bluuebunny/crossref_metadata_2025 huggingface dataset:
Turbine Stator Well CFD Studies: Effects of Coolant Supply Geometry on Cavity Sealing Performance
Authors: Andreini Antonio , Da Soghe Riccardo , Facchini Bruno
Published: October 2010

The increase of aeroengine performance through the improvement of aerodynamic efficiency of core flow is becoming more and more difficult to achieve. However, there are still some devices that could be improved to enhance global engine efficiency. Particularly, investigations on the internal air cooling systems may lead to a reduction of cooling air with a direct benefit to the overall performance. At the same time, further investigations on heat transfer mechanisms within turbine cavities may help to optimize cooling air flows, saving engine life duration. This paper presents a computational fluid dynamics (CFD) study aimed at the characterization of the effects of different geometries for cooling air supply within turbine cavities on wall thermal effectiveness and sealing mass flow rate. Several sealing air supply geometries were considered in order to point out the role of cooling air injection position, swirl number, and jet penetration on the cavities’ sealing performance. Steady state calculations were performed using two different computational domains: the first consists of a sector model of the whole turbine including the second stator well, while the second is a cut-down model of the stator well. Thanks to the simplified geometry of the test rig with respect to actual engines, the study has pointed out clear design suggestions regarding the effects of geometry modification of cooling air supply systems.
Effects of Upstream Wake Phasing on Transonic Axial Compressor Performance
Authors: Nolan S. P. R. , Botros B. B. , Tan C. S. , Adamczyk J. J. , Greitzer E. M. , Gorrell S. E.
Published: October 2010

The effect on rotor work of the phase of an upstream wake relative to the rotor is examined computationally and analytically for a transonic blade row. There can be an important impact on the time-mean performance when the time-dependent circulation of the shed vortices in the wake is phase-locked to the rotor position, as it occurs when there is strong interaction between the rotor static pressure field and the upstream vanes. The rotor work is found to depend on the path of the wake vortices as they travel through the blade passage; for the configurations examined, the calculated change in time-mean rotor work was approximately 3%. It is shown that the effect on work input can be analyzed in terms of the influence of the time-mean relative stagnation pressure nonuniformity associated with the unsteady (but phase-locked) wake vortex flow field, in that the changes in vortex path alter the location of the nonuniformity relative to the rotor. Lower pressure rise and work input occurs when the rotor blade is embedded in a region of low time-mean relative stagnation pressure than when immersed in a region of high relative stagnation pressure. In addition to the work changes, which are essentially two-dimensional effects, it is demonstrated that the location of the wake may affect the tip clearance flow, implying a potential impact on the pressure rise capability and rotor stability limits. Model calculations are presented to give estimates of the magnitude and nature of this phenomenon.
An Investigation of Turbine Wheelspace Cooling Flow Interactions With a Transonic Hot Gas Path—Part 1: Experimental Measurements
Authors: Bunker R. S. , Laskowski G. M. , Bailey J. C. , Palafox P. , Kapetanovic S. , Itzel G. M. , Sullivan M. A. , Farrell T. R.
Published: October 2010

The desire for higher power output combined with lower fuel consumption has focused recent design and research attention on the interaction of required secondary systems cooling flows with the turbine hot gas path. The flow physics associated with the rotor-stator wheelspaces, and in particular the trench and buffer cavity areas just inboard of the hot gas path, demand an increased level of design sophistication to account for the unsteady fluid and thermal effects associated with periodic vane wakes, circumferential pressure gradients, purge flows, and blade lead edge blockages. Part 1 of this study utilizes a wheelspace sector cascade rig for the purpose of gathering fundamental data on flow and thermal effects in a nonrotating environment. This experimental rig is a simplified screening tool for the investigation of basic geometry and flow effects that maintains the bulk of the correct flow physics in the absence of rotation. The test rig is also a validation data generation device for the unsteady CFD modeling efforts described in Part 2. The present cascade is composed of a five-passage annular sector of a transonic turbine inlet guide vane, a complete sector of the upper wheelspace, buffer and trench cavities, and equivalent flow blockages for a blade row represented as leading edge cylinders. The geometry is three-dimensional including all sealing features of the wheelspace. The vane and blade rows can be clocked to any relative position. Secondary cooling flows are adjustable for the wheelspace purge flow and the leakage flow across the vane support. Detailed measurements in the form of static pressures throughout the interaction region, surface temperature distributions, and buffer cavity air temperatures are presented for various clocked positions. The circumferential pressure distribution peak-to-peak variations just aft of the vane are here as much as 18%. These variations are key to the resulting forcing of hot gas inboard of the rim seal. The blade leading edge bow wave is found to have an equal or even greater influence in generating this peak-to-peak variation than the vane trailing edge wake. Buffer cavity cooling effectiveness levels vary with the clocked positions and decrease as cylinder size is increased. Significantly, the effect of the leading edge blockage can reduce buffer cavity cooling effectiveness by a factor of 0.1.
Multistage Compressor and Turbine Modeling for the Prediction of the Maximum Turbine Speed Resulting From Shaft Breakage
Authors: Haake M. , Fiola R. , Staudacher S.
Published: October 2010

A mathematical model for the prediction of the maximum speed of a high pressure turbine following a shaft failure event was developed. The model predicts the high pressure compressor and ducting system pre- and poststall behaviors such as rotating stall and surge after the shaft breakage. The corresponding time-dependent high pressure turbine inlet conditions are used to calculate the turbine maximum speed, taking into account friction and blade and vane tip clearance variations as a result of the rearward movement of the turbine and destruction of the turbine blading. The compressor and ducting system is modeled by a one-dimensional, stage-by-stage approach. The approach uses a finite-difference numerical technique to solve the nonlinear system of equations for continuity, momentum, and energy including source terms for the compressible flow through inlet ducting, compressor, and combustor. The compressor blade forces and shaft work are provided by a set of quasisteady state stage characteristics being valid for prestall and poststall operations. The maximum turbine speed is calculated from a thermodynamic turbine stand-alone model, derived from a performance synthesis program. Friction and blade and vane tip clearance variations are determined iteratively from graphical data depending on the axial rearward movement of the turbine. The compressor and ducting system model was validated in prestall and poststall operation modes with measured high pressure compressor data of a modern two-shaft engine. The turbine model was validated with measured intermediate pressure shaft failure data of a three-shaft engine. The shaft failure model was applied on a modern two-shaft engine. The model was used to carry out a sensitivity study to demonstrate the impact of control system reactions on the resulting maximum high pressure turbine speed following a shaft failure event.
The Effect of Element Thermal Conductivity on Turbulent Convective Heat Transfer From Rough Surfaces
Authors: McClain Stephen T. , Hodge B. Keith , Bons Jeffrey P.
Published: October 2010

The discrete-element model for flows over rough surfaces considers the heat transferred from a rough surface to be the sum of the heat convected from the flat surface and the heat convected from the individual roughness elements to the fluid. In previous discrete-element model developments, heat transfer experiments were performed using metallic or high-thermal conductivity roughness elements. Many engineering applications, however, exhibit roughness with low thermal conductivities. In the present study, the discrete-element model is adapted to consider the effects of finite thermal conductivity of roughness elements on turbulent convective heat transfer. Initially, the boundary-layer equations are solved while the fin equation is simultaneously integrated so that the full conjugate heat transfer problem is solved. However, a simpler approach using a fin efficiency is also investigated. The results of the conjugate analysis and the simpler fin efficiency analysis are compared to experimental measurements for turbulent flows over ordered cone surfaces. Possibilities for extending the fin efficiency method to randomly rough surfaces and the experimental measurements required are discussed.
An Accelerated 3D Navier–Stokes Solver for Flows in Turbomachines
Authors: Brandvik Tobias , Pullan Graham
Published: October 2010

A new three-dimensional Navier–Stokes solver for flows in turbomachines has been developed. The new solver is based on the latest version of the Denton codes but has been implemented to run on graphics processing units (GPUs) instead of the traditional central processing unit. The change in processor enables an order-of-magnitude reduction in run-time due to the higher performance of the GPU. The scaling results for a 16 node GPU cluster are also presented, showing almost linear scaling for typical turbomachinery cases. For validation purposes, a test case consisting of a three-stage turbine with complete hub and casing leakage paths is described. Good agreement is obtained with previously published experimental results. The simulation runs in less than 10 min on a cluster with four GPUs.
Advanced Nonaxisymmetric Endwall Contouring for Axial Compressors by Generating an Aerodynamic Separator—Part II: Experimental and Numerical Cascade Investigation
Authors: Hergt Alexander , Dorfner Christian , Steinert Wolfgang , Nicke Eberhard , Schreiber Heinz-Adolf
Published: October 2010

Modern methods for axial compressor design are capable of shaping the blade surfaces in a three-dimensional way. Linking these methods with automated optimization techniques provides a major benefit to the design process. The application of nonaxisymmetric contoured endwalls is considered to be very successful in turbine rotors and vanes. Concerning axial compressors, nonaxisymmetric endwalls are still a field of research. This two-part paper presents the recent development of a novel endwall design. A vortex created by a nonaxisymmetric endwall groove acts as an aerodynamic separator, preventing the passage vortex from interacting with the suction side boundary layer. This major impact on the secondary flow results in a significant loss reduction by means of load redistribution, reduction in recirculation areas, and suppressed corner separation. Part I of this paper deals with the endwall design and its compressor application. The resulting flow phenomena and physics are described and analyzed in detail. The second paper presents the detailed experimental and numerical investigation of the developed endwall groove. The measurements carried out at the transonic cascade wind tunnel of DLR in Cologne, demonstrated a considerable influence on the cascade performance. A loss reduction and redistribution of the cascade loading were achieved at the aerodynamic design point, as well as near the stall condition of the cascade. This behavior is well predicted by the numerical simulation. The combined analysis of experimental and numerical flow patterns allows a detailed interpretation and description of the resulting flow phenomena. In this context, high fidelity 3D-Reynolds-averaged Navier–Stokes flow simulations are required to analyze the complex blade and endwall boundary layer interaction.
Prestressed Morphing Bistable and Neutrally Stable Shells
Authors: Seffen Keith A. , Guest Simon D.
Published: October 2010

This study deals with prestressed shells, which are capable of “morphing” under large deflexions between very different load-free configurations. Prestressing involves plastically curving a flat, thin shell in orthogonal directions either in the opposite or same sense, resulting in two unique types of behavior for isotropic shells. Opposite-sense prestressing produces a bistable, cylindrically curved shell provided the prestress levels are large enough and similar in size: This effect forms the basis of a child’s “flick” bracelet and is well known. On the other hand, same-sense prestressing results in a novel, neutrally stable shell provided the levels are also sufficiently large but identical: The shell has to be made precisely, otherwise, it is monostable and is demonstrated here by means of a thin, helically curved strip. The equilibrium states associated with both effects are quantified theoretically and new expressions are determined for the requisite prestress levels. Furthermore, each stability response is revealed in closed form where it is shown that the neutrally stable case occurs only for isotropic materials, otherwise, bistability follows for orthotropic materials, specifically, those, which have a shear modulus different from the isotropic value. Finally, prestressing and initial shape are considered together and, promisingly, it is predicted that some shells can be neutrally stable and bistable simultaneously.
Stress Distributions
in Plasma-Sprayed Thermal Barrier Coatings Under Thermal Cycling in a Temperature
Gradient
Authors: Limarga Andi
M. , Vaßen Robert , Clarke David R.
Published: October 2010

The residual stress distribution in plasma-sprayed zirconia thermal barrier coatings subjected to cyclic thermal gradient testing was evaluated using Raman piezospectroscopy and finite element computation. The thermal gradient testing (approximately 440°C/mm at temperature), consisted of repeated front-side heating with a flame and constant cooling of the back-side of the substrate either with front-side radiative cooling only or with additional forced air cooling between the heating cycles. The coatings exhibited characteristic “mud-cracking” with the average crack spacing dependent on the cooling treatment. This is consistent with finite element calculations and Raman spectroscopy measurements in which the sudden drop in coating surface temperature on initial cooling leads to a large biaxial tension at the surface. The key to proper interpretation of the Raman shifts is that the stress-free Raman peaks need to be corrected for shifts associated with the evolution of the metastable tetragonal phase with aging.
Axisymmetric Buckling of an Elastic Plate Containing a Circular Inclusion With Dilative Eigenstrain
Authors: Qiao L. , He L. H. , Ding K. W.
Published: October 2010

An infinite elastically isotropic plate containing a circular inclusion with dilative eigenstrain is studied, and the critical condition for the axisymmetric buckling driven by the eigenstrain is derived analytically.
Copper-plated 50 nm T-gate fabrication
Authors: Oxland Richard K. , Li Xu , Ferguson Susan , Bentley Steven , Thayne Iain G.
Published: October 2010

In this article, the authors report for the first time a route to the realization of scalable sub-100 nm Cu-based T-gates using a fully subtractive, “silicon-compatible” process flow. High resolution electron beam lithography and a low-damage RIE etch process are used to transfer a 50 nm line into ICP-CVD silicon nitride. This pattern forms the T-gate foot. A single blanket metallization is then used to form the Schottky contact, the seed layer for the copper electroplating and a barrier to prevent diffusion of the copper once deposited. A constant potential copper electroplating process has been developed for a Ti/Pt seed layer. Copper films have been deposited with bulk sheet resistance ρsh∼0.1 Ω/◻ (for a 300 nm film) and resistivity ρ=1.8×10−6 Ω cm. The head dimensions of the T-gate are realized by patterning resist on top of the seed prior to electroplating. Heads of width 500 nm were fabricated and shown to have a total gate resistance of Rg=150 Ω mm.
Simultaneous observation of surface topography and elasticity at atomic scale by multifrequency frequency modulation atomic force microscopy
Authors: Naitoh Yoshitaka , Ma Zongmin , Li Yan Jun , Kageshima Masami , Sugawara Yasuhiro
Published: October 2010

The authors integrated the frequency modulation (FM) technique into multifrequency atomic force microscopy (AFM). Based on theoretical considerations, simultaneous excitation of the cantilever oscillation at the first and second flexural modes allows us to acquire the surface topography and surface elasticity simultaneously. The authors performed multifrequency FM-AFM observation using a tungsten-coated silicon cantilever on a Ge(001) surface exhibiting a dimer structure at room temperature. The topography and the elasticity of the surface were successfully obtained at the atomic scale. The authors found that the dimer atoms around a missing dimer defect have higher elasticity than the other dimer atoms. This suggests that stiffer atomic bonding of the dimer atoms occurred as a result of the additional tensile strain field from the defect. Therefore, the multifrequency FM-AFM described in the present study is expected to be useful for the investigation of the surface elasticity at the atomic scale.
Application of contactless electroreflectance to study the epi readiness of m-plane GaN substrates obtained by ammonothermal method
Authors: Kudrawiec R. , Kucharski R. , Rudziński M. , Zając M. , Misiewicz J. , Strupiński W. , Doradziński R. , Dwiliński R.
Published: October 2010

The authors have applied contactless electroreflectance (CER) spectroscopy to study the epi readiness of m-plane GaN substrates obtained by the ammonothermal method. It has been clearly observed that the CER resonance, which is related to the energy gap transition, appears for samples with a well-polished surface. The sharpness of this resonance is directly related to the surface quality. The broadening of energy gap transition can be used as a parameter to quantify the surface quality. For samples polished with optimal conditions, this broadening (γpol) is close to the broadening observed for the cleaved GaN surface (γclev) with m-plane orientation (150–190 vs 135 meV). The quality of the polishing process can be evaluated by analyzing the γclev/γpol ratio, where γclev/γpol=1 corresponds to an excellent polishing process. In the authors’ case, this ratio has been determined to be close to 1 for well-polished samples.
Batch wafer scale fabrication of passivated carbon nanotube transistors for electrochemical sensing applications
Authors: Martin-Fernandez I. , Borrisé X. , Lora-Tamayo E. , Godignon P. , Perez-Murano F.
Published: October 2010

A technological process for batch wafer scale fabrication of electrochemical sensors based on single-walled carbon nanotube (SWCNT) field effect transistors (FETs) is presented. The fabrication of the carbon nanotube (CNT)-FETs is based on the chemical vapor deposition synthesis of the SWCNTs on predefined catalytic areas combined with standard microelectronic processes. Optical lithography is the only patterning method to be used. A fabrication yield close to 20% is achieved, which allows delivering thousands of CNT-FETs per wafer. An additional process to passivate the CNT-FETs is introduced to enable electrochemical sensing applications.
Challenges in the fabrication of an optical frequency ground plane cloak consisting of silicon nanorod arrays
Authors: Blair J. , Brown D. , Tamma V. A. , Park W. , Summers C.
Published: October 2010

The application of transformation optical techniques to photonic crystal-like dielectric structures has facilitated the creation of invisibility cloaks that operate at optical wavelengths. In this article, the authors present the fabrication processes for an all-dielectric ground plane cloak structure that consists of multiple silicon nanorod arrays connected by input and output waveguides. An advantage of this particular design is that it does not use metals to obtain metamaterial-like device behavior. The structure consists only of dielectrics that can be processed by the use of electron beam nanofabrication technologies and is designed to operate in the 1400–1600 nm wavelength range.
Epigenetic Reprogramming in Plant and Animal Development
Authors: Feng Suhua , Jacobsen Steven E. , Reik Wolf
Published: October 2010

Epigenetic modifications of the genome are generally stable in somatic cells of multicellular organisms. In germ cells and early embryos, however, epigenetic reprogramming occurs on a genome-wide scale, which includes demethylation of DNA and remodeling of histones and their modifications. The mechanisms of genome-wide erasure of DNA methylation, which involve modifications to 5-methylcytosine and DNA repair, are being unraveled. Epigenetic reprogramming has important roles in imprinting, the natural as well as experimental acquisition of totipotency and pluripotency, control of transposons, and epigenetic inheritance across generations. Small RNAs and the inheritance of histone marks may also contribute to epigenetic inheritance and reprogramming. Reprogramming occurs in flowering plants and in mammals, and the similarities and differences illuminate developmental and reproductive strategies.
Epigenetics in the Extreme: Prions and the Inheritance of Environmentally Acquired Traits
Authors: Halfmann Randal , Lindquist Susan
Published: October 2010

Prions are an unusual form of epigenetics: Their stable inheritance and complex phenotypes come about through protein folding rather than nucleic acid–associated changes. With intimate ties to protein homeostasis and a remarkable sensitivity to stress, prions are a robust mechanism that links environmental extremes with the acquisition and inheritance of new traits.
Filtering of Visual Information in the Tectum by an Identified Neural Circuit
Authors: Del Bene Filippo , Wyart Claire , Robles Estuardo , Tran Amanda , Looger Loren , Scott Ethan K. , Isacoff Ehud Y. , Baier Herwig
Published: October 2010

Small Is Attractive

The optic tectum of zebrafish larvae is required for the detection, tracking, and capture of small, highly motile prey.

Del Bene
et al.

(p.
669
) applied a combination of optical, genetic, and pharmacological tools to investigate how neural circuits in the optic tectum filter out low-frequency visual information. Most tectal neurons were tuned to respond selectively to small, moving objects in the fish's visual environment and responded very poorly to large stimuli. This spatial filtering mechanism depended on the activity of a small population of GABAergic, inhibitory interneurons at the tectal surface. Inactivation or destruction of these interneurons removed the size selectivity of deeper neurons and the zebrafish lost their ability to catch prey.
Rate of Gas Phase Association of Hydroxyl Radical and Nitrogen Dioxide
Authors: Mollner Andrew K. , Valluvadasan Sivakumaran , Feng Lin , Sprague Matthew K. , Okumura Mitchio , Milligan Daniel B. , Bloss William J. , Sander Stanley P. , Martien Philip T. , Harley Robert A. , McCoy Anne B. , Carter William P. L.
Published: October 2010

Honing in on HONO
2

Modeling air pollution requires knowledge of all the interrelated reactions occurring in the atmosphere. Among the most significant is the formation of nitric acid (HONO
2
) from OH and NO
2
radicals. One sticking point in the study of this reaction has been the uncertainty in how often radicals link through an O-O rather than an O-N bond.

Mollner
et al.

(p.
646
) measured the partitioning coefficient, as well as the overall consumption rate of the radicals, with an array of highly sensitive spectroscopic techniques in the laboratory. The measurements yielded a well-defined rate constant for nitric acid formation, which was applied to the prediction of ozone levels in atmospheric simulations of the Los Angeles basin.
Direct Observation and Quantification of CO
2
Binding Within an Amine-Functionalized Nanoporous Solid
Authors: Vaidhyanathan Ramanathan , Iremonger Simon S. , Shimizu George K. H. , Boyd Peter G. , Alavi Saman , Woo Tom K.
Published: October 2010

Designing Carbon Dioxide Traps

One widely discussed means of stemming the rise in atmospheric carbon dioxide concentration is to capture the gas prior to its emission and then bury it. The materials currently known to best adsorb CO
2
for this purpose tend to involve amine groups; however, the precise molecular details of adsorption often remain murky, and rational improvement of sorbent properties by structural modification has been challenging.

Vaidhyanathan
et al.

(p.
650
; see the Perspective by

Lastoskie

) have crystallographically resolved the binding motifs of CO
2
in an amine-bearing metal-organic framework solid. Accompanying theoretical simulations matched the experimental observations.
Exploiting Entanglement
Dance of the Photons
From Einstein to Quantum Teleportation

by Anton Zeilinger

Farrar, Straus, and Giroux, New York, 2010. 313 pp. $26. ISBN 9780374239664.
Authors: O'Brien Jeremy L.
Published: October 2010

Writing for nonspecialists and the interested public and drawing heavily on research by him and his colleagues, Zeilinger discusses quantum entanglement, the development of our understanding of the phenomenon, and its potential technological uses.
The Tao of Chloride Transporter Structure
Authors: Mindell Joseph A.
Published: October 2010

A protein structure from a heat-loving alga offers insight into the diverse family of CLC chloride channels and transporters.
Forced to Be Unequal
Authors: Grill Stephan W.
Published: October 2010

The distribution of a motor protein generates an unequal contractile force that controls the asymmetric division of eukaryotic cells.
Georges Charpak (1924–2010)
Authors: Quéré Yves
Published: October 2010

A generous Nobel laureate had a passion for particle detectors and reforming science education.
Six-Legged Fun

Insectos em Ordem [Insects in Order]
Patrícia Garcia Pereira and Eva Monteiro, Curators

National Museum of Natural History and Centre for Environmental Biology, University of Lisbon. At the Old Riding School of the College of Nobles, the Polytechnical Museums. Through 28 November 2010. http://bioeventos2010.ul.pt/bioevento/expo_insectosemordem.html
Authors: Cruz Maria
Published: October 2010

This exhibition introduces the insect diversity of Portugal by guiding visitors through a series of questions that allow them to place sample species in their taxonomic order.
Driving U.S. Energy Leadership
Authors: Alberts Bruce
Published: October 2010

I have just returned from a trip to China, where there is a tremendous emphasis on the importance of investing in science and technology for a sustainable future. For the Chinese, business as usual is not an option: It seems obvious to everyone that an economy that continues to expand using available technologies will choke on its own air pollution. Many nations share China's urgent need to shift away from an economy dominated by fossil fuels. Last month, Germany unveiled a bold proposal to move the country toward renewable “green” energies through aggressive policies, which may spur other European nations to follow suit. What about the United States?
Nobelist 'Coach' Takes On U.S. Science Education
Authors: Mervis Jeffrey
Published: October 2010

Carl Wieman took up the job of associate director for science in the White House Office of Science and Technology Policy in September. He sat down with
Science
on 21 October to discuss the state of science, technology, engineering, and math education and how he became involved.
1000 Genomes Project Gives New Map of Genetic Diversity
Authors: Pennisi Elizabeth
Published: October 2010

The 1000 Genomes Project has produced a compendium of millions of previously unknown single-nucleotide polymorphisms and other variants, described in work published this week. A second analysis in this week's issue of
Science
describes an approach for determining another aspect of genetic variation that arises when genes and other stretches of DNA are duplicated.
Data Say Retention Is Better Answer to 'Shortage' Than Recruitment
Authors: Mervis Jeffrey
Published: October 2010

Most efforts to improve education in science, technology, engineering, and mathematics start with recruitment. But working with those teachers already in the classroom may yield a bigger payoff.
What's in a Number?
Authors: Mervis Jeffrey
Published: October 2010

How far would training 10,000 more science, technology, engineering, and math teachers a year for the next 10 years go toward achieving President Barack Obama's goal of making the country No. 1 in math and science education? No one seems to know.
Snapshots From the Meeting
Authors: Gibbons Ann
Published: October 2010

Snapshots from the meeting include a clue to how the large, fleet-footed, meat-eating dinosaurs called abelisaurids used their stubby arms and evidence that climatic shifts can have a "kaleidoscopic" effect, breaking up communities of animals that then reassemble in new patterns.
LIFE SCIENCE TECHNOLOGIES: Structural Genomics Shapes Up Protein Research
Authors: May Mike
Published: October 2010

The three-dimensional structure of a protein determines how it works and interacts with other molecules. To understand complete pathways, processes, and eventually entire organisms, researchers need to know the structure of every protein. For the human proteome alone, researchers estimate that it consists of about one million proteins, when including all of the posttranslational modifications. Determining so many structures–plus millions more added from other organisms–depends on integrating a range of high throughput technologies.
Field Application of the H9M2e Enzyme-Linked Immunosorbent Assay for Differentiation of H9N2 Avian Influenza Virus-Infected Chickens from Vaccinated Chickens
Authors: Kim Min-Chul , Choi Jun-Gu , Kwon Ji-Sun , Kang Hyun-Mi , Paek Mi-Ra , Jeong Ok-Mi , Kwon Jun-Hun , Lee Youn-Jeong
Published: October 2010

Vaccination for control of H9N2 low-pathogenicity avian influenza (LPAI) in chickens began in 2007 in South Korea where the H9N2 virus is prevalent. Recently, an enzyme-linked immunosorbent assay (ELISA) using the extracellular domain of the M2 protein (M2e ELISA) was developed as another strategy to differentiate between vaccinated and infected chickens. Here, an ELISA using the extracellular domain of the M2 protein of H9N2 LPAI virus (H9M2e ELISA) was applied to differentiate infected from vaccinated chickens using the H9N2 LPAI virus M2 peptide. The specificity and sensitivity of the optimized H9M2e ELISA were 96.1% and 83.8% (the absorbance of the sample to the absorbance for the positive control [S/P ratio] ≥ 0.6), respectively, with the cutoff value (S/P ratio = 0.6), and the criterion of avian influenza (AI) infection in a chicken house was established as >20% reactivity of anti-M2e antibody per house with this cutoff value. After infection in naïve chickens and once-vaccinated chickens with a hemagglutination inhibition (HI) assay titer of 9.25 ± 0.75 log
2
units, the sera from infected chickens were confirmed as AI infected when the chickens were 1 week old in both groups, and AI infection lasted for 24 weeks and 9 weeks in naïve and once-vaccinated chickens, respectively, although in twice-vaccinated chickens with a higher HI titer of 11.17 ± 0.37 log
2
units, anti-M2e antibody in infected sera did not reach a level indicating AI infection. In field application, anti-M2e antibody produced in infected chickens after vaccination or in reinfected chickens could be identified as AI infection, although HI test could not distinguish infected from vaccinated sera. These results indicate the utility of H9M2e ELISA as a surveillance tool in control of H9N2 LPAI infections.
Evaluation ofRickettsia japonicaPathogenesis and Reservoir Potential in Dogs by Experimental Inoculation and Epidemiologic Survey
Authors: Inokuma Hisashi , Matsuda Hironori , Sakamoto Leo , Tagawa Michihito , Matsumoto Kotaro
Published: October 2010

Rickettsia japonicapathogenesis and reservoir potential in dogs were evaluated by both experimental inoculation and epidemiologic survey. In the experimental inoculation study, dogs 1 and 2 were pretreated with an immunosuppressive dose of cyclosporine 14 days before inoculation and became ill after exposure toR. japonica.Dogs exhibited clinical signs, including fever, anorexia, depression, and decreased water consumption, between 36 and 96 h after inoculation, but these signs disappeared spontaneously by 5 days after inoculation. Dogs 3 and 4 were not pretreated with cyclosporine, and no clinical signs were detected in them throughout the 14-day observation period. The control dog was clinically normal and had a normal rectal temperature throughout the study period. We attempted to detect rickettsial DNA from peripheral blood and aspiration samples from kidney and spleen by nested PCR, but all samples examined were negative. The control dog lacked detectable titers toR. japonicaantigen on day 14, while positive antibodies toR. japonicawere detected in all four experimentally infected dogs, with titers of 1:160 to 1:80. In the epidemiologic survey, 24 (1.8%) of the 1,363 dogs examined throughout Japan had antibodies againstR. japonica, with titers of 1:40 or more. However, we observed neither clinical signs at the time of sample collection nor nested PCR results indicative of rickettsial infection in these dogs. In conclusion, dogs in Japan can be exposed toR. japonica, and infected dogs with immunosuppressive conditions can temporarily develop clinical symptoms, including fever, anorexia, depression, and decreased water consumption.
Simultaneous Analysis of Multiple Enzymes Increases Accuracy of Pulsed-Field Gel Electrophoresis in Assigning Genetic Relationships among Homogeneous
Salmonella
Strains
Authors: Zheng Jie , Keys Christine E. , Zhao Shaohua , Ahmed Rafiq , Meng Jianghong , Brown Eric W.
Published: October 2010

Due to a highly homogeneous genetic composition, the subtyping of
Salmonella enterica
serovar Enteritidis strains to an epidemiologically relevant level remains intangible for pulsed-field gel electrophoresis (PFGE). We reported previously on a highly discriminatory PFGE-based subtyping scheme for
S. enterica
serovar Enteritidis that relies on a single combined cluster analysis of multiple restriction enzymes. However, the ability of a subtyping method to correctly infer genetic relatedness among outbreak strains is also essential for effective molecular epidemiological traceback. In this study, genetic and phylogenetic analyses were performed to assess whether concatenated enzyme methods can cluster closely related salmonellae into epidemiologically relevant hierarchies. PFGE profiles were generated by use of six restriction enzymes (XbaI, BlnI, SpeI, SfiI, PacI, and NotI) for 74 strains each of
S. enterica
serovar Enteritidis and
S. enterica
serovar Typhimurium. Correlation analysis of Dice similarity coefficients for all pairwise strain comparisons underscored the importance of combining multiple enzymes for the accurate assignment of genetic relatedness among
Salmonella
strains. The mean correlation increased from 81% and 41% for single-enzyme PFGE up to 99% and 96% for five-enzyme combined PFGE for
S. enterica
serovar Enteritidis and
S. enterica
serovar Typhimurium strains, respectively. Data regressions approached 100% correlation among Dice similarities for
S. enterica
serovar Enteritidis and
S. enterica
serovar Typhimurium strains when a minimum of six enzymes were concatenated. Phylogenetic congruence measures singled out XbaI, BlnI, SfiI, and PacI as most concordant for
S. enterica
serovar Enteritidis, while XbaI, BlnI, and SpeI were most concordant among
S. enterica
serovar Typhimurium strains. Together, these data indicate that PFGE coupled with sufficient enzyme numbers and combinations is capable of discerning accurate genetic relationships among
Salmonella
serovars comprising highly homogeneous strain complexes.
Antimicrobial Susceptibility Testing and Profiling of
Nocardia
Species and Other Aerobic Actinomycetes from South Africa: Comparative Evaluation of Broth Microdilution versus the Etest
Authors: Lowman Warren , Aithma Naseema
Published: October 2010

Nocardiosis is an underrecognized clinical entity in South Africa, for which interspecies epidemiological and clinical differences are poorly understood. The taxonomical state of flux and the lack of a simple antimicrobial susceptibility testing method are partly responsible. Definitive identification is molecularly based, which further complicates the study of this ubiquitous organism, as this methodology is beyond the scope of most routine diagnostic laboratories. The Etest methodology has been proposed as an alternative to the reference broth microdilution method, although there have been a limited number of comparative studies. We profiled 51 clinical isolates of aerobic actinomycetes, including 39
Nocardia
species, using sequence-based (16S rRNA) identification. Broth microdilution and Etests were done concurrently on all isolates. The overall level of categorical and essential agreement for broth microdilution and Etest for the
Nocardia
isolates ranged from 67.5 to 100% and 46.2 to 81.6%, respectively. Very major errors were seen with amikacin, amoxicillin-clavulanate, ciprofloxacin, clarithromycin, and imipenem. For
Nocardia
species, uniform susceptibility to co-trimoxazole, amikacin, and linezolid was demonstrated, with a 48.8% susceptibility rate to imipenem.
Nocardia farcinica
(20.5%) and
Nocardia cyriacigeorgica
(15.4%) were the most commonly identified species among the 82% of isolates identified to species level using 16S rRNA sequences. Furthermore, drug susceptibility patterns demonstrated limited concordance with species identification. Our results suggest that, in a routine diagnostic setting, the Etest is not an acceptable alternative to the reference method of broth microdilution for antimicrobial susceptibility testing. Given the diversity and limited understanding of this group of organisms, further widespread evaluation of clinical isolates, from both clinical and diagnostic perspectives, is warranted.
Insertion Sequences as Highly Resolutive Genomic Markers for Sequence Type 1Legionella pneumophilaParis
Authors: Vergnes Mike , Ginevra Christophe , Kay Elisabeth , Normand Philippe , Thioulouse Jean , Jarraud Sophie , Maurin Max , Schneider Dominique
Published: October 2010

The causative agent of legionellosis,Legionella pneumophila, colonizes all natural and human-made water networks, thus constituting the source of contaminated aerosols responsible for airborne human infections. Efficient control of infections, especially during epidemics, necessitates the fastest and most resolutive identification possible of the bacterial source for subsequent disinfection of reservoirs. We thus compared recognized typing approaches forLegionellawith a method based on characterization of insertion sequence (IS) content. A total of 86 clinical or environmental isolates ofL. pneumophila, including 84 Paris isolates, sampled from 25 clinical investigations in France between 2001 and 2007, were obtained from theLegionellaNational Reference Center. All strains were typed by monoclonal antibody subgrouping, sequence-based typing, pulsed-field gel electrophoresis, and restriction fragment length polymorphism based on the presence or absence of IS elements. We identified six different types of IS elements inL. pneumophilaParis and used them as genomic markers in hybridization experiments. One IS type, ISLpn11, revealed a high discriminatory power. Simpson's index of discrimination, calculated from the distribution of IS elements, was higher than that obtained with the other typing methods used forL. pneumophilaParis. Moreover, specific ISLpn11copies were found only in strains isolated from particular cities. In more than half of the cases, each clinical isolate had an ISLpn11profile that was recovered in at least one environmental isolate from the same geographical location, suggesting that our method could identify the infection source. Phylogenetic analysis suggests a clonal expansion for theL. pneumophilaParis strain.
Analyses of Pediatric Isolates of
Cryptococcus neoformans
from South Africa
Authors: Miglia Kathleen J. , Govender Nelesh P. , Rossouw Jenny , Meiring Susan , Mitchell Thomas G.
Published: October 2010

Compared to the incidence in adults, cryptococcosis is inexplicably rare among children, even in sub-Saharan Africa, which has the highest prevalence of coinfection with HIV and
Cryptococcus neoformans
. To explore any mycological basis for this age-related difference in the incidence of cryptococcosis, we investigated isolates of
C. neoformans
recovered from pediatric and adult patients during a 2-year period in South Africa. From reports to the Group for Enteric, Respiratory, and Meningeal Disease Surveillance in South Africa (GERMS-SA), we reviewed all cases of cryptococcosis in 2005 and 2006. We analyzed one isolate of
C. neoformans
from each of 82 pediatric patients (<15 years of age) and determined the multilocus sequence type (ST), mating type, ploidy, and allelic profile. This sample included isolates of all three molecular types of serotype A or
C. neoformans
var.
grubii
(molecular types VNI, VNII, and VNB) and one AD hybrid. Seventy-seven (94%) of the strains possessed the
MAT
α mating type allele, and five were
MAT
a.
Seventy-five (91%) were haploid, and seven were diploid. A total of 24 different STs were identified. The ratios of each mating type and the proportion of haploids were comparable to those for the isolates that were obtained from 86 adult patients during the same period. Notably, the most prevalent pediatric ST was significantly associated with male patients. Overall, these pediatric isolates exhibited high genotypic diversity. They included a relatively large percentage of diploids and the rarely reported
MAT
a
mating type.
Comparative Evaluation of the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 Version 2 Test Using the TaqMan 48 Analyzer and the Abbott RealTi
m
e HIV-1 Assay
Authors: van Rensburg Estrelita Janse , Tait Karen , Watt Alistair , Schall Robert
Published: October 2010

Acceptable precision was achieved in a comparison study of the Abbott RealTi
m
e (RT) and Roche CAP/CTM-48 V2 HIV-1 assays, but viral load quantification was under- and overestimated, respectively, compared to the 2nd HIV-1 WHO International Standard. The same quantification patterns were observed for patient cohorts from Africa and the United States.
Development of a Multilocus Sequence Tool for Typing
Cryptosporidium muris
and
Cryptosporidium andersoni
Authors: Feng Yaoyu , Yang Wenli , Ryan Una , Zhang Longxian , Kváč Martin , Koudela Břetislav , Modrý David , Li Na , Fayer Ronald , Xiao Lihua
Published: October 2010

Although widely used for the characterization of the transmission of intestinal
Cryptosporidium
spp., genotyping tools are not available for
C. muris
and
C. andersoni
, two of the most common gastric
Cryptosporidium
spp. infecting mammals. In this study, we screened the
C. muris
whole-genome sequencing data for microsatellite and minisatellite sequences. Among the 13 potential loci (6 microsatellite and 7 minisatellite loci) evaluated by PCR and DNA sequencing, 4 were eventually chosen. DNA sequence analyses of 27
C. muris
and 17
C. andersoni
DNA preparations showed the presence of 5 to 10 subtypes of
C. muris
and 1 to 4 subtypes of
C. andersoni
at each locus. Altogether, 11
C. muris
and 7
C. andersoni
multilocus sequence typing (MLST) subtypes were detected among the 16
C. muris
and 12
C. andersoni
specimens successfully sequenced at all four loci. In all analyses, the
C. muris
isolate (TS03) that originated from an East African mole rat differed significantly from other
C. muris
isolates, approaching the extent of genetic differences between
C. muris
and
C. andersoni
. Thus, an MLST technique was developed for the high-resolution typing of
C. muris
and
C. andersoni
. It should be useful for the characterization of the population genetics and transmission of gastric
Cryptosporidium
spp.
Meningitis Due to
Providencia stuartii
Authors: Sipahi Oguz Resat , Bardak-Ozcem Selin , Ozgiray Erkin , Aydemir Sohret , Yurtseven Taskin , Yamazhan Tansu , Tasbakan Meltem , Ulusoy Sercan
Published: October 2010

In this report, we present a case of postneurosurgical meningitis due to
Providencia stuartii
, which was treated successfully with meropenem therapy lasting 21 days.
Improved Selective and Differential Medium for Isolation of
Escherichia coli
O157:H7
Authors: Park Sang-Hyun , Ryu Sangryeol , Kang Dong-Hyun
Published: October 2010

GMAC, a modified version of Sorbitol MacConkey medium (SMAC), was produced with a reduced quantity of selective agents and incorporated gentiobiose. GMAC supported a higher recovery rate of heat- or acid-injured
Escherichia coli
O157:H7 cells than SMAC with cefixime and tellurite (CT-SMAC), while differentiating
E. coli
O157:H7 from sorbitol-nonfermenting
Hafnia alvei
.
Mixed-Strain
Mycobacterium tuberculosis
Infections among Patients Dying in a Hospital in KwaZulu-Natal, South Africa
Authors: Cohen Ted , Wilson Douglas , Wallengren Kristina , Samuel Elizabeth Y. , Murray Megan
Published: October 2010

We performed spoligotyping and 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing on
M. tuberculosis
culture-positive biopsy specimens collected from adults dying in a hospital in KwaZulu-Natal. Of 56 culture-positive samples genotyped, we detected mixed strains in five (9%) and clonal heterogeneity in an additional four (7%).
Emergence of a Unique Penicillin-Resistant
Streptococcus pneumoniae
Serogroup 35 Strain
Authors: Stanek Ronald J. , Maher Mary B. , Norton Nancy B. , Mufson Maurice A.
Published: October 2010

We analyzed seven
Streptococcus pneumoniae
serogroup 35 isolates by pulsed-field gel electrophoresis of the genome and
pbp2b
gene nucleotide sequences. Three penicillin-susceptible strains and one penicillin-intermediate-resistant strain exhibited 100% identity to prototype R6. Two resistant strains and one other intermediate strain differed from them and contained a unique sequence.