bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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.
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTA 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

ABSTRACT

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

ABSTRACT

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
.