bluuebunny/crossref_metadata_2025 huggingface dataset:
Singular Perturbation Analysis of the Nonlinear, Flow-Dependent Compressive Stress Relaxation Behavior of Articular Cartilage
Authors: Holmes M. H. , Lai W. M. , Mow V. C.
Published: July 2009

The dominant mechanism giving rise to the viscoelastic response of articular cartilage during compression is the nonlinear diffusive interaction of the fluid and solid phases of the tissue as they flow relative to one another. The present study is concerned with the role of this interaction under uniaxial stress relaxation in compression. The model is a biphasic mixture of fluid and solid which incorporates the strain-dependent permeability found earlier from permeation experiments. When a ramp-displacement is imposed on the articular surface, simple, but accurate, asymptotic approximations are derived for the deformation and stress fields in the tissue for slow and moderately fast rates of compression. They are shown to agree very well with experiment and they provide a simple means for determining the material parameters. Moreover, they lead to important insights into the role of the flow-dependent viscoelastic nature of articular cartilage and other hydrated biological tissues.
A Comparative Evaluation of Unconstrained Optimization Methods Applied to the Thermal Tomography Problem
Authors: Clegg S. T. , Roemer R. B.
Published: July 2009

In cancer hyperthermia treatments, it is important to be able to predict complete tissue temperature fields from sampled temperatures taken at the limited number of locations allowed by clinical constraints. An initial attempt to do this automatically using unconstrained optimization techniques to minimize the differences between experimental temperatures and temperatures predicted from treatment simulations has been previously reported [1]. This paper reports on a comparative study which applies a range of different optimization techniques (relaxation, steepest descent, conjugate gradient, Gauss, Box-Kanemasu, and Modified Box-Kanemasu) to this problem. The results show that the Gauss method converges more rapidly than the others, and that it converges to the correct solution regardless of the initial guess for the unknown blood perfusion vector. A sensitivity study of the error space is also performed, and the relationships between the error space characteristics and the comparative speeds of the optimization techniques are discussed.
Numerical Analysis of the Thermochemical Tooth Damage Induced by Laser Radiation
Authors: Laufer G. , Haber S.
Published: July 2009

A numerical model is developed to predict zones of thermochemical tooth damage induced by laser radiation. Particular attention is devoted to pulp denaturation, enamel fracture and caries sterilization treatment dependence on laser energy and other beam parameters.
Fluid Dynamic Study in a Femoral Artery Branch Casting of Man With Upstream Main Lumen Curvature for Steady Flow
Authors: Back M. R. , Cho Y. I. , Back L. H.
Published: July 2009

An in-vitro, steady flow investigation was conducted in a hollow, transparent vascular replica of the profunda femoris branch of man for a range of physiological flow conditions. The replica casting tested was obtained from a human cadaver and indicated some plaque formation along the main lumen and branch. The flow visualization observations and measured pressure distributions indicated the highly three-dimensional flow characteristics with arterial curvature and branching, and the important role of centrifugal effects in fluid transport mechanisms.
On the Detection of Messages Carried in Arterial Pulse Waves
Authors: Dai K. , Xue H. , Dou R. , Fung Y. C.
Published: July 2009

The hypothesis is made that a disturbance in blood flow at one place can be detected in the arterial pulse waves at a distant site. This hypothesis was motivated by the traditional Chinese medicine which uses arterial pulse waves as a principal means of diagnosis. We formulated a test by asking whether a disturbance to the blood flow in a leg can be detected by changes in the pulse waves in the radial arteries. In particular, we ask whether the radial artery can differentiate a disturbance in the right leg from that in the left leg. We put force transducers on the radial arteries, depressed them by a specific amount, and recorded the force waves in response to a 2-min occlusion of the blood flow in the right or left tibial artery. The results show that the radial artery force waves do change in response to the flow disturbance. For a given individual, the force varies with the location of the force transducer on the radial artery, the specific amount of initial depression, and the right or left leg occlusion. Generally, an occlusion in the right leg reduces the force level in both radial arteries, the more so in the right radial artery than in the left. Although the discrimination is not very strong, the phenomenon is novel, and warrants further investigation.
A Three-Dimensional Computational Simulation of Some Sources of Measurement Artifact in Microvascular Pulsed Ultrasound Doppler Velocimetry
Authors: Brown T. D. , Bell L. D. , Pedersen D. R. , Blair W. F.
Published: July 2009

Recent applications of 20 MHz pulsed ultrasound Doppler velocimetry (PUDVM) in microsurgical research have necessarily employed piezoelectric crystals whose diameter is not negligible compared to the lumen size (1–2 mm) of many vessels of interest. A three-dimensional numerical model was developed to explore relationships between actual and detected flow field parameters, for (steady) Poiseuille flow, when appreciable velocity gradients exist within the PUDVM sample volume. Validation studies showed that highly accurate velocity profiles could be obtained in the limiting case of a very small sample volume (0.1 mm radius), but that for currently employed crystals ( ≈ 0.5 mm radius) there was appreciable underestimation of the centersteam velocity, and appreciable overestimation of the flow stream diameter. Errors in perceived velocity and flow rate were found to be relatively insensitive to perturbations in the sample volume thickness, in the size of the sampling range increment, or in the angle of insonation beam divergence. By contrast, these apparent flow parameters were found to be very sensitive to perturbations of sample volume diameter or of the Dopper angle. Small variations in the degree of partial sample volume overlap of the flowstream periphery were shown to be capable of causing large fluctuations in apparent flow stream diameter.
Analysis of Functional Scoliosis by Means of an Anisotropic Beam Model of the Human Spine
Authors: Lindbeck L.
Published: July 2009

An upright, muscle-relaxed human spine, suffering from a mild functional scoliosis, caused by a small difference in leg length, is modeled as an anisotropic, elastic beam. The lower end of the beam is built-in in a fixed body, i.e., the laterally tilted pelvis. The upper end is rigidly attached to a rigid body, i.e., the supported upper part of the trunk, which is supposed to move freely in the frontal plane. It is shown that the characteristic scoliotic curvature of the spine, observed on an X-ray picture, can be reproduced by means of buckling analysis of the beam model, using realistic values of geometric and loading parameters and a properly chosen bending stiffness, which is found to be in reasonable agreement with earlier experimental findings. The analysis also shows that the muscle-relaxed upright equilibrium position of the spine is mechanically unstable.
Constant Strain Increment for Exponential Tendons in the High-Stress Limit
Authors: Greene P. R.
Published: July 2009

It is theoretically shown that, in the high-stress limit, the exponentially stiffening tendon will have constant strain increment along its length, regardless of changes in cross-sectional area.
Numerical Experiments With a New Differentiation Filter
Authors: Busby H. R. , Trujillo D. M.
Published: July 2009

A dynamic programming filter which provides estimates of the first and second derivative of empirical displacement data is investigated numerically. This filter uses a weighted least squares criteria in estimating the derivatives. The filter equations are presented together with several numerial examples. These examples are taken from references that proposed other techniques.
Elastic Properties of Collapsing and Expanding Trachea
Authors: Winter D. C.
Published: July 2009

The compliance of the canine trachea under positive and negative transmural pressures was measured in an in-vivo preparation. The average compliance values found in eight animals were 11.7×10−6 (dynes/cm2)−1 at zero transmural pressure and 4.9 and 6.9×10−6 (dynes/cm2)−1 at −20 and +20×103 dynes/cm2 transmural pressure, respectively. These compliances were significantly lower than those measured by others in excised preparations. Stress relaxation was noted at all pressure levels.
An Acoustic Plethysmograph to Measure Total Infant Body Volume
Authors: Deskins W. G. , Winter D. C. , Sheng H.-P. , Garza C.
Published: July 2009

An acoustic plethysmograph intended to measure the body volume of premature infants has been developed using the principle of the Helmholtz resonator, in which the resonance frequency is dependent on the volume of the resonating cavity. A prototype system was built and used to measure the volume of inanimate objects and newborn miniature pigs. Results for inanimate objects agree within 1 percent with comparable measurements by water displacement. Results of the animal body volume measurements compare favorably (within an average of 1.1 percent) with those obtained using hydrostatic weighing.
Ultrasonic Characterization of Biological Tissues
Authors: Shung K. K.
Published: July 2009

Ultrasonic imaging has become increasingly important as a diagnostic tool in medicine because it is noninvasive and it can provide valuable information otherwise unattainable. However, at present, clinical interpretation of an ultrasonic image still mostly relies on recognition of boundaries and positional relationship of anatomical structures and a subjective analysis of the distribution or texture of echo amplitudes. Other potentially useful information carried back by the echoes is completely discarded. The aim of ultrasonic tissue characterization research is to develop methods to extract additional information from the returned echoes so that tissue pathology or abnormality can be reliably identifed and severity of the pathology objectively assessed with quantiative criteria. A number of ultrasonic parameters including acoustic velocity, impedance, attentuation and scattering, have been utilized in attempting to achieve this goal. In this paper, recent progress in this research will be discussed and relevant results presented.
Parameter Estimation and Sensitivity Analysis of a Nonlinearly Elastic Static Lung Model
Authors: Ligas J. R. , Saidel G. M. , Primiano F. P.
Published: July 2009

A model for the static pressure-volume behavior of the lung parenchyma based on a pseudo-elastic strain energy function was tested. Values of the model parameters and their variances were estimated by an optimal least-squares fit of the model-predicted pressures to the corresponding data from excised, saline-filled dog lungs. Although the model fit data from twelve lungs very well, the coefficients of variation for parameter values differed greatly. To analyze the sensitivity of the model output to its parameters, we examined an approximate Hessian, H, of the least-squares objective function. Based on the determinant and condition number of H, we were able to set formal criteria for choosing the most reliable estimates of parameter values and their variances. This in turn allowed us to specify a normal range of parameter values for these dog lungs. Thus the model not only describes static pressure-volume data, but also uses the data to estimate parameters from a fundamental constitutive equation. The optimal parameter estimation and sensitivity analysis developed here can be widely applied to other physiologic systems.
A Numerical Simulation of the Flow in a T-Type Bifurcation and Its Application to an “End to Side” Fistula
Authors: Enden G. , Israeli M. , Dinnar U.
Published: July 2009

Some recent surgical procedures such as arteriovenous fistula, or coronary and cerebral by-passes were observed to yield counterdirectional branching blood flows. There is a lack of knowledge about the role of the counterdirectional flow ratio, the angle of anastomosis and the shear stresses in the process of thrombogenesis that leads to shunt occlusion. The program developed to simulate these hemodynamic conditions uses an efficient numerical scheme for the solution of the 2-D Navier-Stokes equations and can be easily adapted to flows in other geometrical configurations.
Structural Models for Human Spinal Motion Segments Based on a Poroelastic View of the Intervertebral Disk
Authors: Simon B. R. , Wu J. S. S. , Carlton M. W. , Evans J. H. , Kazarian L. E.
Published: July 2009

Analytical and finite element models (FEMs) were used to quantify poroelastic material properties for a human intervertebral disk. An axisymmetric FEM based on a poroelastic view of disk constituents was developed for a representative human spinal motion segment (SMS). Creep and steady-state response predicted by FEMs agreed with experimental observations, i.e., long-time creep occurs with flow in the SMS, whereas for rapid steady-state loading an “undrained,” nearly incompressible response is evident. A relatively low value was determined for discal permeability. Transient and long-term creep FE analyses included the study of deformation, pore fluid flow, stress, and pore fluid pressure. Relative fluid motion associated with transient creep is related to nuclear nutrition and the overall mechanical response in the normal disk. Degeneration of the disk may be associated, with an increase in permeability.
In-Vitro Pulsatile Flow Visualization Studies in a Pulmonary Artery Model
Authors: Philpot E. , Yoganathan A. P. , Sung H.-W. , Woo Y.-R. , Franch R. H. , Sahn D. J. , Valdez-Cruz L.
Published: July 2009

In-vitro pulsatile flow visualization studies were conducted in an adult-sized pulmonary artery model to observe the effects of valvular pulmonic stenosis on the flow fields of the main, left and right pulmonary arteries. The flow patterns revealed that as the degree of stenosis increased, the jet-type flow created by the valve became narrower, and it impinged on the far (distal) wall of the left pulmonary artery further downstream from the junction of the bifurcation. This in turn led to larger regions of disturbed turbulent flow, as well as helical-type secondary flow motions in the left pulmonary artery, compared to the right pulmonary artery. The flow field in the main pulmonary artery also became more disturbed and turbulent, especially during peak systole and the deceleration phase. The flow visualization observations have been valuable in helping to conduct further quantitative studies such as pressure and velocity field mapping. Such studies are important to understanding the fluid mechanics characteristics of the main pulmonary artery and its two major branches.
Thermoplastics: New Opportunities for Mechanics
Authors: Stokes Vijay K.
Published: July 2009

The use of thermoplastic polymeric materials in structural applications is increasing. A good example is the all-plastic thermoplastic automotive bumper, made of unfilled nonreinforced thermoplastic resin, which is capable of withstanding an 8 kmph (5 mph) impact. The structural applications of such materials are expected to grow dramatically. These materials behave very differently from metals, and their use in load-bearing applications raises interesting mechanics issues that need to be addressed. This paper discusses some opportunities for new research directions in mechanics, which would impact the use of plastics in load-bearing applications.
Artificial Intelligence and Geometric Reasoning in Manufacturing Technology
Authors: Dixon John R. , Dym Clive L.
Published: July 2009

This article presents a brief review of the current literature on the applications of artificial intelligence (AI) technologies, and especially expert (knowledge-based) systems, to manufacturing. Emphasis is placed on geometric representation and reasoning in design as an aid to manufacturing. Also discussed are applications of AI to process planning and design, process control, assembly, and other phases of manufacturing.
Design for Manufacture: An Overview
Authors: Stoll Henry W.
Published: July 2009

Design for manufacture (DFM) is concerned with defining product design alternatives which facilitate optimization of the manufacturing system as a whole. Recognized as being essential to productivity improvement, interest in the DFM approach has risen dramatically as the result of recent experience with deployment of advanced manufacturing technology. This article critically examines the broad range of activities which are embodied in the DFM approach. Discussion is divided into consideration of DFM principles and rules, quantitative evaluation methodologies, and computer-aided DFM. Underlying organization issues are also discussed.
Commentary on Flexible Fixturing
Authors: Thompson B. S. , Gandhi M. V.
Published: July 2009

One of the significant impediments to the evolution of truly flexible computer-integrated manufacturing systems is the absence of truly adaptable flexible fixturing systems. This article reports on research activities dedicated to synthesizing and developing viable universal flexible fixturing systems, methodologies, and technologies for fixturing parts of various shapes and sizes. Phase-change fixturing, modular fixture kits, and other innovative concepts are discussed. In addition, the article not only contains a state-of-the-art review of this rapidly evolving area of engineering science, but it also highlights the necessity for interdisciplinary research in order to address the frontier problems in this area. These disciplines range from the mechanics of both solids and fluids through dynamics and vibrations to artificial intelligence. This research philosophy is essential for developing viable solutions which can be successfully implemented in the factory-of-the-future.
The Dynamics of Phenotypic Change and the Shrinking Sheep of St. Kilda
Authors: Ozgul Arpat , Tuljapurkar Shripad , Benton Tim G. , Pemberton Josephine M. , Clutton-Brock Tim H. , Coulson Tim
Published: July 2009

Little Lambs

In changing environments, ecological and evolutionary dynamics are intimately intertwined. However, understanding the dynamics of phenotypic traits under natural conditions is still rudimentary.

Ozgul
et al.

(p.
464
; published online 2 July) dissected the dynamics of a phenotypic trait in the context of the contributing ecological and evolutionary processes. In a wild population of Soay sheep where mean body size has fluctuated substantially over the past 25 years and has, on average, gotten smaller, an ecological response to environmental variation is the major driver of the dynamics; evolutionary change has contributed relatively little: The sheep have become smaller because climate change has modified the way that density-dependence influences lamb growth rates.
Pathogenesis and Transmission of Swine-Origin 2009 A(H1N1) Influenza Virus in Ferrets
Authors: Munster Vincent J. , de Wit Emmie , van den Brand Judith M. A. , Herfst Sander , Schrauwen Eefje J. A. , Bestebroer Theo M. , van de Vijver David , Boucher Charles A. , Koopmans Marion , Rimmelzwaan Guus F. , Kuiken Thijs , Osterhaus Albert D. M. E. , Fouchier Ron A. M.
Published: July 2009

“Swine Flu” Pathology

The clinical spectrum of disease caused by the swine-origin 2009 A(H1N1) influenza virus and its transmissibility are not completely understood.

Munster
et al.

(p.
481
; published online 2 July) and

Maines
et al.

(p.
484
; published online 2 July) used ferrets, an established model for human influenza, to evaluate the pathogenesis and transmissibility of a selection of 2009 A(H1N1) virus isolates compared with representative seasonal H1N1 viruses. The results help explain the atypical symptoms seen so far, including the gastrointestinal distress and vomiting observed in many patients. Although results were variable, it seems that the 2009 A(H1N1) virus may be less efficiently transmitted by respiratory droplets in comparison to the highly transmissible seasonal H1N1 virus, suggesting that additional virus adaptation in mammals may be required before we see phenotypes observed in earlier pandemics.
Transmission and Pathogenesis of Swine-Origin 2009 A(H1N1) Influenza Viruses in Ferrets and Mice
Authors: Maines Taronna R. , Jayaraman Akila , Belser Jessica A. , Wadford Debra A. , Pappas Claudia , Zeng Hui , Gustin Kortney M. , Pearce Melissa B. , Viswanathan Karthik , Shriver Zachary H. , Raman Rahul , Cox Nancy J. , Sasisekharan Ram , Katz Jacqueline M. , Tumpey Terrence M.
Published: July 2009

“Swine Flu” Pathology

The clinical spectrum of disease caused by the swine-origin 2009 A(H1N1) influenza virus and its transmissibility are not completely understood.

Munster
et al.

(p.
481
; published online 2 July) and

Maines
et al.

(p.
484
; published online 2 July) used ferrets, an established model for human influenza, to evaluate the pathogenesis and transmissibility of a selection of 2009 A(H1N1) virus isolates compared with representative seasonal H1N1 viruses. The results help explain the atypical symptoms seen so far, including the gastrointestinal distress and vomiting observed in many patients. Although results were variable, it seems that the 2009 A(H1N1) virus may be less efficiently transmitted by respiratory droplets in comparison to the highly transmissible seasonal H1N1 virus, suggesting that additional virus adaptation in mammals may be required before we see phenotypes observed in earlier pandemics.
Experimental Chemotherapy againstTrypanosoma cruziInfection Using Ruthenium Nitric Oxide Donors
Authors: Silva Jean Jerley N. , Pavanelli Wander R. , Pereira José Clayston M. , Silva João S. , Franco Douglas W.
Published: July 2009

The ruthenium NO donors of the grouptrans-[Ru(NO)(NH3)4L]n+, where the ligand (L) is N-heterocyclic H2O, SO32−, or triethyl phosphite, are able to lyseTrypanosoma cruziin vitro and in vivo. Using half-maximal (50%) inhibitory concentrations against bloodstream trypomastigotes (IC50try) and cytotoxicity data on mammalian V-79 cells (IC50V79), the in vitro therapeutic indices (TIs) (IC50V79/IC50try) for these compounds were calculated. Compounds that exhibited an in vitro TI of ≥10 and trypanocidal activity against both epimastigotes and trypomastigotes with an IC50try/epiof ≤100 μM were assayed in a mouse model for acute Chagas' disease, using two different routes (intraperitoneal and oral) for drug administration. A dose-effect relationship was observed, and from that, the ideal dose of 400 nmol/kg of body weight for bothtrans-[Ru(NO)(NH3)4isn](BF4)3(isn, isonicotinamide) andtrans-[Ru(NO)(NH3)4imN](BF4)3(imN, imidazole) and median (50%) effective doses (ED50) of 86 and 190 nmol/kg, respectively, were then calculated. Since the 50% lethal doses (LD50) for both compounds are higher than 125 μmol/kg, the in vivo TIs (LD50/ED50) of the compounds are 1,453 fortrans-[Ru(NO)(NH3)4isn](BF4)3and 658 fortrans-[Ru(NO)(NH3)4imN](BF4)3. Although these compounds exhibit a marked trypanocidal activity and are able to react with cysteine, they exhibit very low activity inT. cruzi-glycosomal glyceraldehyde-3-phosphate dehydrogenase tests, suggesting that this enzyme is not their target. Thetrans-[Ru(NO)(NH3)4isn](BF4)3andtrans-[Ru(NO)(NH3)4imN](BF4)3compounds are able to eliminate amastigote nests in myocardium tissue at 400-nmol/kg doses and ensure the survival of all infected mice, thus opening a novel set of therapies to try against trypanosomatids.
Lipid Segregation Explains Selective Toxicity of a Series of Fragments Derived from the Human Cathelicidin LL-37
Authors: Epand Raquel F. , Wang Guangshun , Berno Bob , Epand Richard M.
Published: July 2009

The only human cathelicidin, the 37-residue peptide LL-37, exhibits antimicrobial activity against both gram-positive and gram-negative bacteria. We studied the ability of several fragments of LL-37, exhibiting different antimicrobial activities, to interact with membranes whose compositions mimic the cytoplasmic membranes of gram-positive or of gram-negative bacteria. These fragments are as follows: KR-12, the smallest active segment of LL-37, with the sequence KRIVQRIKDFLR, which exhibits antimicrobial activity only against gram-negative bacteria; a slightly smaller peptide, RI-10, missing the two cationic residues at the N and C termini of KR-12, which has been shown not to have any antimicrobial activity; a longer peptide, GF-17, which shows antimicrobial activity against gram-positive as well as gram-negative bacteria; and GF-17D3, with 3
d
-amino-acid residues, which is also selective only for gram-negative bacteria. Those fragments with the capacity to cluster anionic lipids away from zwitterionic lipids in a membrane exhibit selective toxicity toward bacteria containing zwitterionic as well as anionic lipids in their cytoplasmic membranes but not toward bacteria with only anionic lipids. This finding allows for the prediction of the bacterial-species selectivity of certain agents and paves the way for designing new antimicrobials targeted specifically toward gram-negative bacteria.
Meropenem Pharmacokinetics in the Newborn
Authors: van den Anker John N. , Pokorna Pavla , Kinzig-Schippers Martina , Martinkova Jirina , de Groot Ronald , Drusano G. L. , Sorgel Fritz
Published: July 2009

We studied meropenem in 23 pre-term (gestational age, 29 to 36 weeks) and 15 full-term (gestational age, 37 to 42 weeks) neonates. Meropenem doses of 10, 20, and 40 mg/kg were administered as single doses (30-min intravenous infusion) on a random basis. Blood was obtained for determining the meropenem concentration nine times. Each child required other antimicrobials for proven/suspected bacterial infections. Samples were assayed by high-performance liquid chromatography analysis. Population pharmacokinetic parameter values were obtained by employing the BigNPAG program. Model building was performed by the likelihood ratio test. The final model included estimated creatinine clearance (CL
cr
) (Schwartz formula) and weight (Wt) in the calculation of clearance (meropenem clearance = 0.00112 × CL
cr
+ 0.0925 × Wt + 0.156 liter/hr). The overall fit of the model to the data was good (observed = 1.037 × predicted − 0.096; r
2
= 0.977). Given the distributions of estimated creatinine clearance and weight between pre-term and full-term neonates, meropenem clearance was substantially higher in the full-term group. A Monte Carlo simulation was performed using the creatinine clearance and weight distributions for pre-term and full-term populations separately, examining 20- and 40-mg/kg doses, 8- and 12-h dosing intervals, and 0.5-h and 4-h infusion times. The 8-h interval produced robust target attainments (both populations). If more resistant organisms were to be treated (MIC of 4 to 8 mg/liter), the 40-mg/kg dose and a prolonged infusion was favored. Treating clinicians need to balance dose choices for optimizing target attainment against potential toxicity. These findings require validation in clinical circumstances.
CraA, a Major Facilitator Superfamily Efflux Pump Associated with Chloramphenicol Resistance in
Acinetobacter baumannii
Authors: Roca I. , Marti S. , Espinal P. , Martínez P. , Gibert I. , Vila J.
Published: July 2009

Acinetobacter baumannii
has been increasingly associated with hospital-acquired infections, and the presence of multidrug resistance strains is of great concern to clinicians.
A. baumannii
is thought to possess a great deal of intrinsic resistance to several antimicrobial agents, including chloramphenicol, although the mechanisms involved in such resistance are not well understood. In this work, we have identified a major facilitator superfamily efflux pump present in most
A. baumannii
strains, displaying strong substrate specificity toward chloramphenicol.
Role of Porins in the Susceptibility of
Mycobacterium smegmatis
and
Mycobacterium chelonae
to Aldehyde-Based Disinfectants and Drugs
Authors: Svetlíková Zuzana , Škovierová Henrieta , Niederweis Michael , Gaillard Jean-Louis , McDonnell Gerald , Jackson Mary
Published: July 2009

Nosocomial outbreaks attributable to glutaraldehyde-resistant, rapidly growing mycobacteria are increasing. Here, evidence is provided that defects in porin expression dramatically increase the resistance of
Mycobacterium smegmatis
and
Mycobacterium chelonae
to glutaraldehyde and another aldehyde disinfectant,
ortho
-phthalaldehyde. Since defects in porin activity also dramatically increased the resistance of
M. chelonae
to drugs, there is thus some concern that the widespread use of glutaraldehyde and
ortho
-phthalaldehyde in clinical settings may select for drug-resistant bacteria.
Metabolism and Cometabolism of Cyclic Ethers by a Filamentous Fungus, aGraphiumsp
Authors: Skinner Kristin , Cuiffetti Lynda , Hyman Michael
Published: July 2009

The filamentous fungusGraphiumsp. (ATCC 58400) grows on gaseousn-alkanes and diethyl ether.n-Alkane-grown mycelia of this strain also cometabolically oxidize the gasoline oxygenate methyltert-butyl ether (MTBE). In this study, we characterized the ability of this fungus to metabolize and cometabolize a range of cyclic ethers, including tetrahydrofuran (THF) and 1,4-dioxane (14D). This strain grew on THF and other cyclic ethers, including tetrahydropyran and hexamethylene oxide. However, more vigorous growth was consistently observed on the lactones and terminal diols potentially derived from these ethers. Unlike the case in all previous studies of microbial THF oxidation, a metabolite, γ-butyrolactone, was observed during growth of this fungus on THF. Growth on THF was inhibited by the samen-alkenes andn-alkynes that inhibit growth of this fungus onn-alkanes, while growth on γ-butyrolactone or succinate was unaffected by these inhibitors. Propane and THF also behaved as mutually competitive substrates, and propane-grown mycelia immediately oxidized THF, without a lag phase. Mycelia grown on propane or THF exhibited comparable high levels of hemiacetal-oxidizing activity that generated methyl formate from mixtures of formaldehyde and methanol. Collectively, these observations suggest that THF andn-alkanes may initially be oxidized by the same monooxygenase and that further transformation of THF-derived metabolites involves the activity of one or more alcohol dehydrogenases. Both propane- and THF-grown mycelia also slowly cometabolically oxidized 14D, although unlike THF oxidation, this reaction was not sustainable. Specific rates of THF, 14D, and MTBE degradation were very similar in THF- and propane-grown mycelia.
SomeListeria monocytogenesOutbreak Strains Demonstrate Significantly Reduced Invasion,inlATranscript Levels, and Swarming Motility In Vitro
Authors: Roberts A. J. , Williams S. K. , Wiedmann M. , Nightingale K. K.
Published: July 2009

Listeria monocytogenescan cause a severe invasive food-borne disease known as listeriosis, and large outbreaks of this disease occur occasionally. Based on molecular-subtype data, epidemic clone (EC) strains have been defined, including ECI and ECIa, which have caused listeriosis outbreaks on different continents. While a number of molecular-subtyping studies of outbreak strains have been reported, few comprehensive data sets of virulence-associated characteristics of these strains are available. We assembled a set of human clinical isolates from 15 outbreaks that occurred worldwide between 1975 and 2002. Initial characterization of these strains showed significant variation in the ability to invade human Caco-2 intestinal epithelial cells and HepG2 hepatic cells; four strains showed consistently reduced invasion in both cell lines. DNA sequencing ofinlA, which encodes a protein required for efficient Caco-2 and HepG2 invasion, showed that none of the invasion-attenuated strains contained known virulence-attenuating mutations ininlA. Phylogenetic analyses ofinlAsequences revealed a well-supported clade containing a fully invasive ECI strain and three invasion-attenuated ECI strains, along with a fully invasive ECIa strain and an invasion-attenuated ECIa strain. Of the four invasion-attenuated strains, one strain showed both reducedinlAtranscript levels and impaired swarming, one strain showed reducedinlAtranscript levels, and two strains showed reduced swarming. Overall, our data show that (i)L. monocytogenesstrains from outbreaks vary significantly in invasion efficiency and (ii) different mechanisms may contribute to reduced invasion efficiency. Association between EC strains and listeriosis outbreaks may involve characteristics other than virulence phenotypes, including survival and growth in food-associated environments.
Pulsed-Field Gel Electrophoresis Profile Changes Resulting from Spontaneous Chromosomal Deletions in Enterohemorrhagic
Escherichia coli
O157:H7 during Passage in Cattle
Authors: Yoshii Noriyo , Ogura Yoshitoshi , Hayashi Tetsuya , Ajiro Takashi , Sameshima Toshiya , Nakazawa Muneo , Kusumoto Masahiro , Iwata Taketoshi , Akiba Masato
Published: July 2009

A total of 905 enterohemorrhagic
Escherichia coli
(EHEC) O157:H7 isolates that were recovered from experimentally infected cattle, in addition to the inoculated strain, were analyzed by pulsed-field gel electrophoresis (PFGE). Twelve PFGE profiles other than that of the inoculated strain were observed. We successfully identified five distinct chromosomal deletions that affected the PFGE profiles using whole-genome PCR scanning and DNA sequencing analysis. The changes in PFGE profiles of EHEC O157:H7 isolates after passage through the intestinal tract of cattle were partially generated by deletion of chromosomal regions.
Development of an Improved Isolation Approach and Simple Sequence Repeat Markers To Characterize
Phytophthora capsici
Populations in Irrigation Ponds in Southern Georgia
Authors: Wang Ziying , Langston David B. , Csinos Alexander S. , Gitaitis Ronald D. , Walcott Ronald R. , Ji Pingsheng
Published: July 2009

Phytophthora capsici
, the causal agent of
Phytophthora
blight, is a major concern in vegetable production in Georgia and many other states in the United States. Contamination of irrigation water sources by
P. capsici
may be an important source of inoculum for the pathogen. A simple method was developed in this study to improve the efficiency of recovering
P. capsici
from fruits used as baits in irrigation ponds. In contrast to direct isolation on agar plates, infected fruit tissues were used to inoculate stems of pepper seedlings, and the infected pepper stems were used for isolation on agar plates. With isolation through inoculation of pepper stems, the frequency of recovering
P. capsici
from infected eggplant and pear fruits increased from 13.9% to 77.7% and 8.1% to 53.5%, respectively, compared with direct isolation on agar plates.
P. capsici
was isolated from seven out of nine irrigation ponds evaluated, with most of the ponds containing both A1 and A2 mating types and a 4:5 ratio of A1 to A2 when isolates from all ponds were calculated. All
P. capsici
isolates were pathogenic on squash plants, and only a small proportion (8.2%) of the isolates were resistant or intermediately sensitive to mefenoxam. Simple sequence repeats (SSRs) were identified through bioinformatics mining of 55,848 publicly available expressed sequence tags of
P. capsici
in dbEST GenBank. Thirty-one pairs of SSR primers were designed, and SSR analysis indicated that the 61
P. capsici
isolates from irrigation ponds were genetically distinct. Cluster analysis separated the isolates into five genetic clusters with no more than two genetic groups in one pond, indicating relatively low
P. capsici
genetic diversity in each pond. The isolation method and SSR markers developed for
P. capsici
in this study could contribute to a more comprehensive understanding of the genetic diversity of this important pathogen.
Protein Engineering of the Transcriptional Activator FhlA To Enhance Hydrogen Production in
Escherichia coli
Authors: Sanchez-Torres Viviana , Maeda Toshinari , Wood Thomas K.
Published: July 2009

Escherichia coli
produces H
2
from formate via the formate hydrogenlyase (FHL) complex during mixed acid fermentation; the FHL complex consists of formate dehydrogenase H (encoded by
fdhF
) for forming 2H
+
, 2e
−
, and CO
2
from formate and hydrogenase 3 (encoded by
hycGE
) for synthesizing H
2
from 2H
+
and 2e
−
. FHL protein production is activated by the σ
54
transcriptional activator FhlA, which activates transcription of
fdhF
and the
hyc
,
hyp
, and
hydN-hypF
operons. Here, through random mutagenesis using error-prone PCR over the whole gene, as well as over the
fhlA
region encoding the first 388 amino acids of the 692-amino-acid protein, we evolved FhlA to increase H
2
production. The amino acid replacements in FhlA133 (Q11H, L14V, Y177F, K245R, M288K, and I342F) increased hydrogen production ninefold, and the replacements in FhlA1157 (M6T, S35T, L113P, S146C, and E363K) increased hydrogen production fourfold. Saturation mutagenesis at the codons corresponding to the amino acid replacements in FhlA133 and at position E363 identified the importance of position L14 and of E363 for the increased activity; FhlA with replacements L14G and E363G increased hydrogen production (fourfold and sixfold, respectively) compared to FhlA. Whole-transcriptome and promoter reporter constructs revealed that the mechanism by which the FhlA133 changes increase hydrogen production is by increasing transcription of all of the genes activated by FhlA (the FHL complex). With FhlA133, transcription of P

fdhF

and P

hyc

is less sensitive to formate regulation, and with FhlA363 (E363G), P

hyc

transcription increases but P

hyp

transcription decreases and hydrogen production is less affected by the repressor HycA.
Application of a Short Intracellular pH Method to Flow Cytometry for Determining
Saccharomyces cerevisiae
Vitality
Authors: Weigert Claudia , Steffler Fabian , Kurz Tomas , Shellhammer Thomas H. , Methner Frank-Jürgen
Published: July 2009

The measurement of yeast's intracellular pH (ICP) is a proven method for determining yeast vitality. Vitality describes the condition or health of viable cells as opposed to viability, which defines living versus dead cells. In contrast to fluorescence photometric measurements, which show only average ICP values of a population, flow cytometry allows the presentation of an ICP distribution. By examining six repeated propagations with three separate growth phases (lag, exponential, and stationary), the ICP method previously established for photometry was transferred successfully to flow cytometry by using the pH-dependent fluorescent probe 5,6-carboxyfluorescein. The correlation between the two methods was good (
r
2
= 0.898,
n
= 18). With both methods it is possible to track the course of growth phases. Although photometry did not yield significant differences between exponentially and stationary phases (
P
= 0.433), ICP via flow cytometry did (
P
= 0.012). Yeast in an exponential phase has a unimodal ICP distribution, reflective of a homogeneous population; however, yeast in a stationary phase displays a broader ICP distribution, and subpopulations could be defined by using the flow cytometry method. In conclusion, flow cytometry yielded specific evidence of the heterogeneity in vitality of a yeast population as measured via ICP. In contrast to photometry, flow cytometry increases information about the yeast population's vitality via a short measurement, which is suitable for routine analysis.
Potentially Pathogenic Bacteria in Shower Water and Air of a Stem Cell Transplant Unit
Authors: Perkins Sarah D. , Mayfield Jennie , Fraser Victoria , Angenent Largus T.
Published: July 2009

Potential pathogens from shower water and aerosolized shower mist (i.e., shower aerosol) have been suggested as an environmental source of infection for immunocompromised patients. To quantify the microbial load in shower water and aerosol samples, we used culture, microscopic, and quantitative PCR methods to investigate four shower stalls in a stem cell transplant unit at Barnes-Jewish Hospital in St. Louis, MO. We also tested membrane-integrated showerheads as a possible mitigation strategy. In addition to quantification, a 16S rRNA gene sequencing survey was used to characterize the abundant bacterial populations within shower water and aerosols. The average total bacterial counts were 2.2 × 10
7
cells/liter in shower water and 3.4 × 10
4
cells/m
3
in shower aerosol, and these counts were reduced to 6.3 × 10
4
cells/liter (99.6% efficiency) and 8.9 × 10
3
cells/m
3
(82.4% efficiency), respectively, after membrane-integrated showerheads were installed. Potentially pathogenic organisms were found in both water and aerosol samples from the conventional showers. Most notable was the presence of
Mycobacterium mucogenicum
(99.5% identity) in the water and
Pseudomonas aeruginosa
(99.3% identity) in the aerosol samples. Membrane-integrated showerheads may protect immunocompromised patients from waterborne infections in a stem cell transplant unit because of efficient capture of vast numbers of potentially pathogenic bacteria from hospital water. However, an in-depth epidemiological study is necessary to investigate whether membrane-integrated showerheads reduce hospital-acquired infections. The microbial load in shower aerosols with conventional showerheads was elevated compared to the load in HEPA-filtered background air in the stem cell unit, but it was considerably lower than typical indoor air. Thus, in shower environments without HEPA filtration, the increase in microbial load due to shower water aerosolization would not have been distinguishable from anticipated variations in background levels.
Bacterial Chemotaxis to Atrazine and Relateds-Triazines
Authors: Liu Xianxian , Parales Rebecca E.
Published: July 2009

Pseudomonassp. strain ADP utilizes the human-mades-triazine herbicide atrazine as the sole nitrogen source. The results reported here demonstrate that atrazine and the atrazine degradation intermediatesN-isopropylammelide and cyanuric acid are chemoattractants for strain ADP. In addition, the nonmetabolizeds-triazine ametryn was also an attractant. The chemotactic response to theses-triazines was not specifically induced during growth with atrazine, and atrazine metabolism was not required for the chemotactic response. A cured variant of strain ADP (ADP M13-2) was attracted tos-triazines, indicating that the atrazine catabolic plasmid pADP-1 is not necessary for the chemotactic response and that atrazine degradation and chemotaxis are not genetically linked. These results indicate that atrazine and relateds-triazines are detected by one or more chromosomally encoded chemoreceptors inPseudomonassp. strain ADP. We demonstrated thatEscherichia coliis attracted to thes-triazine compoundsN-isopropylammelide and cyanuric acid, and anE. colimutant lacking Tap (the pyrimidine chemoreceptor) was unable to respond tos-triazines. These data indicate that pyrimidines and triazines are detected by the same chemoreceptor (Tap) inE. coli. We showed thatPseudomonassp. strain ADP is attracted to pyrimidines, which are the naturally occurring structures closest to triazines, and propose that chemotaxis towards-triazines may be due to fortuitous recognition by a pyrimidine chemoreceptor inPseudomonassp. strain ADP. In competition assays, the presence of atrazine inhibited chemotaxis ofPseudomonassp. strain ADP to cytosine, and cytosine inhibited chemotaxis to atrazine, suggesting that pyrimidines ands-triazines are detected by the same chemoreceptor.
Carbohydrate Metabolism Differences between Subgroup A1 and B2 Strains of
B
acillus anthracis
as Assessed by Comparative Genomics and Functional Genetics
Authors: Sylvestre Patricia , Moya Mary , Haustant Michel , Vaissaire Josée , Mock Michèle
Published: July 2009

In France,
Bacillus anthracis
subgroup B2 strains do not metabolize starch or glycogen but can use gluconate, whereas subgroup A1 strains show the inverse pattern. Functional genetic analysis revealed that mutations in the
amyS
and
gntK
genes encoding an alpha-amylase and a gluconate kinase, respectively, were responsible for these phenotypes.
Single Nucleotide Polymorphism-Based Diagnostic System for Crop-Associated
Sclerotinia
Species
Authors: Andrew Marion , Kohn Linda M.
Published: July 2009

A molecular diagnostic system using single nucleotide polymorphisms (SNPs) was developed to identify four
Sclerotinia
species:
S. sclerotiorum
(Lib.) de Bary,
S. minor
Jagger,
S. trifoliorum
Erikss., and the undescribed species
Sclerotinia
species 1. DNAs of samples are hybridized with each of five 15-bp oligonucleotide probes containing an SNP site midsequence unique to each species. For additional verification, hybridizations were performed using diagnostic single nucleotide substitutions at a 17-bp sequence of the calmodulin locus. The accuracy of these procedures was compared to that of a restriction fragment length polymorphism (RFLP) method based on Southern hybridizations of EcoRI-digested genomic DNA probed with the ribosomal DNA-containing plasmid probe pMF2, previously shown to differentiate
S. sclerotiorum
,
S. minor
, and
S. trifoliorum.
The efficiency of the SNP-based assay as a diagnostic test was evaluated in a blind screening of 48
Sclerotinia
isolates from agricultural and wild hosts. One isolate of
Botrytis cinerea
was used as a negative control. The SNP-based assay accurately identified 96% of
Sclerotinia
isolates and could be performed faster than RFLP profiling using pMF2. This method shows promise for accurate, high-throughput species identification.
H
2
O
2
Activates the Nuclear Localization of Msn2 and Maf1 through Thioredoxins in
Saccharomyces cerevisiae
Authors: Boisnard Stéphanie , Lagniel Gilles , Garmendia-Torres Cecilia , Molin Mikael , Boy-Marcotte Emmanuelle , Jacquet Michel , Toledano Michel B. , Labarre Jean , Chédin Stéphane
Published: July 2009

The cellular response to hydrogen peroxide (H
2
O
2
) is characterized by a repression of growth-related processes and an enhanced expression of genes important for cell defense. In budding yeast, this response requires the activation of a set of transcriptional effectors. Some of them, such as the transcriptional activator Yap1, are specific to oxidative stress, and others, such as the transcriptional activators Msn2/4 and the negative regulator Maf1, are activated by a wide spectrum of stress conditions. How these general effectors are activated in response to oxidative stress remains an open question. In this study, we demonstrate that the two cytoplasmic thioredoxins, Trx1 and Trx2, are essential to trigger the nuclear accumulation of Msn2/4 and Maf1, specifically under H
2
O
2
treatment. Contrary to the case with many stress conditions previously described for yeast, the H
2
O
2
-induced nuclear accumulation of Msn2 and Maf1 does not correlate with the downregulation of PKA kinase activity. Nevertheless, we show that PP2A phosphatase activity is essential for driving Maf1 dephosphorylation and its subsequent nuclear accumulation in response to H
2
O
2
treatment. Interestingly, under this condition, the lack of PP2A activity has no impact on the subcellular localization of Msn2, demonstrating that the H
2
O
2
signaling pathways share a common route through the thioredoxin system and then diverge to activate Msn2 and Maf1, the final integrators of these pathways.