bluuebunny/crossref_metadata_2025 huggingface dataset:
Platelet function in paediatric patients undergoing surgery for cyanotic congenital heart defects
Authors: Rivo J. , Gozal Y. , Raushenbach M. , Varon D. , Katz J.
Published: November 2006

Introduction:  Coagulation abnormalities accompany cardiac surgery in children with cyanotic congenital heart defects (CHD). However the state of primary haemostasis in such patients remains insufficiently investigated.

Methods:  This study conforms to the principles of the Declaration of Helsinki. Nineteen pediatric patients aged 7 days–10 years with cyanotic CHD undergoing correction surgery were enrolled in the study. Citrated venous blood was taken at three points – prior to operation, after termination of cardiopulmonary bypass and neutralization of heparin by protamine and on postoperative day two. Optical platelet aggregometry with adenosine diphosphate, epinephrine, collagen and ristocetin as platelets agonists was used. The results were calculated statistically using Student's t‐test.

Results:  Our results demonstrate that ADP‐induced platelet aggregation was markedly reduced after operation (73.2 ± 19 vs 43.2 ± 24.9; P < 0.005). Similar results were obtained for epinephrine (56.7 ± 28.9 vs 31 ± 29.4; P < 0.05) and ristocetin‐induced platelet aggregation (90.3 ± 25.6 vs 59 ± 21.4; P < 0.001), whereas the effect of collagen had a trend to decrease remaining however statistically insignificant (53.6 ± 40.4 vs 31.2 ± 34.3; P < 0.2). Both haemoglobin and haematocrit levels remained unchanged, whereas platelet count dramatically decreased (from 339.4 ± 159.4 to 138.9 ± 80.3; P < 0.001) that can potentially be explained by platelet destruction during cardiopulmonary bypass. On the second postoperative day, the amount of platelets remained unchanged (180.8 ± 102.0; P > 0.5) whereas platelet aggregation returned to the initial values (77.1 ± 14.2, 73.6 ± 17.1 and 81.0 ± 12.8 for ADP, epinephrine and ristocetin‐induced aggregation, respectively; in all cases P > 0.1 compared with the level before operation). Haemoglobin and haematorcrit levels were similar after operation and on the second day.

Discussion:  As stated in the results section, platelet aggregation recovers on the second postoperative day whereas platelet count remains relatively low. Consequently, changes in platelet aggregation observed immediately after operation cannot be explained only by the decrease in platelet count.

Conclusions:  (i) Platelet aggregation induced by different agonists, as well as platelet count, decrease in children with cyanotic CHD immediately after operation; and (ii) platelet aggregation but not platelet count recovers on the second postoperative day.
Carbohydrate characterization of quail primordial germ cells during migration and gonadal differentiation
Authors: Armengol Clara , Carretero Ana , Nacher Víctor , Ruberte Jesús , Navarro Marc
Published: November 2006

A selection of lectins were used to study changes in the distribution of sugar residues in primordial germ cells (PGCs) during gonadal colonization and differentiation. Although the cytochemical characteristics of PGCs have been described in the chick, little is known about such characteristics in other avian species of interest to experimental biology. Therefore, we studied embryos of Japanese quail (Coturnix coturnix japonica) by light and laser confocal scanning microscopy, using the QH1 antibody as a tool to identify PGCs in both sexes and at all stages. LEA, WGA and RCA‐I bound to PGCs in a similar way to QH1. LEA was the best marker for all stages. The presence of acid phosphatase and the intense reaction of LEA, WGA, RCA‐I and WFA at the cell surface were shown to be a useful tool in the study of the migratory PGCs of the quail. Quails were sexed histologically in younger embryos than in chick; results were confirmed by PCR. The lectin‐binding pattern changed drastically in differentiated gonads. Cell surface reactivity was almost entirely lost. Quail differentiating oogonia showed a characteristic binding pattern to QH1 and to the lectins WGA, RCA‐I and WFA. Binding was observed in intense spots in the Golgi complex, and there was a specific PNA reaction. These results suggest that some selective sugar binding sites on the PGCs play a significant role in their migration, colonization and maturation.
Hazardous Waste Incineration at Sea: EPA Decision Making on Risk
Authors: Ditz Daryl W.
Published: November 2006

This paper critiques the Environmental Protection Agency's assessment of risk for hazardous waste incineration at sea. It reviews operational and transportation risks and considers alternative approaches for managing chlorinated organic hazardous wastes. It concludes that depending on the scale of the program, ocean incineration will either contribute little to the overall management of this waste stream or else it will engender significant risks, especially in the coastal environment. Furthermore, past assessments on the part of EPA have tended to understate the risks of incineration at sea while simultaneously holding out the promise of the technology as a commercial‐scale management option. Finally, this paper observes that the Western European countries that pioneered incineration in the North Sea are now finding practical alternatives. It is recommended that waste reuse, on‐site treatment, and techniques of waste reduction provide viable alternatives and obviate the need for incineration at sea.
Comprehensive Review of Campylobacter and Poultry Processing
Authors: Keener K.M. , Bashor M.P. , Curtis P.A. , Sheldon B.W. , Kathariou S.
Published: November 2006

Campylobacter has been recognized as a leading bacterial cause of human gastroenteritis in the United States, with 40000 documented cases annually. Epidemiological data suggest that contaminated products of animal origin, especially poultry, contribute significantly to campylobacteriosis. Thus, reduction of contamination of raw poultry would have a large impact in reducing incidence of illness. Contamination occurs both on the farm and in poultry slaughter plants. Routine procedures on the farm such as feed withdrawal, poultry handling, and transportation practices have a documented effect on Campylobacter levels at the processing plant. At the plant, defeathering, evisceration, and carcass chillers have been documented to cross‐contaminate poultry carcasses. Carcass washings and the application of processing aids have been shown to reduce populations of Campylobacter in the carcasses by log10 0.5 log10 1.5; however, populations of Campylobacter have been shown to enter a poultry processing plant at levels between log10 5 colony‐forming units (CFU)/mL and log10 8 CFU/mL of carcass rinse. The purpose of this article is to review Campylobacter, the infection that it causes, its association with poultry, contamination sources during processing, and intervention methods.
Distinct fluvial and adfluvial migration patterns of a relict charr, Salvelinus confluentus, stock in a mountainous watershed, Idaho, USA
Authors: Hogen D. M. , Scarnecchia D. L.
Published: November 2006

Abstract –  Sixty‐five large (>385 mm fork length) bull trout (Salvelinus confluentus), a threatened relict charr (Family Salmonidae), were captured in the upper East Fork South Fork Salmon River (EFSFSR), Idaho, USA and implanted with radio tags to investigate their spatial and temporal movements and distribution throughout the South Fork Salmon River (SFSR) basin and beyond. All radio‐tagged fish were migratory. Most fish displayed a fluvial migration pattern. They typically overwintered in the larger rivers downriver of the EFSFSR (SFSR and the Salmon River further downstream), migrated upriver to the EFSFSR in June and further upriver into small (<2 m wide) tributaries to spawn in August and September. Both consecutive‐year and nonconsecutive‐year spawners were found. A typical migration distance between the overwintering habitat and the spawning habitat was 100 km. A minor fraction (<10%) of the fish displayed an adfluvial life history pattern, overwintering in a small (2 ha) 60‐year‐old flooded mine pit in the EFSFSR upstream of the spawning tributaries. The stock exhibited distinct site fidelity for spawning and overwintering. Similar fluvial and adfluvial migration patterns have been reported for bull trout in the region as well as for other charr species worldwide. Effective management of this and other migratory charr stocks will require protection of a wide range of habitats, from large rivers to the smallest tributaries.
Nonlinear Strain Hardening Model for Predicting Clamp Load Loss in Bolted Joints
Authors: Nassar Sayed A. , Matin Payam H.
Published: November 2006

Closed form solution for the amount of clamp load loss due to an externally applied separating force is determined for a bolted assembly in which the fastener is initially tightened beyond its proportional limit. The joint may or may not have been yielded at initial assembly, however. After the initial tightening of the fastener, the joint is subsequently subjected to a tensile separating force, which further increases the fastener tensile stress into the nonlinear range. Such a separating force will simultaneously reduce the clamping force in the bolted joint. Upon the removal of the separating service load, the bolted joint system reaches a new equilibrium point between the fastener tension and the joint clamping force. At the new equilibrium point, the fastener tension is reduced from its value at initial assembly, due to the plastic elongation of the fastener. The reduction in fastener tension translates into a partial—yet permanent—loss of the clamping load, which may lead to joint leakage, loosening, or fatigue failure. A nonlinear strain hardening model is implemented in order to describe the fastener behavior past the proportional limit of its material, and to determine the clamp load loss due to the permanent set in the fastener after the separating force has been removed. In order to study the effect of strain hardening, various rates of strain hardening are used for modeling the behavior of the fastener material. The effect of three nondimensional variables on the amount of clamp load loss is investigated. This includes the joint-to-fastener stiffness ratio, the ratio of initial fastener tension to its elastic limit, and the ratio of the separating force to its maximum value that would cause joint separation to start. Analytical results are presented for a range of stiffness ratios that simulates both soft and hard joint applications.
Mobility of Single-Loop N-Bar Linkage With Active/Passive Prismatic Joints
Authors: Guo W. Z. , Du R.
Published: November 2006

Single-loop N-bar linkages that contain one prismatic joint are common in engineering. This type of mechanism often requires complicated control and, hence, understanding its mobility is very important. This paper presents a systematic study on the mobility of this type of mechanism by introducing the concept of virtual link. It is found that this type of mechanism can be divided into three categories: Class I, Class II, and Class III. For each category, the slide reachable range is cut into different regions: Grashof region, non-Grashof region, and change-point region. In each region, the rotation range of the revolute joint or rotatability of the linkage can be determined based on Ting’s criteria. The characteristics charts are given to describe the rotatability condition. Furthermore, if the prismatic joint is an active joint, the revolvability of the input revolute joint is dependent in non-Grashof region but independent in other regions. If the prismatic joint is a passive joint, the revolvability of the input revolute joint is dependent on the offset distance of the prismatic joint. Two examples are given to demonstrate the presented method. The new method is able to cover all the cases of N-bar planar linkages with one or a set of adjoined prismatic joints. It can also be used to study N-bar open-loop planar robotic mechanisms.
Synthesis of Bistable Periodic Structures Using Topology Optimization and a Genetic Algorithm
Authors: Prasad J. , Diaz A. R.
Published: November 2006

A formulation for the automatic synthesis of two-dimensional bistable, compliant periodic structures is presented, based on standard methods for topology optimization. The design space is parametrized using nonlinear beam elements and a ground structure approach. A performance criterion is suggested, based on characteristics of the load-deformation curve of the compliant structure. A genetic algorithm is used to find candidate solutions. A numerical implementation of this methodology is discussed and illustrated using simple examples.
Computation of Member Stiffness in the Design of Bolted Joints
Authors: Musto Joseph C. , Konkle Nicholas R.
Published: November 2006

In designing bolted connections in machinery applications, it is necessary to estimate the stiffness of the clamped members. The method of Wileman et al. (Wileman, J., Choudhury, M., and Green, I., 1991, ASME J. of Mech. Des., 113, pp. 432–437) has become a standard approach to estimating the member stiffness. In this method, finite element studies are used to estimate the stiffness of the clamped members of a single material type. In this paper, the studies performed by Wileman et al. (Wileman, J., Choudhury, M., and Green, I., 1991, ASME J. of Mech. Des., 113, pp. 432–437) are extended to include the case where the clamped members are of different material types. Results for a steel/aluminum joint are presented in detail, and a generalized technique for estimating the member stiffness for any material combination is derived. The method developed in this brief is shown to provide accurate estimates of member stiffness over a range of aspect ratios and joint compositions.
A Note on the Diagonalizability and the Jordan Form of the 4×4 Homogeneous Transformation Matrix
Authors: Deepak R Sangamesh , Ghosal Ashitava
Published: November 2006

The 4×4 homogeneous transformation matrix is extensively used for representing rigid body displacement in 3D space and has been extensively used in the analysis of mechanisms, serial and parallel manipulators, and in the field of geometric modeling and computed aided design. The properties of the transformation matrix are very well known. One of the well known properties is that a general 4×4 homogeneous transformation matrix cannot be diagonalized, and at best can be reduced to a Jordan form. In this paper, we show that the 4×4 homogeneous transformation matrix can be diagonalized if and only if displacement along the screw axis is zero. For the general transformation with nonzero displacement along the axis, we present an explicit expression for the fourth basis vector of the Jordan basis. We also present a variant of the Jordan form which contains the motion variables along and about the screw axis and the corresponding basis vectors which contains the information only about the screw axis and its location. We present a novel expression for a point on the screw axis closest to the origin, which is then used to form a simple choice of basis for different forms. Finally, the theoretical results are illustrated with a numerical example.
Influences of The Type and Thickness of Electrolyte on Solid Oxide Fuel Cell Hybrid System Performance
Authors: Milewski Jaroslaw , Miller Andrzej
Published: November 2006

This paper sets out the results of mathematical modeling and numerical simulations with regard to the influences of the type and thickness of electrolyte on Solid Oxide Fuel Cell Hybrid System (SOFC-HS) performance. A change of electrolyte materials can result in total hybrid system efficiency increasing from around 48% HHV (53% LHV) to about 65% HHV (72% LHV) in an environment where turbine inlet temperature and gas turbine subsystem pressure ratio remain unchanged. The governing equations of SOFC-HS modeling are given. An adequate simulator of the SOFC stack was made and described. Based on this simulator, a model of the 260kWe Siemens Westinghouse unit was built. The performance of this SOFC-HS with different electrolyte materials and thicknesses is shown, and some characteristics are given and described. The advantages and disadvantages of different electrolyte types from a hybrid system performance point of view are indicated.
Rotating Disk Electrode Study of Supported and Unsupported Catalysts for PEMFC Application
Authors: Dundar F. , Smirnova A. , Dong X. , Ata A. , Sammes N.
Published: November 2006

The electrochemical study of different supported and unsupported Pt-based catalysts used in polymer electrolyte fuel cells (PEMFCs) has been made by means of thin film rotating disk electrode (RDE) method. The comparison of electrochemical surface area (ESA) was made using cyclic voltammetry measurements in H2SO4 or HClO4 at room temperature and scanning rates of 20 and 100mV∕s. Oxygen reduction activity for aerogel-supported and carbon-supported Pt catalysts was evaluated at various rotation speeds in the range of 0-2500rpm and compared to the catalytic activity of unsupported Pt-black catalyst. The calculated values of Levich constant for the oxygen reduction reaction (ORR) indicate dependence on the applied voltage and either 4 or 2–4 electron transfer mechanism. The hydrogen peroxide by-product formation was determined with a rotating ring disk electrode (RRDE) and was observed to take place mostly at voltages below 0.6V due to the limitations from mass transport effects. The results obtained at different Pt loadings in the range of 10-46.5wt% Pt demonstrated that XC-72 and aerogel-based catalysts are foreseen to have higher ESA in comparison to other tested supported and unsupported commercially available catalysts.
SIMULINK-FEMLAB Integrated Dynamic Simulation Model for a PEM Fuel Cell System
Authors: Radu R. , Taccani R.
Published: November 2006

The necessity for reliable simulation models, able to support the fuel cell systems development activity, has increased continuously during the last years. The present work proposes a model which integrates the finite element method in a dynamic simulation, in order to achieve higher accuracy and the possibility to investigate the influence of various parameters on the fuel cell dynamics. The model is implemented using MATLAB/SIMULINK and consists of two interacting main subsystems that calculates the fuel cell power response and the stack thermal behavior. The first simulates the mass transport and electrochemical phenomena using a model implemented in FEMLAB, and considers as input parameters the stack geometry, reactants pressure, flow rate and composition, and the stack average temperature. The last parameter is also evaluated by the second model, implemented also in FEMLAB, which considers the stack geometry, cooling air flow rate and ambient temperature. Both models were validated using the experimental data acquired on a Ballard Nexa 1.5kWe proton exchange membrane (PEM) system. The results prove that integrated model simulates with accuracy the dynamics of the proton exchange membrane fuel cell type (PEMFC) system and the interaction between the stack and the auxiliaries. The proposed model was used as a predictive tool for two situations. In the first simulation, with a relative fast dynamic, the model demonstrates that the cooling fan control strategy is essential for transient conditions characterized by a significant load decreasing. In the second, the model estimates the variation of the PEMFC main parameters on a 24h cycle, confirming its reliability.
Investigation of the Reaction of Ethanol-Steam Mixtures in a YSZ Electrochemical Reactor Operated in a Fuel Cell Mode
Authors: Poulianitis Constantinos , Maragou Vasiliki , Yan Aiyu , Song Shuqin , Tsiakaras Panagiotis
Published: November 2006

In the present investigation ethanol-water mixtures were directly fed to a yttria stabilized zirconia (YSZ) electrochemical reactor operated in a fuel cell mode and the preliminary results are presented and discussed. Polycrystalline films of platinum (Pt) and silver (Ag) were, respectively, tested as anode catalysts in a wide range of experimental conditions while the cathode was exposed to the atmospheric air. The single direct ethanol solid oxide fuel cell (DE-SOFC) tests were performed in order to investigate separately Pt and Ag’s activities towards ethanol steam reaction and fuel cell performance (Pt‐DESOFC and Ag‐DESOFC). In both cases the products were on-line analyzed by a mass spectrograph, a gas chromatograph and a series of gas analysers under fuel cell mode of operation. The results showed that even at high temperature values (>750°C) the main products were CH3CHO, CH4, CO, H2, and CO2. Furthermore, as expected the single DESOFC performance was improved as the temperature increased. However, a relatively poor fuel cell performance has been obtained in both cases, which could be attributed to the following reasons: the relatively low (for YSZ electrolyte) operation temperature, the presence of homogeneous reactions, and the cell configuration.
Aerogel-Based PEMFC Catalysts Operating at Room Temperature
Authors: Smirnova A. , Dong X. , Hara H. , Sammes N.
Published: November 2006

A carbon-aerogel-supported Pt catalyst with 22nm pore size distribution and low Pt loading (0.1mg∕cm2) has been tested in a proton exchange membrane fuel cell (PEMFC). The performance of the PEMFC and kinetic parameters of the catalyst at room temperature are discussed in terms of microstructure of the support and sulfonated tetrafluoroethylene (Nafion) distribution. The PEMFCs demonstrated power densities up to 0.5mW∕cm2 at 0.6V in air∕hydrogen and 2atm backpressure on both cathode and anode. Continuous cycling with upper potential sweep limits of 1.0 and 1.2V leads to degradation effects that result in decreasing of the electrochemical surface area (ESA) of the catalyst. The comparison of an ESA decrease for a 1.0 and 1.2V sweep limit after 1000cycles indicated that the higher degradation effects are due to the oxidation of carbon support.
Reduction and Reoxidation Processes of NiO∕YSZ Composite for Solid Oxide Fuel Cell Anodes
Authors: Modena Stefano , Ceschini Sergio , Tomasi Andrea , Montinaro Dario , Sglavo Vincenzo M.
Published: November 2006

Solid oxide fuel cells (SOFCs) are an emerging technology in hydrogen-based energy production, thanks to their high performance, high power density, high efficiency, and reduced emissions over conventional power generation technologies. For these reasons, a great attention has been addressed in these years to SOFCs materials and technologies. An important issue related to the utilization of SOFCs as power generators is the capability of SOFCs materials to resist to thermal cycles in different atmospheres. The present work proposes an experimental investigation on the reduction process of NiO∕YSZ anode into Ni∕YSZ cermet, which is the best candidate for anode material in SOFCs, its reoxidation into NiO∕YSZ and the following rereduction into Ni∕YSZ. Anodes with different NiO∕YSZ ratios were analyzed through different physical and chemical techniques, such as scanning electron microscopy (SEM) and porosity measurements. The reduction, reoxidation and rereduction behaviors were studied by thermogravimetric analysis (TGA) in a unique long experiment, at different temperatures in the range of 700–800°C. The kinetics of the processes was studied and thermodynamic parameters such as activation energy were also calculated and correlated to the compositions and microstructure of the materials. The study clears up the effect of anode composition and microstructure on the reduction, reoxidation, and rereduction processes.
Fabrication and Performance of Anode-Supported Micro-Tubular Solid Oxide Fuel Cells
Authors: Pusz Jakub , Mohammadi Alidad , Sammes Nigel M.
Published: November 2006

A solid oxide fuel cell was fabricated using standard NiO/8YSZ cermet anode, 8mol% yttria stabilized zirconia (YSZ) electrolyte, and lanthanum strontium manganite cathode. The anodes were extruded using an hydraulic ram extruder. An electrolyte was deposited using a novel technique allowing obtaining a 3-5μm thin and dense YSZ layer. The cathode was deposited by brush painting. The cells were operated under different temperature and fuel conditions, and showed excellent performance of up approximately 0.6Wcm−2 at 890°C. Performance data as well as scanning electron microscopy micrographs of the cells are presented.
Teaching College Physics at the Local Elementary School
Authors: Hagedorn Eric A.
Published: November 2006

For several years physics faculty at the University of Texas at El Paso (UTEP) have taught physics to pre-service elementary and middle school teachers in an unusual location: the local elementary school! The participating pre-service elementary and middle school teachers are typically in their last semester and are fully immersed in their internships (called “student teaching” elsewhere. See Fig. 1). Rather than bringing the students back to campus for class during four of their field semesters, UTEP sends education, mathematics, and physics faculty out to the schools as part of what is referred to as the “field-based program” (FBP) even though some of this program occurs on campus.
Seeing the Light: Visibility of the July '45 Trinity Atomic Bomb Test from the Inner Solar System
Authors: Reed B. Cameron
Published: November 2006

In his The Making of the Atomic Bomb, Richard Rhodes remarks of the July 16, 1945, Trinity atomic bomb test in New Mexico that “had astronomers been watching they could have seen it reflected from the moon, literal moonshine,” an allusion to Ernest Rutherford's famous dismissal of the prospect of atomic energy.1 Investigating this impressive claim makes for a nice exercise in exploring astronomical magnitudes and leads to other intriguing questions: Just how bright would the explosion have appeared to an observer on the Moon, say, as compared to Venus? What about an observer on Mars or otherwise located in the solar system? What fraction of the bomb's yield was in the form of visible light?
Second-Generation Automatic Problem Grading
Authors: Greene Ronald L.
Published: November 2006

Recent years have seen widespread adoption of automatic grading of physics homework problems. Although first-generation homework management systems1–3 provide feedback and assign scores based only on the answers, problem-solving performance on exams seems to be no worse for students using these systems than for those who receive detailed comments from manually graded homework. Apparently immediate feedback, which encourages students to continue to work on a problem until they “get it right,” is as effective as detailed, but delayed, comments on a complete written solution. Second-generation homework systems should combine the two approaches by using immediate feedback in grading complete solutions.
Genes That Enhance the Ecological Fitness of
Shewanella oneidensis
MR-1 in Sediments Reveal the Value of Antibiotic Resistance
Authors: Groh Jennifer L. , Luo Qingwei , Ballard Jimmy D. , Krumholz Lee R.
Published: November 2006

Environmental bacteria persist in various habitats, yet little is known about the genes that contribute to growth and survival in their respective ecological niches. Signature-tagged mutagenesis (STM) of
Shewanella oneidensis
MR-1 coupled with a screen involving incubations of mutant strains in anoxic aquifer sediments allowed us to identify 47 genes that enhance fitness in sediments. Gene functions inferred from annotations provide us with insight into physiological and ecological processes that environmental bacteria use while growing in sediment ecosystems. Identification of the
mexF
gene and other potential membrane efflux components by STM demonstrated that homologues of multidrug resistance genes present in pathogens are required for sediment fitness of nonpathogenic bacteria. Further studies with a
mexF
deletion mutant demonstrated that the multidrug resistance pump encoded by
mexF
is required for resistance to antibiotics, including chloramphenicol and tetracycline. Chloramphenicol-adapted cultures exhibited mutations in the gene encoding a TetR family regulatory protein, indicating a role for this protein in regulating expression of the
mexEF
operon. The relative importance of
mexF
for sediment fitness suggests that antibiotic efflux may be a required process for bacteria living in sediment systems.
Novel Role for
Aeromonas jandaei
as a Digestive Tract Symbiont of the North American Medicinal Leech
Authors: Siddall Mark E. , Worthen Paul L. , Johnson Matthew , Graf Joerg
Published: November 2006

The gut bacteria of the North American medicinal leech,
Macrobdella decora
, were characterized. Biochemical tests and DNA sequences indicated that
Aeromonas jandaei
is the dominant culturable symbiont in leeches from a broad geographic area. In this work we identified a new habitat for
A. jandaei
, and here we suggest that there is unexpected specificity between leeches and
Aeromonas
species.
Degradation and Mineralization of Nanomolar Concentrations of the Herbicide Dichlobenil and Its Persistent Metabolite 2,6-Dichlorobenzamide by
Aminobacter
spp. Isolated from Dichlobenil-Treated Soils
Authors: Sørensen Sebastian R. , Holtze Maria S. , Simonsen Allan , Aamand Jens
Published: November 2006

2,6-Dichlorobenzamide (BAM), a persistent metabolite from the herbicide 2,6-dichlorobenzonitrile (dichlobenil), is the pesticide residue most frequently detected in Danish groundwater. A BAM-mineralizing bacterial community was enriched from dichlobenil-treated soil sampled from the courtyard of a former plant nursery. A BAM-mineralizing bacterium (designated strain MSH1) was cultivated and identified by 16S rRNA gene sequencing and fatty acid analysis as being closely related to members of the genus
Aminobacter
, including the only cultured BAM degrader,
Aminobacter
sp. strain ASI1. Strain MSH1 mineralized 15 to 64% of the added [
ring
-U-
14
C]BAM to
14
CO
2
with BAM at initial concentrations in the range of 7.9 nM to 263.1 μM provided as the sole carbon, nitrogen, and energy source. A quantitative enzyme-linked immunoassay analysis with antibodies against BAM revealed residue concentrations of 0.35 to 18.05 nM BAM following incubation for 10 days, corresponding to a BAM depletion of 95.6 to 99.9%. In contrast to the
Aminobacter
sp. strain ASI1, strain MSH1 also mineralized the herbicide itself along with several metabolites, including
ortho
-chlorobenzonitrile,
ortho
-chlorobenzoic acid, and benzonitrile, making it the first known dichlobenil-mineralizing bacterium.
Aminobacter
type strains not previously exposed to dichlobenil or BAM were capable of degrading nonchlorinated structural analogs. Combined, these results suggest that closely related
Aminobacter
strains may have a selective advantage in BAM-contaminated environments, since they are able to use this metabolite or structurally related compounds as a carbon and nitrogen source.
Biotransformation of Patulin by
Gluconobacter oxydans
Authors: Ricelli A. , Baruzzi F. , Solfrizzo M. , Morea M. , Fanizzi F. P.
Published: November 2006

A bacterium isolated from patulin-contaminated apples was capable of degrading patulin to a less-toxic compound, ascladiol. The bacterium was identified as
Gluconobacter oxydans
by 16S rRNA gene sequencing, whereas ascladiol was identified by liquid chromatography-tandem mass spectrometry and proton and carbon nuclear magnetic resonance. Degradation of up to 96% of patulin was observed in apple juices containing up to 800 μg/ml of patulin and incubated with
G. oxydans
.
Use of
Tetrahymena thermophila
To Study the Role of Protozoa in Inactivation of Viruses in Water
Authors: Pinheiro Marcel D. O. , Power Mary E. , Butler Barbara J. , Dayeh Vivian R. , Slawson Robin , Lee Lucy E. J. , Lynn Denis H. , Bols Niels C.
Published: November 2006

The ability of a ciliate to inactivate bacteriophage was studied because these viruses are known to influence the size and diversity of bacterial populations, which affect nutrient cycling in natural waters and effluent quality in sewage treatment, and because ciliates are ubiquitous in aquatic environments, including sewage treatment plants.
Tetrahymena thermophila
was used as a representative ciliate; T4 was used as a model bacteriophage. The T4 titer was monitored on
Escherichia coli
B in a double-agar overlay assay. T4 and the ciliate were incubated together under different conditions and for various times, after which the mixture was centrifuged through a step gradient, producing a top layer free of ciliates. The T4 titer in this layer decreased as coincubation time increased, but no decrease was seen if phage were incubated with formalin-fixed
Tetrahymena
. The T4 titer associated with the pellet of living ciliates was very low, suggesting that removal of the phage by
Tetrahymena
inactivated T4. When
Tetrahymena
cells were incubated with SYBR gold-labeled phage, fluorescence was localized in structures that had the shape and position of food vacuoles. Incubation of the phage and ciliate with cytochalasin B or at 4°C impaired T4 inactivation. These results suggest the active removal of T4 bacteriophage from fluid by macropinocytosis, followed by digestion in food vacuoles. Such ciliate virophagy may be a mechanism occurring in natural waters and sewage treatment, and the methods described here could be used to study the factors influencing inactivation and possibly water quality.
Morphogenesis of the
Bacillus anthracis
Spore
Authors: Giorno Rebecca , Bozue Joel , Cote Christopher , Wenzel Theresa , Moody Krishna-Sulayman , Mallozzi Michael , Ryan Matthew , Wang Rong , Zielke Ryszard , Maddock Janine R. , Friedlander Arthur , Welkos Susan , Driks Adam
Published: November 2006

Bacillus
spp. and
Clostridium
spp. form a specialized cell type, called a spore, during a multistep differentiation process that is initiated in response to starvation. Spores are protected by a morphologically complex protein coat. The
Bacillus anthracis
coat is of particular interest because the spore is the infective particle of anthrax. We determined the roles of several
B. anthracis
orthologues of
Bacillus subtilis
coat protein genes in spore assembly and virulence. One of these,
cotE
, has a striking function in
B. anthracis
: it guides the assembly of the exosporium, an outer structure encasing
B. anthracis
but not
B. subtilis
spores. However, CotE has only a modest role in coat protein assembly, in contrast to the
B. subtilis
orthologue.
cotE
mutant spores are fully virulent in animal models, indicating that the exosporium is dispensable for infection, at least in the context of a
cotE
mutation. This has implications for both the pathophysiology of the disease and next-generation therapeutics. CotH, which directs the assembly of an important subset of coat proteins in
B. subtilis
, also directs coat protein deposition in
B. anthracis
. Additionally, however, in
B. anthracis
, CotH effects germination; in its absence, more spores germinate than in the wild type. We also found that SpoIVA has a critical role in directing the assembly of the coat and exosporium to an area around the forespore. This function is very similar to that of the
B. subtilis
orthologue, which directs the assembly of the coat to the forespore. These results show that while
B. anthracis
and
B. subtilis
rely on a core of conserved morphogenetic proteins to guide coat formation, these proteins may also be important for species-specific differences in coat morphology. We further hypothesize that variations in conserved morphogenetic coat proteins may play roles in taxonomic variation among species.
Anaerobic Central Metabolic Pathways in
Shewanella oneidensis
MR-1 Reinterpreted in the Light of Isotopic Metabolite Labeling
Authors: Tang Yinjie J. , Meadows Adam L. , Kirby James , Keasling Jay D.
Published: November 2006

It has been proposed that during growth under anaerobic or oxygen-limited conditions,
Shewanella oneidensis
MR-1 uses the serine-isocitrate lyase pathway common to many methylotrophic anaerobes, in which formaldehyde produced from pyruvate is condensed with glycine to form serine. The serine is then transformed through hydroxypyruvate and glycerate to enter central metabolism at phosphoglycerate. To examine its use of the serine-isocitrate lyase pathway under anaerobic conditions, we grew
S. oneidensis
MR-1 on [1-
13
C]lactate as the sole carbon source, with either trimethylamine
N
-oxide (TMAO) or fumarate as an electron acceptor. Analysis of cellular metabolites indicated that a large percentage (>70%) of lactate was partially oxidized to either acetate or pyruvate. The
13
C isotope distributions in amino acids and other key metabolites indicate that under anaerobic conditions, although glyoxylate synthesized from the isocitrate lyase reaction can be converted to glycine, a complete serine-isocitrate pathway is not present and serine/glycine is, in fact, oxidized via a highly reversible degradation pathway. The labeling data also suggest significant activity in the anapleurotic (malic enzyme and phosphoenolpyruvate carboxylase) reactions. Although the tricarboxylic acid (TCA) cycle is often observed to be incomplete in many other anaerobes (absence of 2-oxoglutarate dehydrogenase activity), isotopic labeling supports the existence of a complete TCA cycle in
S. oneidensis
MR-1 under certain anaerobic conditions, e.g., TMAO-reducing conditions.
RamB, the Transcriptional Regulator of Acetate Metabolism in
Corynebacterium glutamicum
, Is Subject to Regulation by RamA and RamB
Authors: Cramer Annette , Auchter Marc , Frunzke Julia , Bott Michael , Eikmanns Bernhard J.
Published: November 2006

In
Corynebacterium glutamicum
, the transcriptional regulator RamB negatively controls the expression of genes involved in acetate metabolism. Here we show that RamB represses its own expression by direct interaction with a 13-bp motif in the
ramB
promoter region. Additionally,
ramB
expression is subject to carbon source-dependent positive control by RamA.
Derepression of Excision of Integrative and Potentially Conjugative Elements from
Streptococcus thermophilus
by DNA Damage Response: Implication of a cI-Related Repressor
Authors: Bellanger Xavier , Morel Catherine , Decaris Bernard , Guédon Gérard
Published: November 2006

A DNA-damaging agent, mitomycin C, derepresses the site-specific excision of two integrative and potentially conjugative elements from
Streptococcus thermophilus
, ICE
St1
and ICE
St3
. The regulation pathway involves a repressor related to phage lambda cI repressor. It could also involve a putative regulator related to another type of phage repressors, the “cI-like” repressors.
Genetic Characterization and Virulence Role of the RALP3/LSA Locus Upstream of the Streptolysin S Operon in Invasive M1T1 Group AStreptococcus
Authors: Kwinn Laura A. , Khosravi Arya , Aziz Ramy K. , Timmer Anjuli M. , Doran Kelly S. , Kotb Malak , Nizet Victor
Published: November 2006

Group AStreptococcus(GAS) is a leading human pathogen associated with a wide spectrum of mucosal and invasive infections. GAS expresses a large number of virulence determinants whose expression is under the control of several transcriptional regulatory networks. Here we performed the first mutational analysis of a genetic locus immediately upstream of the streptolysin S biosynthetic operon in several GAS genome sequences, including that of the M1T1 serotype, the leading isolates associated with serious invasive disease. The locus consists of a predicted RofA-like stand-alone transcriptional regulator (RALP3) and the largest open reading frame in the GAS genome, encoding a predicted LPXSG motif cell wall-anchored protein we have named LSA (for “large surface-anchored” protein). Comparative reverse transcription-PCR analysis of wild-type M1T1 GAS and an isogenic RALP3-deficient mutant identifies RALP3 as a global transcriptional regulator affecting expression of numerous virulence factor genes, including those for strong repression of the hyaluronic acid capsule and cysteine protease production. RALP3 contributed to GAS epithelial cell invasion and bloodstream survival. LSA was found to be under negative regulation by RALP3 and to influence GAS-epithelial cell interactions and GAS antimicrobial peptide sensitivity. Isogenic M1T1 GAS mutants lacking either RALP3 or LSA were attenuated in a murine model of systemic infection, indicating that this locus plays a role in the virulence potential of the organism.
Bacillus subtilis
Genome Diversity
Authors: Earl Ashlee M. , Losick Richard , Kolter Roberto
Published: November 2006

Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species
Bacillus subtilis
. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.
Translation Control of
trpG
from Transcripts Originating from the Folate Operon Promoter of
Bacillus subtilis
Is Influenced by Translation-Mediated Displacement of Bound TRAP, While Translation Control of Transcripts Originating from a Newly Identified
trpG
Promoter Is Not
Authors: Yakhnin Helen , Yakhnin Alexander V. , Babitzke Paul
Published: November 2006

Bacillus subtilis trpG
encodes a glutamine amidotransferase subunit that participates in the biosynthesis of both tryptophan and folic acid. TRAP inhibits translation of
trpG
in response to tryptophan by binding to a site that overlaps the
trpG
Shine-Dalgarno sequence, thereby blocking ribosome binding. Similar mechanisms regulate
trpP
and
ycbK
translation. The equilibrium binding constants of tryptophan-activated TRAP for the
trpG
,
ycbK
, and
trpP
transcripts were determined to be 8, 3, and 50 nM, respectively. Despite TRAP having a higher affinity for the
trpG
transcript, TRAP exhibited the least control of
trpG
expression. The
trpG
Shine-Dalgarno sequence overlaps the stop codon of the upstream
pabB
gene, while six of nine triplet repeats within the TRAP binding site are located upstream of the
pabB
stop codon. Thus, ribosomes translating the upstream
pabB
cistron could be capable of reducing TRAP-dependent control of TrpG synthesis by displacing bound TRAP. Expression studies using
pabB-trpG
′
-
′
lacZ
fusions in the presence or absence of an engineered stop codon within
pabB
suggest that translation-mediated displacement of bound TRAP reduces TRAP-dependent inhibition of TrpG synthesis from transcripts originating from the folate operon promoter (

P
pabB

). A new
trpG
promoter (

P
trpG

) was identified in the
pabB
coding sequence that makes a larger contribution to
trpG
expression than does

P
pabB

. We found that TRAP-dependent regulation of
trpG
expression is more extensive for a transcript originating from

P
trpG

and that transcripts originating from

P
trpG

are not subject to translation-mediated displacement of bound TRAP.
Functional Reconstitution of SdcS, a Na
+
-Coupled Dicarboxylate Carrier Protein from
Staphylococcus aureus
Authors: Hall Jason A. , Pajor Ana M.
Published: November 2006

In
Staphylococcus aureus
, the transport of dicarboxylates is mediated in part by the Na
+
-linked carrier protein SdcS. This transporter is a member of the divalent-anion/Na
+
symporter (DASS) family, a group that includes the mammalian Na
+
/dicarboxylate cotransporters NaDC1 and NaDC3. In earlier work, we cloned and expressed SdcS in
Escherichia coli
and found it to have transport properties similar to those of its eukaryotic counterparts (J. A. Hall and A. M. Pajor, J. Bacteriol.
187:
5189-5194, 2005). Here, we report the partial purification and subsequent reconstitution of functional SdcS into liposomes. These proteoliposomes exhibited succinate counterflow activity, as well as Na
+
electrochemical-gradient-driven transport. Examination of substrate specificity indicated that the minimal requirement necessary for transport was a four-carbon terminal dicarboxylate backbone and that productive substrate-transporter interaction was sensitive to substitutions at the substrate C-2 and C-3 positions. Further analysis established that SdcS facilitates an electroneutral symport reaction having a 2:1 cation/dicarboxylate ratio. This study represents the first characterization of a reconstituted Na
+
-coupled DASS family member, thus providing an effective method to evaluate functional, as well as structural, aspects of DASS transporters in a system free of the complexities and constraints associated with native membrane environments.
Identification of Diverse Archaeal Proteins with Class III Signal Peptides Cleaved by Distinct Archaeal Prepilin Peptidases
Authors: Szabó Zalán , Stahl Adriana Oliveira , Albers Sonja-V. , Kissinger Jessica C. , Driessen Arnold J. M. , Pohlschröder Mechthild
Published: November 2006

Most secreted archaeal proteins are targeted to the membrane via a tripartite signal composed of a charged N terminus and a hydrophobic domain, followed by a signal peptidase-processing site. Signal peptides of archaeal flagellins, similar to class III signal peptides of bacterial type IV pilins, are distinct in that their processing sites precede the hydrophobic domain, which is crucial for assembly of these extracytoplasmic structures. To identify the complement of archaeal proteins with class III signal sequences, a PERL program (FlaFind) was written. A diverse set of proteins was identified, and many of these FlaFind positives were encoded by genes that were cotranscribed with homologs of pilus assembly genes. Moreover, structural conservation of primary sequences between many FlaFind positives and subunits of bacterial pilus-like structures, which have been shown to be critical for pilin assembly, have been observed. A subset of pilin-like FlaFind positives contained a conserved
d
omain of
u
nknown
f
unction (DUF361) within the signal peptide. Many of the genes encoding these proteins were in operons that contained a gene encoding a novel
e
uryarchaeal
p
repilin-
p
eptidase, EppA, homolog. Heterologous analysis revealed that
Methanococcus maripaludis
DUF361-containing proteins were specifically processed by the EppA homolog of this archaeon. Conversely,
M. maripaludis
preflagellins were cleaved only by the archaeal preflagellin peptidase FlaK. Together, the results reveal a diverse set of archaeal proteins with class III signal peptides that might be subunits of as-yet-undescribed cell surface structures, such as archaeal pili.