bluuebunny/crossref_metadata_2025 huggingface dataset:
Cadmium‐induced cell death in BY‐2 cell culture starts with vacuolization of cytoplasm and terminates with necrosis
Authors: Kutik Jaromir , Kuthanova Andrea , Smertenko Andrei , Fischer Lukas , Opatrny Zdenek
Published: November 2013

Cadmium is a potent inducer of programmed cell death (PCD) in plants but the morphological changes in cells exposed to cadmium are poorly characterized. Using light and transmission electron microscopy (TEM) we have investigated the changes in ultrastructure of tobacco BY‐2 cells treated with 50 µM CdSO4. The cadmium‐induced alterations in cell morphology occurred gradually over a period of 3–4 days and the first stages of the response resembled vacuolar type of cell death. The initial formation of numerous small cytoplasmic vacuoles and dilation of endoplasmic reticulum was followed first by fusion of smaller vacuoles with each other and with big vacuoles, and then by the appearance of autophagic vacuoles containing autophagic bodies. The final stages of cell death were accompanied by necrotic features including loss of plasmalemma integrity, shrinkage of the protoplast and unprocessed cellular components. In addition, we observed a gradual degradation of nuclear material. Our results demonstrate that cadmium‐induced plant cell death is a slow process featuring elements of vacuolar cell death and terminating with necrosis.
Extracellular calcium chelation and attenuation of calcium entry decrease in vivo cholinergic‐induced eccrine sweating sensitivity in humans
Authors: Metzler‐Wilson Kristen , Sammons Dawn L. , Ossim Megan A. , Metzger Natalie R. , Jurovcik Andrew J. , Krause B. Andrew , Wilson Thad E.
Published: November 2013

New Findings

What is the central question of this study?

Calcium is an important second messenger in eccrine sweating; however, whether modulation of extracellular Ca2+ and Ca2+ entry has the capacity to modulate sweat rate in non‐glabrous human skin has not been explored.

What is the main finding and its importance?

Acetylcholine to sweat rate dose–response relationships identify that local in vivo Ca2+ chelation and L‐type Ca2+ channel antagonism have the capacity to attenuate the cholinergic sensitivity of eccrine sweat glands. Importantly, these data translate previous glabrous in vitro animal studies into non‐glabrous in vivo human skin.

Calcium is an important second messenger in eccrine sweating, with both internal and external sources being identified in vitro. It is unclear whether in vivo modulation of extracellular Ca2+ levels or influx has the capacity to modulate sweat rate in non‐glabrous human skin. To test the hypothesis that lowering interstitial Ca2+ levels would decrease the sensitivity of the ACh to sweat rate (via capacitance hygrometry) dose–response relationship, nine healthy subjects received six ACh doses (1 × 10−5 to 1 × 100 m in 10‐fold increments) with and without a Ca2+ chelator (12.5 mg ml−1 EDTA) via forearm intradermal microdialysis (protocol 1). To test the hypothesis that attenuating Ca2+ influx via L‐type Ca2+ channels would also decrease the sensitivity of the ACh to sweat rate dose–response relationship, 10 healthy subjects received similar ACh doses with and without a phenylalkylamine Ca2+ channel blocker (1 mm verapamil; protocol 2). Non‐linear regression curve fitting identified a right‐shifted ED50 in EDTA‐treated sites compared with ACh alone (−1.0 ± 0.1 and −1.5 ± 0.1 logm, respectively; P < 0.05), but unchanged maximal sweat rate (0.60 ± 0.07 and 0.58 ± 0.11 mg cm−2 min−1, respectively; P > 0.05) in protocol 1. Protocol 2 also resulted in a right‐shifted ED50 (verapamil, −0.9 ± 0.1 logm; ACh alone, −1.6 ± 0.2 logm; P < 0.05), with unchanged maximal sweat rate (verapamil, 0.45 ± 0.08 mg cm−2 min−1; ACh alone, 0.35 ± 0.06 mg cm−2 min−1; P > 0.05). Thus, local in vivo Ca2+ chelation and L‐type Ca2+ channel antagonism have the capacity to attenuate in vivo cholinergic sensitivity of eccrine sweat glands. These data suggest that interstitial Ca2+ and its influx via Ca2+ channels play a functional role in eccrine sweating in intact non‐glabrous human skin.
Elastohydrodynamic Lubrication of Inhomogeneous Materials Using the Equivalent Inclusion Method
Authors: Wang Zhanjiang , Zhu Dong , Wang Qian
Published: November 2013

Solid materials forming the boundaries of a lubrication interface may be elastoplastic, heat treated, coated with multilayers, or functionally graded. They may also be composites reinforced by particles or have impurities and defects. Presented in this paper is a model for elastohydrodynamic lubrication interfaces formed with these realistic materials. This model considers the surface deformation and subsurface stresses influenced by material inhomogeneities, where the inhomogeneities are replaced by inclusions with properly determined eigenstrains by means of the equivalent inclusion method. The surface displacement or deformation caused by inhomogeneities is introduced to the film thickness equation. The stresses are the sum of those caused by the fluid pressure and the eigenstrains. The lubrication of a material with a single inhomogeneity, multiple inhomogeneities, and functionally graded coatings are analyzed to reveal the influence of inhomogeneities on film thickness, pressure distribution, and subsurface stresses.
Numerical Methods for Simulating the Reduction of Iron Ore in Blast Furnace Shaft
Authors: Fu Dong , Zhou Chenn Q. , Chen Yan
Published: November 2013

The blast furnace process is a counter-current moving bed chemical reactor to reduce iron oxides to iron, which involves complex transport phenomena and chemical reactions. The iron ore and coke are alternatively charged into the blast furnace, forming a layer by layer structural burden which is slowly descending in the counter-current direction of the ascending gas flow. A new methodology was proposed to efficiently simulate the gas and solid burden flow in the counter-current moving bed in blast furnace shaft. The gas dynamics, burden movement, chemical reactions, heat and mass transfer between the gas phase and solid phase are included. The new methodology has been developed to explicitly consider the effects of the layer thickness thermally and chemically in the CFD model.
Radial Turbine Rotor Response to Pulsating Inlet Flows
Authors: Cao Teng , Xu Liping , Yang Mingyang , Martinez-Botas Ricardo F.
Published: November 2013

The performance of automotive turbocharger turbines has long been realized to be quite different under pulsating flow conditions compared to that under the equivalent steady and quasi-steady conditions on which the conventional design concept is based. However, the mechanisms of this phenomenon are still intensively investigated nowadays. This paper presents an investigation of the response of a stand-alone rotor to inlet pulsating flow conditions by using a validated unsteady Reynolds-averaged Navier–Stokes solver (URANS). The effects of the frequency, the amplitude, and the temporal gradient of pulse waves on the instantaneous and cycle integrated performance of a radial turbine rotor in isolation were studied, decoupled from the upstream turbine volute. A numerical method was used to help gain the physical understanding of these effects. A validation of the numerical method against the experiments on a full configuration of the turbine was performed prior to the numerical tool being used in the investigation. The rotor was then taken out to be studied in isolation. The results show that the turbine rotor alone can be treated as a quasi-steady device only in terms of cycle integrated performance; however, instantaneously, the rotor behaves unsteadily, which increasingly deviates from the quasi-steady performance as the local reduced frequency of the pulsating wave is increased. This deviation is dominated by the effect of quasi-steady time lag; at higher local reduced frequency, the transient effects also become significant. Based on this study, an interpretation and a model of estimating the quasi-steady time lag have been proposed; a criterion for unsteadiness based on the temporal local reduced frequency concept is developed, which reduces to the Λ criterion proposed in the published literature when cycle averaged. This in turn emphasizes the importance of the pressure wave gradient in time.
Development of a Turning Mid Turbine Frame With Embedded Design—Part I: Design and Steady Measurements
Authors: Spataro Rosario , Göttlich Emil , Lengani Davide , Faustmann Christian , Heitmeir Franz
Published: November 2013

The paper presents a new setup for the two-stage two-spool facility located at the Institute for Thermal Turbomachinery and Machine Dynamics (ITTM) of Graz University of Technology. The rig was designed in order to simulate the flow behavior of a transonic turbine followed by a counter-rotating low pressure (LP) stage like the spools of a modern high bypass aeroengine. The meridional flow path of the machine is characterized by a diffusing S-shaped duct between the two rotors. The role of turning struts placed into the mid turbine frame is to lead the flow towards the LP rotor with appropriate swirl. Experimental and numerical investigations performed on the setup over the last years, which were used as baseline for this paper, showed that wide chord vanes induce large wakes and extended secondary flows at the LP rotor inlet flow. Moreover, unsteady interactions between the two turbines were observed downstream of the LP rotor. In order to increase the uniformity and to decrease the unsteady content of the flow at the inlet of the LP rotor, the mid turbine frame was redesigned with two zero-lifting splitters embedded into the strut passage. In this first part of the paper the design process of the splitters and its critical points are presented, while the time-averaged field is discussed by means of five-hole probe measurements and oil flow visualizations. The comparison between the baseline case and the embedded design configuration shows that the new design is able to reduce the flow gradients downstream of the turning struts, providing a more suitable inlet condition for the low pressure rotor. The improvement in the flow field uniformity is also observed downstream of the turbine and it is, consequently, reflected in an enhancement of the LP turbine performance. In the second part of this paper the influence of the embedded design on the time-resolved field is investigated.
Influence of Circumferential Inflow Distortion on the Performance of a Low Speed, High Aspect Ratio Contra Rotating Axial Fan
Authors: Mistry Chetan , Pradeep A. M.
Published: November 2013

The influence of circumferential inflow distorted on the performance and flow behavior of a high aspect ratio, low speed contra rotating fan is reported in this paper. The total pressure at the inlet is artificially distorted by means of 90 deg mesh sector with a porosity of 0.70. The performance of the contra rotating fan was studied under different speed combinations of the two rotors under clean and distorted inflow conditions. Detailed flow analyses were conducted under design and off-design conditions. In order to understand the effect of distortion and its extent, the distortion sector was rotated circumferentially at intervals of 15 deg to cover the entire annulus. Detailed measurements of the total pressure, velocity components, and flow angles were carried out at the inlet of the first rotor, between the two rotors, and at the exit of the second rotor. The study reveals a few interesting aspects on the effect of inflow distortion on the performance of a contra-rotating stage. For the design speed combination and lower rotational speed of rotor-2, a reduction in the overall operating range with a shift of the peak pressure point towards higher mass flow rate, was observed. It is observed that the effect of inflow distortion at the inlet of rotor-1 gets transferred in the direction of rotor-1 rotation and spreads across the entire annulus. The opposite sense of rotation of rotor-2 causes the distortion effect to get transferred in the direction of rotation of rotor-2 with an associated reduction in the total pressure near the hub. It is observed that a higher rotational speed of the second rotor has a beneficial effect on the overall performance due to the strong suction by generated higher rotational speed of rotor-2.
Aerodynamic Interactions Between a High-Pressure Turbine and the First Low-Pressure Stator
Authors: Gougeon Pierre , Ngo Boum Ghislaine
Published: November 2013

The accurate prediction of turbines performance and flow fields requires the assessment of unsteady numerical simulations. This paper presents a numerical study on the interaction between a single-stage high-pressure turbine and the first vane row of a low-pressure turbine. It focuses on the simulation of the flow within the interturbine duct and the loss generated in the downstream low-pressure vane. Former experiments provided steady and unsteady measurements in the interturbine duct and after the low-pressure vane. A 3D unsteady Reynolds-averaged Navier–Stokes (URANS) approach with phase-lagged boundary conditions is used to characterize the unsteady periodic effects in the interturbine channel and downstream in the low-pressure vane. For the numerical study, two different configurations are considered: a single-stage high-pressure turbine configuration and a high-pressure rotor coupled with a low-pressure vane. For the second one, two inlet boundary conditions are implemented upstream of the rotor: a circumferentially uniform boundary condition and a circumferentially nonuniform rotating boundary condition. The resulting flow fields are compared within the intermediate duct. A harmonic Fourier analysis is carried out to underline the effects of the high-pressure rotor. An unsteady Adamczyk decomposition of the flow field within the duct gives the influence of the different components and the levels of unsteadiness. Comparisons with experimental data show a reasonable good agreement.
Using Topology Optimization to Numerically Improve Barriers to Reverse Engineering
Authors: LeBaron Devin D. , Mattson Christopher A.
Published: November 2013

Here explored is a method by which designers can use the tool of topology optimization to numerically improve barriers to reverse engineering. Recently developed metrics, which characterize the time (T) to reverse engineer a product, enable this optimization. A key parameter used in the calculation of T is information content (K). The method presented in this paper pursues traditional topology optimization objectives while simultaneously maximizing K, and thus T, in the resulting topology. New aspects of this paper include algorithms to (1) evaluate K for any topology, (2) increase K for a topology by manipulating macroscale geometry and microscale crystallographic information for each element, and (3) simultaneously maximize K and minimize structural compliance (a traditional topology optimization objective). These algorithms lead designers to desirable topologies with increased barriers to reverse engineering. The authors conclude that barriers to reverse engineering can indeed be increased without sacrificing the desirable structural characteristic of compliance. This has been shown through the example of a novel electrical contact for a consumer electronics product.
Magnetorheologically Damped Compliant Foot for Legged Robotic Application
Authors: Kostamo Esa , Focchi Michele , Guglielmino Emanuele , Kostamo Jari , Semini Claudio , Buchli Jonas , Pietola Matti , Caldwell Darwin
Published: November 2013

This paper presents an innovative solution for bounce reduction between a robotic leg and the ground by means of a semi-active compliant foot. The aim of this work is to enhance the controllability and the balance of a legged robot by improving the traction between the foot tip and the ground. The compliant foot is custom-designed for quadruped walking robots and it consists of a linear spring and a magnetorheological (MR) damper. By utilizing magnetorheological technology in the damper element, the damping coefficient of the compliant foot can be altered across a wide range without any additional moving parts. The content of this paper is twofold. In the first part the design, a prototype and a model of the semi-active compliant foot are presented, and the performance of the magnetorheological damper is experimentally studied in quasi-static and dynamic cases. Based on the quasi-static measurements, the damping force can be controlled in a range from 15 N to 310 N. From the frequency response measurements, it can be shown that the controllable damping force has a bandwidth higher than 100 Hz. The second part of this paper presents an online stiffness identification algorithm and a mathematical model of the robotic leg. A critical damping control law is proposed and implemented in order to demonstrate the effectiveness of the device that makes use of smart materials. Further on, drop tests have been carried out to assess the performance of the proposed control law in terms of bounce reduction and settling time. The results demonstrate that by real-time control of the damping force 98% bounce reduction with settling time of 170 ms can be achieved.
Investigation of Residual Stress Development During Swage Autofrettage, Using Finite Element Analysis
Authors: Gibson Michael C. , Hameed Amer , Hetherington John G.
Published: November 2013

Swaging is one method of autofrettage, a means of prestressing high-pressure vessels to increase their fatigue lives and load bearing capacity. Swaging achieves the required deformation through physical interference between an oversized mandrel and the bore diameter of the tube, as it is pushed through the tube. A finite element model of the swaging process was developed, in ansys, and systematically refined, to investigate the mechanism of deformation and subsequent development of residual stresses. A parametric study was undertaken, of various properties such as mandrel slope angle, parallel section length, and friction coefficient. It is observed that the axial stress plays a crucial role in the determination of the residual hoop stress and reverse yielding. The model, and results obtained from it, provides a means of understanding the swaging process and how it responds to different parameters. This understanding, coupled with future improvements to the model, potentially allows the swaging process to be refined, in terms of residual stresses development and mandrel driving force.
Effects of Contact Force Model and Size Distribution on Microsized Granular Packing
Authors: Dou Xin , Mao Yijin , Zhang Yuwen
Published: November 2013

Granular packing of microsized particles with different size distributions and contact force models is studied using discrete element method (DEM). Three kinds of size distributions, monosized, uniform, and Gaussian, with mean diameter of 50, 60, and 70 μm are studied. Two aspects of microscale particle packing issues are addressed: one is the importance of van der Waals force when the particle size approaching to microscale, the other one is the structure variation caused by different contact force models. The results indicate that compared with contact force, the van der Waals force contributes very insignificantly to the final packing structure. The packing structures obtained using two different force models are similar to each other. The effects of particle size and its distribution on the packing structure are more significant than the force model.
Large Eddy Simulation for Prediction of Entropy Generation in a Nonpremixed Turbulent Jet Flame
Authors: Safari Mehdi , Sheikhi M. Reza H.
Published: November 2013

Local entropy generation in a turbulent nonpremixed jet flame (Sandia Flame D) is predicted using large eddy simulation (LES) with inclusion of entropy transport. The filtered form of entropy transport equation contains several unclosed source terms which represent irreversibilities due to viscous dissipation, heat conduction, mass diffusion, and chemical reaction. The subgrid scale (SGS) closure is accounted for by the entropy filtered density function (En-FDF) methodology to include complete statistical information about SGS variation of scalars and entropy. The En-FDF provides closed forms for the chemical reaction effects. The methodology is applied for LES of Sandia Flame D and predictions are validated against experimental data. Entropy statistics are shown to compare favorably with the data. All individual irreversible processes in this flame are predicted and analyzed. It is shown that heat conduction and chemical reaction are the main sources of entropy generation in this flame.
On the Observability of Loosely Coupled Global Positioning System/Inertial Navigation System Integrations With Five Degree of Freedom and Four Degree of Freedom Inertial Measurement Units
Authors: Ryan Jonathan G. , Bevly David M.
Published: November 2013

This article examines the observability of a modified loosely coupled global positioning system/inertial navigation system (GPS/INS) filter and analyzes the sideslip and attitude estimation capability of the filter. The modified filter is a loosely coupled integration which does not include a pitch rate gyro and which uses GPS course information as a measurement of heading when the vehicle is driving straight. Experimental tests are conducted which show that the modified filter has the same observability characteristics as a standard loosely coupled filter during turning events. The observability of a loosely coupled integration using only a four degree of freedom (DOF) inertial measurement unit (IMU) is also discussed and examined by experiment, as well as the sideslip and roll angle estimation performance. Finally, the error characteristics of the modified loosely coupled integration with the five DOF IMU when the filter is unobservable are studied. Monte Carlo simulations of long periods of straight driving with various sensor qualities are presented to show the worst case attitude errors when the filter is unobservable.
Gas flow through microtubes with different internal surface coatings
Authors: Hadj Nacer M. , Graur I. , Perrier P. , Méolans J. G. , Wuest M.
Published: November 2013

An experimental setup based on the constant volume technique is developed to measure the mass flow rate through microtubes under isothermal stationary flow conditions. Four different working gases (helium, nitrogen, argon, and carbon dioxide), and two surface materials (stainless steel and Sulfinert) are considered. The Knudsen number calculated for the experimental conditions varies from ∼10−4 (hydrodynamic regime) to ∼ 5 (transitional regime). In the reduced range (10−4−0.1) corresponding to the hydrodynamic and slip regimes, an approach based on the analytical solution of the Stokes equation subjected to a first order velocity slip boundary condition is used. The velocity slip coefficient and the tangential momentum accommodation coefficient are extracted from the experimental data of the mass flow rate using their analytical expressions. The results are summarized in the tables representing the accommodation coefficients for the corresponding gas-surface material combinations. The influence of the molecular mass on the tangential momentum accommodation coefficient is discussed. In addition, an original technique is proposed to extract the accommodation coefficient in the whole experimentally available range (10−4−5) of the gas rarefaction. The accommodation coefficients obtained using this technique are close to those found in the slip regime.
Predicting objective function weights from patient anatomy in prostate IMRT treatment planning
Authors: Lee Taewoo , Hammad Muhannad , Chan Timothy C. Y. , Craig Tim , Sharpe Michael B.
Published: November 2013

Purpose:

Intensity‐modulated radiation therapy (IMRT) treatment planning typically combines multiple criteria into a single objective function by taking a weighted sum. The authors propose a statistical model that predicts objective function weights from patient anatomy for prostate IMRT treatment planning. This study provides a proof of concept for geometry‐driven weight determination.

Methods:

A previously developed inverse optimization method (IOM) was used to generate optimal objective function weights for 24 patients using their historical treatment plans (i.e., dose distributions). These IOM weights were around 1% for each of the femoral heads, while bladder and rectum weights varied greatly between patients. A regression model was developed to predict a patientˈs rectum weight using the ratio of the overlap volume of the rectum and bladder with the planning target volume at a 1 cm expansion as the independent variable. The femoral head weights were fixed to 1% each and the bladder weight was calculated as one minus the rectum and femoral head weights. The model was validated using leave‐one‐out cross validation. Objective values and dose distributions generated through inverse planning using the predicted weights were compared to those generated using the original IOM weights, as well as an average of the IOM weights across all patients.

Results:

The IOM weight vectors were on average six times closer to the predicted weight vectors than to the average weight vector, usingl2 distance. Likewise, the bladder and rectum objective values achieved by the predicted weights were more similar to the objective values achieved by the IOM weights. The difference in objective value performance between the predicted and average weights was statistically significant according to a one‐sided sign test. For all patients, the difference in rectum V54.3 Gy, rectum V70.0 Gy, bladder V54.3 Gy, and bladder V70.0 Gy values between the dose distributions generated by the predicted weights and IOM weights was less than 5 percentage points. Similarly, the difference in femoral head V54.3 Gy values between the two dose distributions was less than 5 percentage points for all but one patient.

Conclusions:

This study demonstrates a proof of concept that patient anatomy can be used to predict appropriate objective function weights for treatment planning. In the long term, such geometry‐driven weights may serve as a starting point for iterative treatment plan design or may provide information about the most clinically relevant region of the Pareto surface to explore.
Patient‐specific QA and delivery verification of scanned ion beam at NIRS‐HIMAC
Authors: Furukawa Takuji , Inaniwa Taku , Hara Yousuke , Mizushima Kota , Shirai Toshiyuki , Noda Koji
Published: November 2013

Purpose:

To evaluate a patient‐specific QA program and system for constancy checking of a scanning delivery system developed at the National Institute of Radiological Sciences.

Methods:

For the patient‐specific QA, all the planned beams are recalculated on a water phantom with treatment planning software (TPS). The recalculated dose distributions are compared with the measured distributions using a 2D ionization chamber array at several depths, and evaluated using gamma index analysis with criteria of 3% and 3 mm and a pass rate of 90%. For the constancy check, the authors developed the multiwire proportional chamber (MWPC), which can record the delivered 2D fluence images in a slice‐by‐slice manner. During irradiation for dosimetric QA with the 2D ionization chamber array and an accordion‐type water phantom, the 2D fluence images are recorded using the MWPC in the delivery system. These recorded images are then compared to those taken in the treatment session to check the constancy check. This analysis also employs gamma index analysis using the same criteria as in the patient‐specific QA. These patient‐specific QA and constancy check evaluations were performed using the data of 122 patients.

Results:

In the patient‐specific QA, the measured dose distributions agreed well with those calculated by the TPS, and the QA criteria were satisfied in all measurements. The additional check of the fluence comparison ensured the constancy of the delivered field during each treatment irradiation.

Conclusions:

The authors established a patient‐specific QA program and additional check of delivery constancy in every treatment session. Fluence comparison is a strong tool for constancy checking of the delivery system.
A multimodal corpus of speech to infant and adult listeners
Authors: Johnson Elizabeth K. , Lahey Mybeth , Ernestus Mirjam , Cutler Anne
Published: November 2013

An audio and video corpus of speech addressed to 28 11-month-olds is described. The corpus allows comparisons between adult speech directed toward infants, familiar adults, and unfamiliar adult addressees as well as of caregivers' word teaching strategies across word classes. Summary data show that infant-directed speech differed more from speech to unfamiliar than familiar adults, that word teaching strategies for nominals versus verbs and adjectives differed, that mothers mostly addressed infants with multi-word utterances, and that infants' vocabulary size was unrelated to speech rate, but correlated positively with predominance of continuous caregiver speech (not of isolated words) in the input.
Regular Patterns in Frictional Resistance of Ice-Stream Beds Seen by Surface Data Inversion
Authors: Sergienko Olga V. , Hindmarsh Richard C. A.
Published: November 2013

Banding Together

It is important to understand how and where the Antarctic Ice Sheet and underlying ground are coupled, if we want to predict the glacial contribution to sea level rise.
Sergienko and Hindmarsh
(p.
1086
, published online 7 November) used observations of ice surface velocities, ice surface elevations, and bed elevations to perform inverse calculations of basal shear stress. Areas of high basal stress were distributed in riblike patterns embedded in much larger areas of no basal shear stress, which may affect the rates at which ice is discharged into the ocean.
A Mechanism for Reorientation of Cortical Microtubule Arrays Driven by Microtubule Severing
Authors: Lindeboom Jelmer J. , Nakamura Masayoshi , Hibbel Anneke , Shundyak Kostya , Gutierrez Ryan , Ketelaar Tijs , Emons Anne Mie C. , Mulder Bela M. , Kirik Viktor , Ehrhardt David W.
Published: November 2013

Light Turns the Array

The organization of cortical microtubule arrays in higher plant cells is essential for organizing cell and tissue morphogenesis, but it is not clear how specific architectures are acquired and reconfigured in response to environmental cues.

Lindeboom
et al.

(
10.1126/science.1245533
, published online 7 November; see the Perspective by

Roll-Mecak

) used live-cell imaging and genetic studies to show that the microtubule-severing protein, katanin, plays a crucial role in reorienting cortical arrays from transverse to longitudinal in
Arabidopsis
seedlings in response to blue light perception. Katanin localized to microtubule intersections where, stimulated by blue light receptors, it preferentially catalyzed the severing of the newer microtubule. The microtubule “plus” end created by severing were observed to grow preferentially, effectively building a new population of microtubules orthogonal to the initial array. The net effect of this process steers the growing seedling toward light.
Metaproteomics Analysis Reveals the Adaptation Process for the Chicken Gut Microbiota
Authors: Tang Yue , Underwood Anthony , Gielbert Adriana , Woodward Martin J. , Petrovska Liljana
Published: November 2013

The animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identified
Clostridiales
,
Bacteroidaceae
, and
Lactobacillaceae
species as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged to
Lactobacillus
spp., 155 belonged to
Clostridium
spp., and 66 belonged to
Streptococcus
spp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.
Nanoscale Cell Wall Deformation Impacts Long-Range Bacterial Adhesion Forces on Surfaces
Authors: Chen Yun , Harapanahalli Akshay K. , Busscher Henk J. , Norde Willem , van der Mei Henny C.
Published: November 2013

Adhesion of bacteria occurs on virtually all natural and synthetic surfaces and is crucial for their survival. Once they are adhering, bacteria start growing and form a biofilm, in which they are protected against environmental attacks. Bacterial adhesion to surfaces is mediated by a combination of different short- and long-range forces. Here we present a new atomic force microscopy (AFM)-based method to derive long-range bacterial adhesion forces from the dependence of bacterial adhesion forces on the loading force, as applied during the use of AFM. The long-range adhesion forces of wild-type
Staphylococcus aureus
parent strains (0.5 and 0.8 nN) amounted to only one-third of these forces measured for their more deformable isogenic Δ
pbp4
mutants that were deficient in peptidoglycan cross-linking. The measured long-range Lifshitz-Van der Waals adhesion forces matched those calculated from published Hamaker constants, provided that a 40% ellipsoidal deformation of the bacterial cell wall was assumed for the Δ
pbp4
mutants. Direct imaging of adhering staphylococci using the AFM peak force-quantitative nanomechanical property mapping imaging mode confirmed a height reduction due to deformation in the Δ
pbp4
mutants of 100 to 200 nm. Across naturally occurring bacterial strains, long-range forces do not vary to the extent observed here for the Δ
pbp4
mutants. Importantly, however, extrapolating from the results of this study, it can be concluded that long-range bacterial adhesion forces are determined not only by the composition and structure of the bacterial cell surface but also by a hitherto neglected, small deformation of the bacterial cell wall, facilitating an increase in contact area and, therewith, in adhesion force.
Polysulfides as Intermediates in the Oxidation of Sulfide to Sulfate by Beggiatoa spp
Authors: Berg Jasmine S. , Schwedt Anne , Kreutzmann Anne-Christin , Kuypers Marcel M. M. , Milucka Jana
Published: November 2013

Zero-valent sulfur is a key intermediate in the microbial oxidation of sulfide to sulfate. Many sulfide-oxidizing bacteria produce and store large amounts of sulfur intra- or extracellularly. It is still not understood how the stored sulfur is metabolized, as the most stable form of S
0
under standard biological conditions, orthorhombic α-sulfur, is most likely inaccessible to bacterial enzymes. Here we analyzed the speciation of sulfur in single cells of living sulfide-oxidizing bacteria via Raman spectroscopy. Our results showed that under various ecological and physiological conditions, all three investigated
Beggiatoa
strains stored sulfur as a combination of cyclooctasulfur (S
8
) and inorganic polysulfides (S

n

2−
). Linear sulfur chains were detected during both the oxidation and reduction of stored sulfur, suggesting that S

n

2−
species represent a universal pool of bioavailable sulfur. Formation of polysulfides due to the cleavage of sulfur rings could occur biologically by thiol-containing enzymes or chemically by the strong nucleophile HS
−
as
Beggiatoa
migrates vertically between oxic and sulfidic zones in the environment. Most
Beggiatoa
spp. thus far studied can oxidize sulfur further to sulfate. Our results suggest that the ratio of produced sulfur and sulfate varies depending on the sulfide flux. Almost all of the sulfide was oxidized directly to sulfate under low-sulfide-flux conditions, whereas only 50% was oxidized to sulfate under high-sulfide-flux conditions leading to S
0
deposition. With Raman spectroscopy we could show that sulfate accumulated in
Beggiatoa
filaments, reaching intracellular concentrations of 0.72 to 1.73 M.
Genes Similar to the Vibrio parahaemolyticus Virulence-Related Genes
tdh
,
tlh
, and
vscC2
Occur in Other Vibrionaceae Species Isolated from a Pristine Estuary
Authors: Klein Savannah L. , Gutierrez West Casandra K. , Mejia Diana M. , Lovell Charles R.
Published: November 2013

Detection of the human pathogen
Vibrio parahaemolyticus
often relies on molecular biological analysis of species-specific virulence factor genes. These genes have been employed in determinations of
V. parahaemolyticus
population numbers and the prevalence of pathogenic
V. parahaemolyticus
strains. Strains of the
Vibrionaceae
species
Photobacterium damselae
,
Vibrio diabolicus
,
Vibrio harveyi
, and
Vibrio natriegens
, as well as strains similar to
Vibrio tubiashii
, were isolated from a pristine salt marsh estuary. These strains were examined for the
V. parahaemolyticus
hemolysin genes
tdh
,
trh
, and
tlh
and for the
V. parahaemolyticus
type III secretion system 2α gene
vscC2
using established PCR primers and protocols. Virulence-related genes occurred at high frequencies in non-
V. parahaemolyticus Vibrionaceae
species.
V. diabolicus
was of particular interest, as several strains were recovered, and the large majority (>83%) contained virulence-related genes. It is clear that detection of these genes does not ensure correct identification of virulent
V. parahaemolyticus
. Further, the occurrence of
V. parahaemolyticus
-like virulence factors in other vibrios potentially complicates tracking of outbreaks of
V. parahaemolyticus
infections.
In Silico
Rational Design and Systems Engineering of Disulfide Bridges in the Catalytic Domain of an Alkaline α-Amylase from Alkalimonas amylolytica To Improve Thermostability
Authors: Liu Long , Deng Zhuangmei , Yang Haiquan , Li Jianghua , Shin Hyun-dong , Chen Rachel R. , Du Guocheng , Chen Jian
Published: November 2013

High thermostability is required for alkaline α-amylases to maintain high catalytic activity under the harsh conditions used in textile production. In this study, we attempted to improve the thermostability of an alkaline α-amylase from
Alkalimonas amylolytica
through
in silico
rational design and systems engineering of disulfide bridges in the catalytic domain. Specifically, 7 residue pairs (P35-G426, Q107-G167, G116-Q120, A147-W160, G233-V265, A332-G370, and R436-M480) were chosen as engineering targets for disulfide bridge formation, and the respective residues were replaced with cysteines. Three single disulfide bridge mutants—P35C-G426C, G116C-Q120C, and R436C-M480C—of the 7 showed significantly enhanced thermostability. Combinational mutations were subsequently assessed, and the triple mutant P35C-G426C/G116C-Q120C/R436C-M480C showed a 6-fold increase in half-life at 60°C and a 5.2°C increase in melting temperature compared with the wild-type enzyme. Interestingly, other biochemical properties of this mutant also improved: the optimum temperature increased from 50°C to 55°C, the optimum pH shifted from 9.5 to 10.0, the stable pH range extended from 7.0 to 11.0 to 6.0 to 12.0, and the catalytic efficiency (
k
cat
/

K
m

) increased from 1.8 × 10
4
to 2.4 × 10
4
liters/g · min. The possible mechanism responsible for these improvements was explored through comparative analysis of the model structures of wild-type and mutant enzymes. The disulfide bridge engineering strategy used in this work may be applied to improve the thermostability of other industrial enzymes.
Characterization of Escherichia coli O157:H7 Strains from Contaminated Raw Beef Trim during “High Event Periods”
Authors: Arthur Terrance M. , Bono James L. , Kalchayanand Norasak
Published: November 2013

The development and implementation of effective antimicrobial interventions by the beef processing industry in the United States have dramatically reduced the incidence of beef trim contamination by
Escherichia coli
O157:H7. However, individual processing plants still experience sporadic peaks in contamination rates where multiple
E. coli
O157:H7-positive lots are clustered in a short time frame. These peaks have been referred to as “high event periods” (HEP) of contamination. The results reported here detail the characterization of
E. coli
O157:H7 isolates from 21 HEP across multiple companies and processing plants to gain insight regarding the mechanisms causing these incidents. Strain genotypes were determined by pulsed-field gel electrophoresis, and isolates were investigated for characteristics linking them to human illness. Through these analyses, it was determined that individual HEP show little to no diversity in strain genotypes. Hence, each HEP has one strain type that makes up most, if not all, of the contamination. This is shown to differ from the genotypic diversity of
E. coli
O157:H7 found on the hides of cattle entering processing plants. In addition, it was found that a large proportion (81%) of HEP are caused by strain types associated with human illness. These results pose a potential challenge to the current model for finished product contamination during beef processing.
Genome Sequence of Border Disease Virus Strain JSLS12-01, Isolated from Sheep in China
Authors: Liu Xia , Mao Li , Li Wenliang , Yang Leilei , Zhang Wenwen , Wei Jianzhong , Jiang Jieyuan
Published: November 2013

Border disease virus (BDV) is a recognized virus in the genus
Pestivirus
and causes border disease (BD) in sheep and goats. Here, a novel BDV strain, JSLS12-01, was identified from sheep in Jiangsu Province, China. The complete coding sequence (CDS) was finished, which provides a better understanding of the molecular evolution of BDV isolates.
Draft Genome Sequence of Mycobacterium abscessus subsp.
bolletii
INCQS 00594
Authors: Leão Sylvia Cardoso , Matsumoto Cristianne Kayoko , Viana-Niero Cristina , Ramos Rommel Thiago Jucá , Carneiro Adriana Ribeiro , Barbosa Maria Silvanira , Lima Karla Valéria Batista , Lopes Maria Luiza , Azevedo Vasco , Silva Artur
Published: November 2013

An epidemic of surgical-site infections by a single strain of
Mycobacterium abscessus
subsp.
bolletii
affected >1,700 patients in Brazil from 2004 to 2008. The genome of the epidemic prototype strain
M. abscessus
subsp.
bolletii
INCQS 00594, deposited in the collection of the National Institute for Health Quality Control (INCQS), was sequenced.
Draft Genome Sequence of Beta-Hemolytic Streptococcus iniae KCTC 11634
Authors: Choi Hye Sung , Kwon Mun Gyeong , Kim Myoung Sug , Park Myoung Ae , Kim Dong-Wook , Park Jin-Young , Kim Ji-Sun , Na Yun-Jeong , Kim Min-Young , Kim Dae-Soo , Chae Sung-Hwa , Seo Jung Soo
Published: November 2013

Streptococcus iniae
is a beta-hemolytic, Gram-positive coccus, which affects a broad range of freshwater and marine fish species, causing substantial economic losses in the aquaculture industry worldwide. Thus, it is very important to derive a complete genome sequence of the bacterium to aid in the development of vaccines and methods for preventing fish streptococcosis and zoonotic infections in humans. Here, we present the draft genome sequence of
S. iniae
KCTC 11634 (1,955,615 bp, with a G+C content of 36.6%), which contains 1,868 putative coding sequences.
Draft Genome Sequence of the Clinical Isolate Acinetobacter nosocomialis Strain M2
Authors: Carruthers Michael D. , Harding Christian M. , Baker Beth D. , Bonomo Robert A. , Hujer Kristine M. , Rather Philip N. , Munson Robert S.
Published: November 2013

We report the 3.78-Mbp high-quality draft assembly of the genome from a clinical isolate of
Acinetobacter nosocomialis
called strain M2 (previously known as
Acinetobacter baumannii
strain M2).
Sequence Determination of Burkholderia pseudomallei Strain NCTC 13392 Colony Morphology Variants
Authors: Vipond Julia , Kane Jennifer , Hatch Graham , McCorrison Jamison , Nierman William C. , Losada Liliana
Published: November 2013

Burkholderia pseudomallei
is a biothreat and the causative agent of melioidosis. There are at least seven known colony morphotypes of
B. pseudomallei
that appear to have different virulence properties in animal models. We report the genome sequence of
B. pseudomallei
strain NCTC 13392 and the genomic variations of its eight morphotype derivatives.
Curious case of missing (A) in coeliac disease with type 1 diabetes mellitus
Authors: Joshi Ameya S , Varthakavi Premlata K , Bhagwat Nikhil M , Dalwadi Pradip
Published: November 2013

Coeliac screening in type 1 diabetes mellitus (T1DM) is universally recommended, but not all authorities recommend serum IgA estimation before using an IgA-based test. We report a case of T1DM with poor glycaemic control and recurrent episodes of hypoglycaemias and diabetic ketoacidosis (DKA). Recurrent oromucosal and respiratory infections further complicated the course of illness, resulting in the increasing proneness to DKA. The patient was screened for coeliac disease but the IgA-based screening test was negative (IgA tissue transglutaminase) due to the low IgA level, whereas the IgG antigliadin was positive. The patient benefited from initiation of a gluten-free diet.
Isolated caecal tuberculosis mimicking a neoplastic tumour in an immunocompetent woman
Authors: Cherif Eya , Ben Hassine Lamia , Azzabi Samira , Khalfallah Narjess
Published: November 2013

Although tuberculosis is endemic in Tunisia, only a few cases of intestinal disease have been reported. This entity is usually associated with pulmonary tuberculosis. Any part of the gastrointestinal tract may be affected but usually with ileocaecal involvement. Diagnosis is extremely difficult because the clinical presentation is so variable. The disease frequently mimics other chronic inflammatory intra-abdominal diseases or even malignancy. We report a case of isolated colonic tuberculosis presenting as circumferential ulcerovegetative lesions in the caecal region.