serotypes. Therefore, this study suggested that strain CZ130302 represents a novel variant serotype ofS. suis(designated serotype Chz) which has a high potential to be virulent and associated with meningitis in animals.
De Novo
Amino Acid Biosynthesis Contributes to Salmonella enterica Growth in Alfalfa Seedling Exudates
Authors: Kwan Grace , Pisithkul Tippapha , Amador-Noguez Daniel , Barak Jeri
Published: November 2014

Salmonella enterica
is a member of the plant microbiome. Growth of
S. enterica
in sprouting-seed exudates is rapid; however, the active metabolic networks essential in this environment are unknown. To examine the metabolic requirements of
S. enterica
during growth in sprouting-seed exudates, we inoculated alfalfa seeds and identified 305
S. enterica
proteins extracted 24 h postinoculation from planktonic cells. Over half the proteins had known metabolic functions, and they are involved in over one-quarter of the known metabolic reactions. Ion and metabolite transport accounted for the majority of detected reactions. Proteins involved in amino acid transport and metabolism were highly represented, suggesting that amino acid metabolic networks may be important for
S. enterica
growth in association with roots. Amino acid auxotroph growth phenotypes agreed with the proteomic data; auxotrophs in amino acid-biosynthetic pathways that were detected in our screen developed growth defects by 48 h. When the perceived sufficiency of each amino acid was expressed as a ratio of the calculated biomass requirement to the available concentration and compared to growth of each amino acid auxotroph, a correlation between nutrient availability and bacterial growth was found. Furthermore, glutamate transport acted as a fitness factor during
S. enterica
growth in association with roots. Collectively, these data suggest that
S. enterica
metabolism is robust in the germinating-alfalfa environment; that single-amino-acid metabolic pathways are important but not essential; and that targeting central metabolic networks, rather than dedicated pathways, may be necessary to achieve dramatic impacts on bacterial growth.
Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle
Authors: Seedorf Henning , Kittelmann Sandra , Janssen Peter H.
Published: November 2014

Sequencing and analyses of 16S rRNA gene amplicons were performed to estimate the composition of the rumen methanogen community in 252 samples from eight cohorts of sheep and cattle, separated into 16 different sample groups by diet, and to determine which methanogens are most prominent in the rumens of farmed New Zealand ruminants.
Methanobacteriales
(relative abundance ± standard deviation, 89.6% ± 9.8%) and
Methanomassiliicoccales
(10.4% ± 9.8%) were the two major orders and contributed 99.98% (±0.1%) to the rumen methanogen communities in the samples. Sequences from
Methanobacteriales
were almost entirely from only four different species (or clades of very closely related species). Each was detectable in at least 89% of the samples. These four species or clades were the
Methanobrevibacter gottschalkii
clade and
Methanobrevibacter ruminantium
clade with a mean abundance of 42.4% (±19.5% standard deviation) and 32.9% (±18.8%), respectively, and
Methanosphaera
sp. ISO3-F5 (8.2% ± 6.7%) and
Methanosphaera
sp. group5 (5.6% ± 5.7%). These four species or clades appeared to be primarily represented by only one or, in one case, two dominant sequence types per species or clade when the sequences were grouped into operational taxonomic units (OTUs) at 99% sequence identity. The mean relative abundance of
Methanomassiliicoccales
in the samples was relatively low but exceeded 40% in some of the treatment groups. Animal feed affected the apparent methanogen community structure of both orders, as evident from differences in relative abundances of the major OTUs in animals under different feeding regimens.
A Regulatory Feedback Loop between RpoS and SpoT Supports the Survival of Legionella pneumophila in Water
Authors: Trigui Hana , Dudyk Paulina , Oh Jinrok , Hong Jong-In , Faucher Sebastien P.
Published: November 2014

Legionella pneumophila
is a waterborne pathogen, and survival in the aquatic environment is central to its transmission to humans. Therefore, identifying genes required for its survival in water could help prevent Legionnaires' disease outbreaks. In the present study, we investigate the role of the sigma factor RpoS in promoting survival in water, where
L. pneumophila
experiences severe nutrient deprivation. The
rpoS
mutant showed a strong survival defect compared to the wild-type strain in defined water medium. The transcriptome of the
rpoS
mutant during exposure to water revealed that RpoS represses genes associated with replication, translation, and transcription, suggesting that the mutant fails to shut down major metabolic programs. In addition, the
rpoS
mutant is transcriptionally more active than the wild-type strain after water exposure. This could be explained by a misregulation of the stringent response in the
rpoS
mutant. Indeed, the
rpoS
mutant shows an increased expression of
spoT
and a corresponding decrease in the level of (p)ppGpp, which is due to the presence of a negative feedback loop between RpoS and SpoT. Therefore, the lack of RpoS causes an aberrant regulation of the stringent response, which prevents the induction of a successful response to starvation.
Lipopolysaccharide O-Chain Core Region Required for Cellular Cohesion and Compaction of
In Vitro
and Root Biofilms Developed by Rhizobium leguminosarum
Authors: Russo Daniela M. , Abdian Patricia L. , Posadas Diana M. , Williams Alan , Vozza Nicolás , Giordano Walter , Kannenberg Elmar , Downie J. Allan , Zorreguieta Angeles
Published: November 2014

The formation of biofilms is an important survival strategy allowing rhizobia to live on soil particles and plant roots. Within the microcolonies of the biofilm developed by
Rhizobium leguminosarum
, rhizobial cells interact tightly through lateral and polar connections, forming organized and compact cell aggregates. These microcolonies are embedded in a biofilm matrix, whose main component is the acidic exopolysaccharide (EPS). Our work shows that the O-chain core region of the
R. leguminosarum
lipopolysaccharide (LPS) (which stretches out of the cell surface) strongly influences bacterial adhesive properties and cell-cell cohesion. Mutants defective in the O chain or O-chain core moiety developed premature microcolonies in which lateral bacterial contacts were greatly reduced. Furthermore, cell-cell interactions within the microcolonies of the LPS mutants were mediated mostly through their poles, resulting in a biofilm with an altered three-dimensional structure and increased thickness. In addition, on the root epidermis and on root hairs, O-antigen core-defective strains showed altered biofilm patterns with the typical microcolony compaction impaired. Taken together, these results indicate that the surface-exposed moiety of the LPS is crucial for proper cell-to-cell interactions and for the formation of robust biofilms on different surfaces.
MS2 Virus Inactivation by Atmospheric-Pressure Cold Plasma Using Different Gas Carriers and Power Levels
Authors: Wu Yan , Liang Yongdong , Wei Kai , Li Wei , Yao Maosheng , Zhang Jue , Grinshpun Sergey A.
Published: November 2014

In this study, airborne MS2 bacteriophages were exposed for subsecond time intervals to atmospheric-pressure cold plasma (APCP) produced using different power levels (20, 24, and 28 W) and gas carriers (ambient air, Ar-O
2
[2%, vol/vol], and He-O
2
[2%, vol/vol]). In addition, waterborne MS2 viruses were directly subjected to the APCP treatment for up to 3 min. MS2 viruses with and without the APCP exposure were examined by scanning electron microscopy (SEM), reverse transcription-PCR (RT-PCR), and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Viral inactivation was shown to exhibit linear relationships with the APCP generation power and exposure time (
R
2
> 0.95 for all energy levels tested) up to 95% inactivation (1.3-log reduction) after a subsecond airborne exposure at 28 W; about the same inactivation level was achieved for waterborne viruses with an exposure time of less than 1 min. A larger amount of reactive oxygen species (ROS), such as atomic oxygen, in APCP was detected for a higher generation power with Ar-O
2
and He-O
2
gas carriers. SEM images, SDS-PAGE, and agarose gel analysis of exposed waterborne viruses showed various levels of damage to both surface proteins and their related RNA genes after the APCP exposure, thus leading to the loss of their viability and infectivity.