bluuebunny/crossref_metadata_2025 huggingface dataset:
A SIMPLE PHOTOGRAMMETRIC TECHNIQUE TO MEASURE SPERM WHALES AT SEA
Authors: Jaquet Nathalie
Published: May 2006

Abstract

Knowledge of whale length is important to ecological studies. However, photographic techniques to measure sperm whales traditionally require high vantage points or a complicated stereo system. Furthermore, these traditional techniques require an alongside approach that often prevents individual identification. For simple and fast size measurements at sea, I used a laser range finder alongside a digital camera to obtain distance to the fluke at the same time as photo‐identification. The camera/lens and laser range finder were calibrated on objects of known lengths. The coefficient of variation (CV) for test objects was low (CV = 0.21%). Forty‐seven individually identified sperm whales were measured repetitively on up to 12 different occasions, and the CV was lower (CV = 1.3%) than for other photogrammetric techniques (CV = 4.4%–5.1%). A regression of log fluke span to log total length from whaling and stranding data yielded an r 2 of 0.87 (CV of residuals = 6.7%). Thirty‐eight female/immature sperm whales were measured in the Gulf of Mexico (median = 9.3 m, range = 7.1–12.3 m), 167 in the Gulf of California (median = 10.7 m, range = 8.4–13.1 m) and 13 bachelor males off Kaikoura, New Zealand (median = 14.2, range = 11.7–15.8 m). The results were within known sperm whale size and suggested that the population in the Gulf of Mexico was made up of smaller animals than that of the Gulf of California. This technique is easy to implement and allows the measurement of identified individuals.
Partially-Averaged Navier-Stokes Model for Turbulence: A Reynolds-Averaged Navier-Stokes to Direct Numerical Simulation Bridging Method
Authors: Girimaji Sharath S.
Published: May 2006

A turbulence bridging method purported for any filter-width or scale resolution—fully averaged to completely resolved—is developed. The method is given the name partially averaged Navier-Stokes (PANS) method. In PANS, the model filter width (extent of partial averaging) is controlled through two parameters: the unresolved-to-total ratios of kinetic energy (fk) and dissipation (fε). The PANS closure model is derived formally from the Reynolds-averaged Navier-Stokes (RANS) model equations by addressing the following question: if RANS represents the closure for fully averaged statistics, what is the corresponding closure for partially averaged statistics? The PANS equations vary smoothly from RANS equations to Navier-Stokes (direct numerical simulation) equations, depending on the values of the filter-width control parameters. Preliminary results are very encouraging.
Growth Rate Exponents of Richtmyer-Meshkov Mixing Layers
Authors: Clark Timothy T. , Zhou Ye
Published: May 2006

The Richtmyer-Meshkov mixing layer is initiated by the passing of a shock over an interface between fluid of differing densities. The energy deposited during the shock passage undergoes a relaxation process during which the fluctuational energy in the flow field decays and the spatial gradients of the flow field decrease in time. This late stage of Richtmyer-Meshkov mixing layers is studied from the viewpoint of self-similarity. Analogies with weakly anisotropic turbulence suggest that both the bubble-side and spike-side widths of the mixing layer should evolve as power-laws in time, with the same power-law exponent and virtual time origin for both sides. The analogy also bounds the power-law exponent between 2∕7 and 1∕2. It is then shown that the assumption of identical power-law exponents for bubbles and spikes yields fits that are in good agreement with experiment at modest density ratios.
Development of a Continuous Model for Simulation of Turbulent Flows
Authors: Yousuff Hussaini M. , Thangam Siva , Woodruff Stephen L. , Zhou Ye
Published: May 2006

The development of a continuous turbulence model that is suitable for representing both the subgrid scale stresses in large eddy simulation and the Reynolds stresses in the Reynolds averaged Navier-Stokes formulation is described. A recursion approach is used to bridge the length scale disparity from the cutoff wave number to those in the energy-containing range. The proposed model is analyzed in conjunction with direct numerical simulations of Kolmogorov flows.
Analysis, Modeling, and Validation for the Thermal Dynamics of a Polymer Electrolyte Membrane Fuel Cell System
Authors: Müller Eric A. , Stefanopoulou Anna G.
Published: May 2006

A control-oriented mathematical model of a polymer electrolyte membrane (PEM) fuel cell stack is developed and experimentally verified. The model predicts the bulk fuel cell transient temperature and voltage as a function of the current drawn and the inlet coolant conditions. The model enables thermal control synthesis and optimization and can be used for estimating the transient system performance. Unlike other existing thermal models, it includes the gas supply system, which is assumed to be capable of controlling perfectly the air and hydrogen flows. The fuel cell voltage is calculated quasistatically. Measurement data of a 1.25kW, 24-cell fuel cell stack with an integrated membrane-type humidification section is used to identify the system parameters and to validate the performance of the simulation model. The predicted thermal response is verified during typical variations in load, coolant flow, and coolant temperature. A first-law control volume analysis is performed to separate the relevant from the negligible contributions to the thermal dynamics and to determine the sensitivity of the energy balance to sensor errors and system parameter deviations.
Numerical Analysis of Unsteady Viscous Flow Through a Weis-Fogh-Type Ship Propulsion Mechanism Using the Advanced Vortex Method
Authors: Ro Kideok , Zhu Baoshan , Kang Hokeun
Published: May 2006

The velocity and pressure field of a ship’s Weis-Fogh-type propulsion mechanism are studied in this paper using an advanced vortex method. The wing (NACA0010 airfoil) and channel are approximated by source and vortex panels, and free vortices are introduced away from the body surfaces. The viscous diffusion of fluid is represented using the core-spreading model to the discrete vortices. The velocity is calculated on the basis of the generalized Biot-Savart law and the pressure field is calculated from an integral, based on the instantaneous velocity and vorticity distributions in the flow field. Two-dimensional unsteady viscous flow calculations of this propulsion mechanism are shown, and the calculated results agree qualitatively with the measured thrust and drag due to unmodeled large fluctuations in the measured data.
Dynamic Simulation of an Integrated Solid Oxide Fuel Cell System Including Current-Based Fuel Flow Control
Authors: Mueller Fabian , Brouwer Jacob , Jabbari Faryar , Samuelsen Scott
Published: May 2006

A two-dimensional dynamic model was created for a Siemens Westinghouse type tubular solid oxide fuel cell (SOFC). This SOFC model was integrated with simulation modules for other system components (e.g., reformer, combustion chamber, and dissipater) to comprise a system model that can simulate an integrated 25kw SOFC system located at the University of California, Irvine. A comparison of steady-state model results to data suggests that the integrated model can well predict actual system power performance to within 3%, and temperature to within 5%. In addition, the model predictions well characterize observed voltage and temperature transients that are representative of tubular SOFC system performance. The characteristic voltage transient due to changes in SOFC hydrogen concentration has a time scale that is shown to be on the order of seconds while the characteristic temperature transient is on the order of hours. Voltage transients due to hydrogen concentration change are investigated in detail. Particularly, the results reinforce the importance of maintaining fuel utilization during transient operation. The model is shown to be a useful tool for investigating the impacts of component response characteristics on overall system dynamic performance. Current-based flow control (CBFC), a control strategy of changing the fuel flow rate in proportion to the fuel cell current is tested and shown to be highly effective. The results further demonstrate the impact of fuel flow delay that may result from slow dynamic responses of control valves, and that such flow delays impose major limitations on the system transient response capability.
Semiempirical Model for Determining PEM Electrolyzer Stack Characteristics
Authors: Harrison Kevin W. , Hernández-Pacheco Eduardo , Mann Michael , Salehfar Hossein
Published: May 2006

A semiempirical equation was used to represent the performance characteristics of a 20-cell proton exchange membrane electrolyzer stack. The coefficients of the equation are the exchange current densities and membrane conductivity. These coefficients were determined using experimental data and a nonlinear curve fitting method. The anode exchange current density was found to be 1.65×10−8Acm−2, the cathode exchange current density 0.09Acm−2, and the membrane conductivity 0.075Scm−1. External programmable power supplies were used to obtain the (I‐V) characteristic curve of a commercial proton exchange membrane electrolyzer. Stack current, voltage, and system temperature were monitored while 1A current steps were applied to the electrolyzer stack.
A Computational Study of the Flow Around an Isolated Wheel in Contact With the Ground
Authors: McManus James , Zhang Xin
Published: May 2006

The flow around an isolated wheel in contact with the ground is computed by the Unsteady Reynolds-Averaged Navier-Stokes (URANS) method. Two cases are considered, a stationary wheel on a stationary ground and a rotating wheel on a moving ground. The computed wheel geometry is a detailed and accurate representation of the geometry used in the experiments of Fackrell and Harvey. The time-averaged computed flow is examined to reveal both new flow structures and new details of flow structures known from previous experiments. The mechanisms of formation of the flow structures are explained. A general schematic picture of the flow is presented. Surface pressures and pressure lift and drag forces are computed and compared to experimental results and show good agreement. The grid sensitivity of the computations is examined and shown to be small. The results have application to the design of road vehicles.
Numerical Simulations and Experimental Study of Liquid Metal Flow Around Sand Core
Authors: Bakhtiyarov Sayavur I.
Published: May 2006

This paper presents the results of experimental and numerical studies of the hot distortion phenomenon in the phenolic urethane cold box systems used in metal casting. Dual Pushrod Dilatometry has been used to measure a thermal expansion/contraction of phenolic urethane cold box sand core specimens at temperatures ranging from 20°C to 600°C. High temperature tensile tests showed that the tensile strength of the phenolic urethane cold box sand cores is significantly affected by the bench life, temperature and binders level. High temperature hot distortion furnace tests on cylindrical cores showed that some coatings increase the temperature limit when distortion starts, but application of coating cannot prevent distortion. The hot distortion test during metal casting showed that regardless of the application of coating, the type of coating, and anti-veining additives, all cores with density greater than the density of the molten metal (magnesium alloy) were significantly distorted. Numerical simulations of the liquid metal flow around the cylindrical sand core and analysis of dynamic forces acting on the core during the fill process showed that a buoyancy force is the major contributor to the hot distortion. It is concluded that the one of the solutions in preventing the hot distortion of sand cores is optimizing their weight, which will balance the buoyancy force and will bring the resultant force to the minimum. The hot distortion test castings using optimized sand cores with density almost equal to the density of the molten magnesium proved our predictions, and hot distortion has been prevented.
Anisotropy-Invariant Mapping of Turbulence in a Flow Past an Unswept Airfoil at High Angle of Attack
Authors: Jovičić N. , Breuer M. , Jovanović J.
Published: May 2006

Turbulence investigations of the flow past an unswept wing at a high angle of attack are reported. Detailed predictions were carried out using large-eddy simulations (LES) with very fine grids in the vicinity of the wall in order to resolve the near-wall structures. Since only a well-resolved LES ensures reliable results and hence allows a detailed analysis of turbulence, the Reynolds number investigated was restricted to Rec=105 based on the chord length c. Admittedly, under real flight conditions Rec is considerably higher (about (35-40)∙106). However, in combination with the inclination angle of attack α=18 deg this Rec value guarantees a practically relevant flow behavior, i.e., the flow exhibits a trailing-edge separation including some interesting flow phenomena such as a thin separation bubble, transition, separation of the turbulent boundary layer, and large-scale vortical structures in the wake. Due to the fine grid resolution applied, the aforementioned flow features are predicted in detail. Thus, reliable results are obtained which form the basis for advanced turbulence analysis. In order to provide a deeper insight into the nature of turbulence, the flow was analyzed using the invariant theory of turbulence by Lumley and Newman (J. Fluid Mech., 82, 161–178, 1977). Therefore, the anisotropy of various portions of the flow was extracted and displayed in the invariant map. This allowed us to examine the state of turbulence in distinct regions and provided an improved illustration of what happens in the turbulent flow. Thus, turbulence itself and the way in which it develops were extensively investigated, leading to an improved understanding of the physical mechanisms involved, not restricted to a standard test case such as channel flow but for a realistic, practically relevant flow problem at a moderate Reynolds number.
The Importance of the Mean Elevation in Predicting Skin Friction for Flow Over Closely Packed Surface Roughness
Authors: McClain Stephen T. , Collins S. Patrick , Hodge B. Keith , Bons Jeffrey P.
Published: May 2006

The discrete-element surface roughness model is used to provide insight into the importance of the mean elevation of surface roughness in predicting skin friction over rough surfaces. Comparison of experimental data and extensive computational results using the discrete-element model confirm that the appropriate surface for the imposition of the no-slip condition is the mean elevation of the surface roughness. Additionally, the use of the mean elevation in the Sigal-Danberg approach relating their parameter to the equivalent sand-grain roughness height results in replacing three different piecewise expressions with a single relation. The appropriate mean elevation for closely-packed spherical roughness is also examined.
An improved MLC segmentation algorithm and software for step‐and‐shoot IMRT delivery without tongue‐and‐groove error
Authors: Luan Shuang , Wang Chao , Chen Danny Z. , Hu Xiaobo S. , Naqvi Shahid A. , Wu Xingen , Yu Cedric X.
Published: May 2006

We present an improved multileaf collimator (MLC) segmentation algorithm, denoted by (static leaf sequencing with no tongue‐and‐groove error), for step‐and‐shoot intensity‐modulated radiation therapy (IMRT) delivery. is an improvement over the MLC segmentation algorithm called SLS that was developed by Luan et al. [Med. Phys. 31(4), 695–707 (2004)], which did not consider tongue‐and‐groove error corrections. The aims of are (1) shortening the treatment times of IMRT plans by minimizing their numbers of segments and (2) minimizing the tongue‐and‐groove errors of the computed IMRT plans. The input to is intensity maps (IMs) produced by current planning systems, and its output is (modified) optimized leaf sequences without tongue‐and‐groove error. Like the previous SLS algorithm [Luan et al., Med. Phys. 31(4), 695–707 (2004)], is also based on graph algorithmic techniques in computer science. It models the MLC segmentation problem as a weighted minimum‐cost path problem, where the weight of the path is the number of segments and the cost of the path is the amount of tongue‐and‐groove error. Our comparisons of with CORVUS indicated that for the same intensity maps, the numbers of segments computed by are up to 50% less than those by CORVUS 5.0 on the Elekta LINAC system. Our clinical verifications have shown that the dose distributions of the plans do not have tongue‐and‐groove error and match those of the corresponding CORVUS plans, thus confirming the correctness of . Comparing with existing segmentation methods, also has two additional advantages: (1) can compute leaf sequences whose tongue‐and‐groove error is minimized subject to a constraint on the maximum allowed number of segments, which may be desirable in clinical situations where a treatment with the complete correction of tongue‐and‐groove error takes too much time, and (2) can be used to minimize a more general type of error called the tongue‐or‐groove error.
The Sand Seas of Titan: Cassini RADAR Observations of Longitudinal Dunes
Authors: Lorenz R. D. , Wall S. , Radebaugh J. , Boubin G. , Reffet E. , Janssen M. , Stofan E. , Lopes R. , Kirk R. , Elachi C. , Lunine J. , Mitchell K. , Paganelli F. , Soderblom L. , Wood C. , Wye L. , Zebker H. , Anderson Y. , Ostro S. , Allison M. , Boehmer R. , Callahan P. , Encrenaz P. , Ori G. G. , Francescetti G. , Gim Y. , Hamilton G. , Hensley S. , Johnson W. , Kelleher K. , Muhleman D. , Picardi G. , Posa F. , Roth L. , Seu R. , Shaffer S. , Stiles B. , Vetrella S. , Flamini E. , West R.
Published: May 2006

The most recent Cassini RADAR images of Titan show widespread regions (up to 1500 kilometers by 200 kilometers) of near-parallel radar-dark linear features that appear to be seas of longitudinal dunes similar to those seen in the Namib desert on Earth. The Ku-band (2.17-centimeter wavelength) images show â¼100-meter ridges consistent with duneforms and reveal flow interactions with underlying hills. The distribution and orientation of the dunes support a model of fluctuating surface winds of â¼0.5 meter per second resulting from the combination of an eastward flow with a variable tidal wind. The existence of dunes also requires geological processes that create sand-sized (100- to 300-micrometer) particulates and a lack of persistent equatorial surface liquids to act as sand traps.
B Cell Ligand Discrimination Through a Spreading and Contraction Response
Authors: Fleire S. J. , Goldman J. P. , Carrasco Y. R. , Weber M. , Bray D. , Batista F. D.
Published: May 2006

B cells recognize foreign antigens by virtue of cell surface immunoglobulin receptors and are most effectively activated by membrane-bound ligands. Here, we show that in the early stages of this process, B cells exhibit a two-phase response in which they first spread over the antigen-bearing membrane and then contract, thereby collecting bound antigen into a central aggregate. The extent of this response, which is both signaling- and actin-dependent, determines the quantity of antigen accumulated and hence the degree of B cell activation. Brownian dynamic simulations reproduce essential features of the antigen collection process and suggest a possible basis for affinity discrimination. We propose that dynamic spreading is an important step of the immune response.
Catalytic Production of Olefin Block Copolymers via Chain Shuttling Polymerization
Authors: Arriola Daniel J. , Carnahan Edmund M. , Hustad Phillip D. , Kuhlman Roger L. , Wenzel Timothy T.
Published: May 2006

We report a catalytic system that produces olefin block copolymers with alternating semicrystalline and amorphous segments, achieved by varying the ratio of α-olefin to ethylene in the two types of blocks. The system uses a chain shuttling agent to transfer growing chains between two distinct catalysts with different monomer selectivities in a single polymerization reactor. The block copolymers simultaneously have high melting temperatures and low glass transition temperatures, and therefore they maintain excellent elastomeric properties at high temperatures. Furthermore, the materials are effectively produced in economically favorable, continuous polymerization processes.
Structure of the Multidrug Transporter EmrD from
Escherichia coli
Authors: Yin Yong , He Xiao , Szewczyk Paul , Nguyen That , Chang Geoffrey
Published: May 2006

EmrD is a multidrug transporter from the Major Facilitator Superfamily that expels amphipathic compounds across the inner membrane of
Escherichia coli
. Here, we report the x-ray structure of EmrD determined to a resolution of 3.5 angstroms. The structure reveals an interior that is composed mostly of hydrophobic residues, which is consistent with its role transporting amphipathic molecules. Two long loops extend into the inner leaflet side of the cell membrane. This region can serve to recognize and bind substrate directly from the lipid bilayer. We propose that multisubstrate specificity, binding, and transport are facilitated by these loop regions and the internal cavity.
Metal Reduction and Iron Biomineralization by a Psychrotolerant Fe(III)-Reducing Bacterium,
Shewanella
sp. Strain PV-4
Authors: Roh Yul , Gao Haichun , Vali Hojatollah , Kennedy David W. , Yang Zamin K. , Gao Weimin , Dohnalkova Alice C. , Stapleton Raymond D. , Moon Ji-Won , Phelps Tommy J. , Fredrickson James K. , Zhou Jizhong
Published: May 2006

A marine psychrotolerant, dissimilatory Fe(III)-reducing bacterium,
Shewanella
sp. strain PV-4, from the microbial mat at a hydrothermal vent of Loihi Seamount in the Pacific Ocean has been further characterized, with emphases on metal reduction and iron biomineralization. The strain is able to reduce metals such as Fe(III), Co(III), Cr(VI), Mn(IV), and U(VI) as electron acceptors while using lactate, formate, pyruvate, or hydrogen as an electron donor. Growth during iron reduction occurred over the pH range of 7.0 to 8.9, a sodium chloride range of 0.05 to 5%, and a temperature range of 0 to 37°C, with an optimum growth temperature of 18°C. Unlike mesophilic dissimilatory Fe(III)-reducing bacteria, which produce mostly superparamagnetic magnetite (<35 nm), this psychrotolerant bacterium produces well-formed single-domain magnetite (>35 nm) at temperatures from 18 to 37°C. The genome size of this strain is about 4.5 Mb. Strain PV-4 is sensitive to a variety of commonly used antibiotics except ampicillin and can acquire exogenous DNA (plasmid pCM157) through conjugation.
Determination of Cyanobacterial Diversity during Algal Blooms in Daechung Reservoir, Korea, on the Basis of
cpcBA
Intergenic Spacer Region Analysis
Authors: Kim Song-Gun , Rhee Sung-Keun , Ahn Chi-Yong , Ko So-Ra , Choi Gang-Guk , Bae Jin-Woo , Park Yong-Ha , Oh Hee-Mock
Published: May 2006

The detection and prevention of cyanobacterial blooms are important issues in water quality management. As such, the diversity and community dynamics of cyanobacteria during cyanobacterial bloom in the Daechung Reservoir, Korea, were studied by analyzing the intergenic spacer (IGS) region between phycocyanin subunit genes
cpcB
and
cpcA
(
cpcBA
IGS). To amplify the
cpcBA
IGS from environmental samples, new PCR primers that could cover a wider range of cyanobacteria than previously known primers were designed. In the samples taken around the bloom peak (2 September 2003), seven groups of
cpcBA
IGS sequences were detected, and none of the amplified
cpcBA
IGSs was closely related to the
cpcBA
IGS from chloroplasts. Apart from the
Microcystis
-,
Aphanizomenon
(
Anabaena
)-,
Pseudanabaena-
, and
Planktothrix
(
Oscillatoria
)-like groups, the three other groups of
cpcBA
IGS sequences were only distantly related to previously reported sequences (<85% similarity to their closest relatives). The most prominent changes during the bloom were the gradual decrease and eventual disappearance of the
Aphanizomenon
(
Anabaena
)-like group before the bloom peak and the gradual increase and sudden disappearance of
Planktothrix
(
Oscillatoria
)-like groups right after the bloom peak. The community succession profile obtained based on the
cpcBA
IGS analysis was also supported by a PCR-denaturing gradient gel electrophoresis analysis of the 16S rRNA genes.
Glycosylphosphatidylinositol-Anchored Ecm33p Influences Conidial Cell Wall Biosynthesis in
Aspergillus fumigatus
Authors: Chabane Sandrine , Sarfati Jacqueline , Ibrahim-Granet Oumaima , Du Chen , Schmidt Christine , Mouyna Isabelle , Prevost Marie-Christine , Calderone Richard , Latgé Jean-Paul
Published: May 2006

ECM33
encodes a glycosylphosphatidylinositol-anchored protein whose orthologs in yeast are essential for sporulation.
Aspergillus fumigatus
Ecm33p is unique and has an apparent mass of 55 kDa. Disruption of
A. fumigatus ECM33
results in a mutant with several morphogenetic aberrations, including the following: (i) a defect in conidial separation, (ii) an increase in the diameter of the conidia of the mutant associated with an increase in the concentration of the cell wall chitin, (iii) conidia that were sensitive to the absence of aeration during long-term storage, and (iv) conidia that were more resistant to killing by phagocytes, whereas the mycelium was more easily killed by neutrophils.
Interaction of
Escherichia coli
and Soil Particles in Runoff
Authors: Muirhead Richard William , Collins Robert Peter , Bremer Philip James
Published: May 2006

A laboratory-scale model system was developed to investigate the transport mechanisms involved in the horizontal movement of bacteria in overland flow across saturated soils. A suspension of
Escherichia coli
and bromide tracer was added to the model system, and the bromide concentration and number of attached and unattached
E. coli
cells in the overland flow were measured over time. Analysis of the breakthrough curves indicated that the
E. coli
and bromide were transported together, presumably by the same mechanism. This implied that the
E. coli
was transported by advection with the flowing water. Overland-flow transport of
E. coli
could be significantly reduced if the cells were preattached to large soil particles (>45 μm). However, when unattached cells were inoculated into the system, the
E. coli
appeared to attach predominantly to small particles (<2 μm) and hence remained unattenuated during transport. These results imply that in runoff generated by saturation-excess conditions, bacteria are rapidly transported across the surface and have little opportunity to interact with the soil matrix.
Engineering of a Xylose Metabolic Pathway in
Corynebacterium glutamicum
Authors: Kawaguchi Hideo , Vertès Alain A. , Okino Shohei , Inui Masayuki , Yukawa Hideaki
Published: May 2006

The aerobic microorganism
Corynebacterium glutamicum
was metabolically engineered to broaden its substrate utilization range to include the pentose sugar xylose, which is commonly found in agricultural residues and other lignocellulosic biomass. We demonstrated the functionality of the corynebacterial
xylB
gene encoding xylulokinase and constructed two recombinant
C. glutamicum
strains capable of utilizing xylose by cloning the
Escherichia coli
gene
xylA
encoding xylose isomerase, either alone (strain CRX1) or in combination with the
E. coli
gene
xylB
(strain CRX2). These genes were provided on a high-copy-number plasmid and were under the control of the constitutive promoter
trc
derived from plasmid pTrc99A. Both recombinant strains were able to grow in mineral medium containing xylose as the sole carbon source, but strain CRX2 grew faster on xylose than strain CRX1. We previously reported the use of oxygen deprivation conditions to arrest cell replication in
C. glutamicum
and divert carbon source utilization towards product production rather than towards vegetative functions (M. Inui, S. Murakami, S. Okino, H. Kawaguchi, A. A. Vertès, and H. Yukawa, J. Mol. Microbiol. Biotechnol.
7
:182-196, 2004). Under these conditions, strain CRX2 efficiently consumed xylose and produced predominantly lactic and succinic acids without growth. Moreover, in mineral medium containing a sugar mixture of 5% glucose and 2.5% xylose, oxygen-deprived strain CRX2 cells simultaneously consumed both sugars, demonstrating the absence of diauxic phenomena relative to the new
xylA-xylB
construct, albeit glucose-mediated regulation still exerted a measurable influence on xylose consumption kinetics.
Proteomic Analysis of Extracellular Proteins from
Aspergillus oryzae
Grown under Submerged and Solid-State Culture Conditions
Authors: Oda Ken , Kakizono Dararat , Yamada Osamu , Iefuji Haruyuki , Akita Osamu , Iwashita Kazuhiro
Published: May 2006

Filamentous fungi are widely used for the production of homologous and heterologous proteins. Recently, there has been increasing interest in
Aspergillus oryzae
because of its ability to produce heterologous proteins in solid-state culture. To provide an overview of protein secretion by
A. oryzae
in solid-state culture, we carried out a comparative proteome analysis of extracellular proteins in solid-state and submerged (liquid) cultures. Extracellular proteins prepared from both cultures sequentially from 0 to 40 h were subjected to two-dimensional electrophoresis, and protein spots at 40 h were identified by peptide mass fingerprinting using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. We also attempted to identify cell wall-bound proteins of the submerged culture. We analyzed 85 spots from the solid-state culture and 110 spots from the submerged culture. We identified a total of 29 proteins, which were classified into 4 groups. Group 1 consisted of extracellular proteins specifically produced in the solid-state growth condition, such as glucoamylase B and alanyl dipeptidyl peptidase. Group 2 consisted of extracellular proteins specifically produced in the submerged condition, such as glucoamylase A (GlaA) and xylanase G2 (XynG2). Group 3 consisted of proteins produced in both conditions, such as xylanase G1. Group 4 consisted of proteins that were secreted to the medium in the solid-state growth condition but trapped in the cell wall in the submerged condition, such as α-amylase (TAA) and β-glucosidase (Bgl). A Northern analysis of seven genes from the four groups suggested that the secretion of TAA and Bgl was regulated by trapping these proteins in the cell wall in submerged culture and that secretion of GlaA and XynG2 was regulated at the posttranscriptional level in the solid-state culture.
Classification Tree Method for Bacterial Source Tracking with Antibiotic Resistance Analysis Data
Authors: Price Bertram , Venso Elichia A. , Frana Mark F. , Greenberg Joshua , Ware Adam , Currey Lee
Published: May 2006

Various statistical classification methods, including discriminant analysis, logistic regression, and cluster analysis, have been used with antibiotic resistance analysis (ARA) data to construct models for bacterial source tracking (BST). We applied the statistical method known as classification trees to build a model for BST for the Anacostia Watershed in Maryland. Classification trees have more flexibility than other statistical classification approaches based on standard statistical methods to accommodate complex interactions among ARA variables. This article describes the use of classification trees for BST and includes discussion of its principal parameters and features. Anacostia Watershed ARA data are used to illustrate the application of classification trees, and we report the BST results for the watershed.
Diversity and Seasonal Dynamics of
Actinobacteria
Populations in Four Lakes in Northeastern Germany
Authors: Allgaier Martin , Grossart Hans-Peter
Published: May 2006

The phylogenetic diversity and seasonal dynamics of freshwater
Actinobacteria
populations in four limnologically different lakes of the Mecklenburg-Brandenburg Lake District (northeastern Germany) were investigated. Fluorescence in situ hybridization was used to determine the seasonal abundances and dynamics of total
Actinobacteria
(probe HGC69a) and the three actinobacterial subclusters
acI
,
acI-A
, and
acI-B
(probes AcI-852, AcI-840-1, and AcI-840-2). Seasonal means of total
Actinobacteria
abundances in the epilimnia of the lakes varied from 13 to 36%, with maximum values of 30 to 58%, of all DAPI (4′,6′-diamidino-2-phenylindole)-stained cells. Around 80% of total
Actinobacteria
belonged to the
acI
cluster. The two subclusters
acI-A
and
acI-B
accounted for 60 to 91% of the
acI
cluster and showed seasonal means of 49% (
acI-B
) and 23% (
acI-A
) in relation to the
acI
cluster. Total
Actinobacteria
and members of the clusters
acI
and
acI-B
showed distinct seasonal changes in their absolute abundances, with maxima in late spring and fall/winter. In eight clone libraries constructed from the lakes, a total of 76 actinobacterial 16S rRNA gene sequences were identified from a total of 177 clones. The majority of the
Actinobacteria
sequences belonged to the
acI
and
acIV
cluster. Several new clusters and subclusters were found (
acSTL
,
scB1-4
, and
acIVA-D
). The majority of all obtained 16S rRNA gene sequences are distinct from those of already-cultured freshwater
Actinobacteria
.
Population Dynamics within a Microbial Consortium during Growth on Diesel Fuel in Saline Environments
Authors: Kleinsteuber Sabine , Riis Volker , Fetzer Ingo , Harms Hauke , Müller Susann
Published: May 2006

The diversity and dynamics of a bacterial community extracted from an exploited oil field with high natural soil salinity near Comodoro Rivadavia in Patagonia (Argentina) were investigated. Community shifts during long-term incubation with diesel fuel at four salinities between 0 and 20% NaCl were monitored by single-strand conformation polymorphism community fingerprinting of the PCR-amplified V4-V5 region of the 16S rRNA genes. Information obtained by this qualitative approach was extended by flow cytometric analysis to follow quantitatively the dynamics of community structures at different salinities. Dominant and newly developing clusters of individuals visualized via their DNA patterns versus cell sizes were used to identify the subcommunities primarily involved in the degradation process. To determine the most active species, subcommunities were separated physically by high-resolution cell sorting and subsequent phylogenetic identification by 16S rRNA gene sequencing. Reduced salinity favored the dominance of
Sphingomonas
spp., whereas at elevated salinities,
Ralstonia
spp. and a number of halophilic genera, including
Halomonas
,
Dietzia
, and
Alcanivorax
, were identified. The combination of cytometric sorting with molecular characterization allowed us to monitor community adaptation and to identify active and proliferating subcommunities.
The General Secretory Pathway of
Burkholderia gladioli
pv. agaricicola BG164R Is Necessary for Cavity Disease in White Button Mushrooms
Authors: Chowdhury Piklu Roy , Heinemann Jack A.
Published: May 2006

Cavity disease in white button mushrooms is caused by
Burkholderia gladioli
pv. agaricicola. We describe the isolation and characterization of six mutants of the strain BG164R that no longer cause this disease on mushrooms. The mutations were mapped to genes of the general secretory pathway (GSP). This is the first report of the association of the type II secretion pathway with a disease in mushrooms. Phenotypes of the six avirulent mutants were the following: an inability to degrade mushroom tissue, a highly reduced capacity to secrete chitinase and protease, and a reduced number of flagella. Using these mutants, we also made the novel observation that the factors causing mushroom tissue degradation, thereby leading to the expression of cavity disease, can be separated from mycelium inhibition because avirulent mutants continued to inhibit the growth of actively growing mushroom mycelia. The GSP locus of
B. gladioli
was subsequently cloned and mapped and compared to the same locus in closely related species, establishing that the genetic organization of the
gsp
operon of
B. gladioli
pv. agaricicola is consistent with that of other species of the genus. We also identify the most common indigenous bacterial population present in the mushroom fruit bodies from a New Zealand farm, one of which,
Ewingella americana
, was found to be an apparent antagonist of
B. gladioli
pv. agaricicola. While other investigators have reported enhanced disease symptoms due to interactions between endogenous and disease-causing bacteria in other mushroom diseases, to the best of our knowledge this is the first report of an antagonistic effect.
RNA-Based Stable Isotope Probing and Isolation of Anaerobic Benzene-Degrading Bacteria from Gasoline-Contaminated Groundwater
Authors: Kasai Yuki , Takahata Yoh , Manefield Mike , Watanabe Kazuya
Published: May 2006

Stable isotope probing (SIP) of benzene-degrading bacteria in gasoline-contaminated groundwater was coupled to denaturing gradient gel electrophoresis (DGGE) of DNA fragments amplified by reverse transcription-PCR from community 16S rRNA molecules. Supplementation of the groundwater with [
13
C
6
]benzene together with an electron acceptor (nitrate, sulfate, or oxygen) showed that a phylotype affiliated with the genus
Azoarcus
specifically appeared in the
13
C-RNA fraction only when nitrate was supplemented. This phylotype was also observed as the major band in DGGE analysis of bacterial 16S rRNA gene fragments amplified by PCR from the gasoline-contaminated groundwater. In order to isolate the
Azoarcus
strains, the groundwater sample was streaked on agar plates containing nonselective diluted CGY medium, and the DGGE analysis was used to screen colonies formed on the plates. This procedure identified five bacterial isolates (from 60 colonies) that corresponded to the SIP-identified
Azoarcus
phylotype, among which two strains (designated DN11 and AN9) degraded benzene under denitrifying conditions. Incubation of these strains with [
14
C]benzene showed that the labeled carbon was mostly incorporated into
14
CO
2
within 14 days. These results indicate that the
Azoarcus
population was involved in benzene degradation in the gasoline-contaminated groundwater under denitrifying conditions. We suggest that RNA-based SIP identification coupled to phylogenetic screening of nonselective isolates facilitates the isolation of enrichment/isolation-resistant microorganisms with a specific function.
Uranium(VI) Reduction by
Anaeromyxobacter dehalogenans
Strain 2CP-C
Authors: Wu Qingzhong , Sanford Robert A. , Löffler Frank E.
Published: May 2006

Previous studies demonstrated growth of
Anaeromyxobacter dehalogenans
strain 2CP-C with acetate or hydrogen as the electron donor and Fe(III), nitrate, nitrite, fumarate, oxygen, or
ortho
-substituted halophenols as electron acceptors. In this study, we explored and characterized U(VI) reduction by strain 2CP-C. Cell suspensions of fumarate-grown 2CP-C cells reduced U(VI) to U(IV). More-detailed growth studies demonstrated that hydrogen was the required electron donor for U(VI) reduction and could not be replaced by acetate. The addition of nitrate to U(VI)-reducing cultures resulted in a transitory increase in U(VI) concentration, apparently caused by the reoxidation of reduced U(IV), but U(VI) reduction resumed following the consumption of N-oxyanions. Inhibition of U(VI) reduction occurred in cultures amended with Fe(III) citrate, or citrate. In the presence of amorphous Fe(III) oxide, U(VI) reduction proceeded to completion but the U(VI) reduction rates decreased threefold compared to control cultures. Fumarate and 2-chlorophenol had no inhibitory effects on U(VI) reduction, and both electron acceptors were consumed concomitantly with U(VI). Since cocontaminants (e.g., nitrate, halogenated compounds) and bioavailable ferric iron are often encountered at uranium-impacted sites, the metabolic versatility makes
Anaeromyxobacter dehalogenans
a promising model organism for studying the complex interaction of multiple electron acceptors in U(VI) reduction and immobilization.
Characterization of a Culturable Alphaproteobacterial Symbiont Common to Many Marine Sponges and Evidence for Vertical Transmission via Sponge Larvae
Authors: Enticknap Julie J. , Kelly Michelle , Peraud Olivier , Hill Russell T.
Published: May 2006

A closely related group of alphaproteobacteria were found to be present in seven genera of marine sponges from several locations and were shown to be transferred between sponge generations through the larvae in one of these sponges. Isolates of the alphaproteobacterium were cultured from the spongesAxinella corrugata,Mycale laxissima,Monanchora unguifera, andNiphates digitalisfrom Key Largo, Florida;Didiscus oxeataandMonanchora unguiferafrom Discovery Bay, Jamaica; anAcanthostronglyophorasp. from Manado, Indonesia; andMicrociona proliferafrom the Cheasapeake Bay in Maryland. Isolates were very similar to each other on the basis of 16S rRNA gene sequence (>99% identity) and are closely related toPseudovibrio denitrificans. The bacterium was never isolated from surrounding water samples and was cultured from larvae ofM. laxissima, indicating that it is a vertically transmitted symbiont in this sponge. Denaturing gradient gel electrophoresis, 16S rRNA gene clone library analysis, and fluorescent in situ hybridization with probes specific to the alphaproteobacterium confirmed the presence of this bacterium in theM. laxissimalarvae. The alphaproteobacterium was densely associated with the larvae rather than being evenly distributed throughout the mesohyl. This is the first report of the successful culture of a bacterial symbiont of a sponge that is transferred through the gametes.
Involvement of Coenzyme M during Aerobic Biodegradation of Vinyl Chloride and Ethene by
Pseudomonas putida
Strain AJ and
Ochrobactrum
sp. Strain TD
Authors: Danko Anthony S. , Saski Christopher A. , Tomkins Jeffrey P. , Freedman David L.
Published: May 2006

The involvement of coenzyme M in aerobic biodegradation of vinyl chloride and ethene in
Pseudomonas putida
strain AJ and
Ochrobactrum
sp. strain TD was demonstrated using PCR, hybridization, and enzyme assays. The results of this study extend the range of eubacteria known to use epoxyalkane:coenzyme M transferase.
Assessment of the Effectiveness of Low-Pressure UV Light for Inactivation of
Helicobacter pylori
Authors: Hayes Samuel L. , White Karen M. , Rodgers Mark R.
Published: May 2006

Three strains of
Helicobacter pylori
were exposed to UV light from a low-pressure source to determine log inactivation versus applied fluence. Results indicate that
H. pylori
is readily inactivated at UV fluences typically used in water treatment regimens. Greater than 4-log
10
inactivation was demonstrated on all three strains at fluences of less than 8 mJ cm
−2
.
Development and Optimization of High-Throughput Methods To MeasurePlasmodium falciparum-Specific Growth Inhibitory Antibodies
Authors: Persson Kristina E. M. , Lee Chee T. , Marsh Kevin , Beeson James G.
Published: May 2006

Antibodies that inhibit replication ofPlasmodium falciparumin erythrocytes are thought to be important both in acquired immunity to malaria and as mediators of immunity generated by candidate blood-stage vaccines. However, several constraints have limited the study of these functional antibodies in population studies and vaccine trials. We report the development and optimization of high-throughput growth inhibition assays with improved sensitivity that use minimal volumes of test serum. The major inhibitory activity of serum from exposed donors was antibody mediated, but nonspecific inhibitory factors were found in untreated serum. Culture volumes could be effectively reduced to 25 μl to limit amounts of test serum or inhibitors used in assays. Performing inhibition assays over two cycles of parasite replication gave greater sensitivity than single-cycle assays, and a simple two-cycle inhibition assay was developed that yielded highly reproducible results. Determination of parasite growth by flow cytometry was most suitable for high-throughput assays using small culture volumes and was more sensitive than parasite lactate dehydrogenase assays and less prone to error and variation than microscopy. We evaluated and optimized methods to remove antimalarials and nonspecific inhibitory factors from serum that are suitable for use with small volumes of samples that are typically obtained from clinical studies. Both microdialysis and immunoglobulin purification by ammonium sulfate precipitation were effective and practical. These methods should facilitate evaluation of vaccine trials and clinical studies of immunity and are also suitable for testing drugs and other compounds for antimalarial activity.
Identification of a Novel 74-Kilodalton Immunodominant Antigen ofPythium insidiosumRecognized by Sera from Human Patients with Pythiosis
Authors: Krajaejun Theerapong , Kunakorn Mongkol , Pracharktam Rungnapa , Chongtrakool Piriyaporn , Sathapatayavongs Boonmee , Chaiprasert Angkana , Vanittanakom Nongnuch , Chindamporn Ariya , Mootsikapun Piroon
Published: May 2006

The oomycetous, fungus-like, aquatic organismPythium insidiosumis the etiologic agent of pythiosis, a life-threatening infectious disease of humans and animals that has been increasingly reported from tropical, subtropical, and temperate countries. Human pythiosis is endemic in Thailand, and most patients present with arteritis, leading to limb amputation and/or death, or cornea ulcer, leading to enucleation. Diagnosis of pythiosis is time-consuming and difficult. Radical surgery is the main treatment for pythiosis because conventional antifungal drugs are ineffective. The aims of this study were to evaluate the use of Western blotting for diagnosis of human pythiosis, to identify specific immunodominant antigens ofP. insidiosum, and to increase understanding of humoral immune responses against the pathogen. We performed Western blot analysis on 16P. insidiosumisolates using 12 pythiosis serum samples. These specimens were derived from human patients with pythiosis who had different forms of infection and lived in different geographic areas throughout Thailand. We have identified a 74-kDa immunodominant antigen in allP. insidiosumisolates tested. The 74-kDa antigen was also recognized by sera from all patients with pythiosis but not by control sera from healthy individuals, patients with thalassemia, and patients with various infectious diseases, indicating that Western blot analysis could facilitate diagnosis of pythiosis. Therefore, the 74-kDa antigen is a potential target for developing rapid serodiagnostic tests as well as a therapeutic vaccine for pythiosis. These advances could lead to early diagnosis and effective treatment, crucial factors for better prognosis for patients with pythiosis.