bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of an Acetate-Fed Denitrifying Microbial Community by Stable Isotope Probing, Full-Cycle rRNA Analysis, and Fluorescent In Situ Hybridization-Microautoradiography
Authors: Ginige Maneesha P. , Keller Jürg , Blackall Linda L.
Published: December 2005

The acetate-utilizing microbial consortium in a full-scale activated sludge process was investigated without prior enrichment using stable isotope probing (SIP). [
13
C]acetate was used in SIP to label the DNA of the denitrifiers. The [
13
C]DNA fraction that was extracted was subjected to a full-cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the
13
C library were closely related to the bacterial families
Comamonadaceae
and
Rhodocyclaceae
in the class
Betaproteobacteria
. Seven oligonucleotide probes for use in fluorescent in situ hybridization (FISH) were designed to specifically target these clones. Application of these probes to the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated for 16 days revealed that there was a significant positive correlation between the CFDSBR denitrification rate and the relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH-microautoradiography demonstrated that the DEN581 and DEN124 probe-targeted cells that dominated the CFDSBR were capable of taking up [
14
C]acetate under anoxic conditions. Initially, DEN444 and DEN1454 probe-targeted bacteria also dominated the CFDSBR biomass, but eventually DEN581 and DEN124 probe-targeted bacteria were the dominant bacterial groups. All probe-targeted bacteria assessed in this study were denitrifiers capable of utilizing acetate as a source of carbon. The rapid increase in the number of organisms positively correlated with the immediate increase in denitrification rates observed by plant operators when acetate is used as an external source of carbon to enhance denitrification. We suggest that the impact of bacteria on activated sludge subjected to intermittent acetate supplementation should be assessed prior to the widespread use of acetate in the wastewater industry to enhance denitrification.
Application of Stereolithographic Custom Models for Studying the Impact of Biofilms and Mineral Precipitation on Fluid Flow
Authors: Stoner D. L. , Watson S. M. , Stedtfeld R. D. , Meakin P. , Griffel L. K. , Tyler T. L. , Pegram L. M. , Barnes J. M. , Deason V. A.
Published: December 2005

Here we introduce the use of transparent experimental models fabricated by stereolithography for studying the impacts of biomass accumulation, minerals precipitation, and physical configuration of flow paths on liquid flow in fracture apertures. The internal configuration of the models ranged in complexity from simple geometric shapes to those that incorporate replicated surfaces of natural fractures and computationally derived fracture surfaces. High-resolution digital time-lapse imaging was employed to qualitatively observe the migration of colloidal and soluble dyes through the flow models. In this study, aSphingomonassp. andSporosarcina (Bacillus) pasteuriiinfluenced the fluid dynamics by physically altering flow paths. Microbial colonization and calcite deposition enhanced the stagnant regions adjacent to solid boundaries. Microbial growth and calcite precipitation occurred to a greater extent in areas behind the fabricated obstacles and less in high-velocity orifices.
Desulfotomaculum
and
Methanobacterium
spp. Dominate a 4- to 5-Kilometer-Deep Fault
Authors: Moser Duane P. , Gihring Thomas M. , Brockman Fred J. , Fredrickson James K. , Balkwill David L. , Dollhopf Michael E. , Lollar Barbara Sherwood , Pratt Lisa M. , Boice Erik , Southam Gordon , Wanger Greg , Baker Brett J. , Pfiffner Susan M. , Lin Li-Hung , Onstott T. C.
Published: December 2005

Alkaline, sulfidic, 54 to 60°C, 4 to 53 million-year-old meteoric water emanating from a borehole intersecting quartzite-hosted fractures >3.3 km beneath the surface supported a microbial community dominated by a bacterial species affiliated with
Desulfotomaculum
spp. and an archaeal species related to
Methanobacterium
spp. The geochemical homogeneity over the 650-m length of the borehole, the lack of dividing cells, and the absence of these microorganisms in mine service water support an indigenous origin for the microbial community. The coexistence of these two microorganisms is consistent with a limiting flux of inorganic carbon and SO
4
2−
in the presence of high pH, high concentrations of H
2
and CH
4
, and minimal free energy for autotrophic methanogenesis. Sulfide isotopic compositions were highly enriched, consistent with microbial SO
4
2−
reduction under hydrologic isolation. An analogous microbial couple and similar abiogenic gas chemistry have been reported recently for hydrothermal carbonate vents of the Lost City near the Mid-Atlantic Ridge (D. S. Kelly et al., Science
307:
1428-1434, 2005), suggesting that these features may be common to deep subsurface habitats (continental and marine) bearing this geochemical signature. The geochemical setting and microbial communities described here are notably different from microbial ecosystems reported for shallower continental subsurface environments.
Engineering
Pseudomonas fluorescens
for Biodegradation of 2,4-Dinitrotoluene
Authors: Monti Mariela R. , Smania Andrea M. , Fabro Georgina , Alvarez María E. , Argaraña Carlos E.
Published: December 2005

Using the genes encoding the 2,4-dinitrotoluene degradation pathway enzymes, the nonpathogenic psychrotolerant rhizobacterium
Pseudomonas fluorescens
ATCC 17400 was genetically modified for degradation of this priority pollutant. First, a recombinant strain designated MP was constructed by conjugative transfer from
Burkholderia
sp. strain DNT of the pJS1 megaplasmid, which contains the
dnt
genes for 2,4-dinitrotoluene degradation. This strain was able to grow on 2,4-dinitrotoluene as the sole source of carbon, nitrogen, and energy at levels equivalent to those of
Burkholderia
sp. strain DNT. Nevertheless, loss of the 2,4-dinitrotoluene degradative phenotype was observed for strains carrying pJS1. The introduction of
dnt
genes into the
P.fluorescens
ATCC 17400 chromosome, using a suicide chromosomal integration Tn
5
-based delivery plasmid system, generated a degrading strain that was stable for a long time, which was designated RE. This strain was able to use 2,4-dinitrotoluene as a sole nitrogen source and to completely degrade this compound as a cosubstrate. Furthermore,
P. fluorescens
RE, but not
Burkholderia
sp. strain DNT, was capable of degrading 2,4-dinitrotoluene at temperatures as low as 10°C. Finally, the presence of
P. fluorescens
RE in soils containing levels of 2,4-dinitrotoluene lethal to plants significantly decreased the toxic effects of this nitro compound on
Arabidopsis thaliana
growth. Using synthetic medium culture,
P. fluorescens
RE was found to be nontoxic for
A.thaliana
and
Nicotiana tabacum
, whereas under these conditions
Burkholderia
sp. strain DNT inhibited
A.thaliana
seed germination and was lethal to plants. These features reinforce the advantageous environmental robustness of
P. fluorescens
RE compared with
Burkholderia
sp. strain DNT.
Structural Characterization of Glucooligosaccharide Oxidase from
Acremonium strictum
Authors: Lee Meng-Hwan , Lai Wen-Lin , Lin Shuen-Fuh , Hsu Cheng-Sheng , Liaw Shwu-Huey , Tsai Ying-Chieh
Published: December 2005

Glucooligosaccharide oxidase from
Acremonium strictum
was screened for potential applications in oligosaccharide acid production and carbohydrate detection. This protein is a unique covalent flavoenzyme which catalyzes the oxidation of a variety of carbohydrates with high selectivity for cello- and maltooligosaccharides. Kinetic measurements suggested that this enzyme possesses an open carbohydrate-binding groove, which is mainly composed of two glucosyl-binding subsites. The encoding gene was subsequently cloned, and one intron was detected in the genomic DNA. Large amounts of active enzymes were expressed in
Pichia pastoris
, with a yield of 300 mg per liter medium. The protein was predicted to share structural homology with plant cytokinin dehydrogenase and related flavoproteins that share a conserved flavin adenine dinucleotide (FAD)-binding domain. The closest sequence matches are those of plant berberine bridge enzyme-like proteins, particularly the characteristic flavinylation site. Unexpectedly, mutation of the putative FAD-attaching residue, H70, to alanine, serine, cysteine, and tyrosine did not abolish the covalent FAD linkage and had little effect on the

K
m

. Instead, the variants displayed
k
cat
values that were 50- to 600-fold lower, indicating that H70 is crucial for efficient redox catalysis, perhaps through modulation of the oxidative power of the flavin.
Cell Adsorption and Selective Desorption for Separation of Microbial Cells by Using Chitosan-Immobilized Silica
Authors: Kubota Munehiro , Matsui Masayoshi , Chiku Hiroyuki , Kasashima Nobuyuki , Shimojoh Manabu , Sakaguchi Kengo
Published: December 2005

Cell adsorption and selective desorption for separation of microbial cells were conducted by using chitosan-immobilized silica (CIS). When chitosan was immobilized onto silica surfaces with glutaraldehyde, bacterial cells adsorbed well and retained viability. Testing of the adsorption and desorption ability of CIS using various microbes such as
Escherichia coli
,
Aeromonas hydrophila
,
Pseudomonas aeruginosa
,
Bacillus subtilis
,
Micrococcus luteus
,
Staphylococcus aureus
,
Staphylococcus epidermidis
,
Lactobacillus casei
,
Streptococcus mutans
,
Streptococcus sobrinus
,
Streptococcus salivarius
,
Saccharomyces cerevisiae
,
Saccharomyces ludwigii
, and
Schizosaccharomyces pombe
revealed that most microbes could be adsorbed and selectively desorbed under different conditions. In particular, recovery was improved when
l
-cysteine was added. A mixture of two bacterial strains adsorbed onto CIS could also be successfully separated by use of specific solutions for each strain. Most of the desorbed cells were alive. Thus, quantitative and selective fractionation of cells is readily achievable by employing chitosan, a known antibacterial material.
Plasmids for Nicotine-Dependent and -Independent Gene Expression in
Arthrobacter nicotinovorans
and Other
Arthrobacter
Species
Authors: Sandu Cristinel , Chiribau Calin-Bogdan , Sachelaru Paula , Brandsch Roderich
Published: December 2005

The first inducible
Arthrobacter
overexpression system, based on the promoter/operator and the repressor of the 6-
d
-hydroxynicotine oxidase gene of
Arthrobacter nicotinovorans
, is described here. Nicotine-dependent overproduction and affinity purification of recombinant proteins are presented. The system will allow the production of complex enzymes and genetic complementation studies in
Arthrobacter
species.
Heterologous Production of Functional Forms of
Rhizopus oryzae
Lipase in
Escherichia coli
Authors: Di Lorenzo Mirella , Hidalgo Aurelio , Haas Michael , Bornscheuer Uwe T.
Published: December 2005

To date, expression of the lipase from
Rhizopus oryzae
(ROL) in
Escherichia coli
always led to the formation of inclusion bodies and inactive protein. However, the production of active ROL and its precursor ProROL in soluble form was achieved when
E. coli
Origami(DE3) and pET-11d were used as expression systems.
Growth and Multiplexed Analysis of Microorganisms on a Subdivided, Highly Porous, Inorganic Chip Manufactured from Anopore
Authors: Ingham Colin J. , van den Ende Maaike , Pijnenburg Dirk , Wever Peter C. , Schneeberger Peter M.
Published: December 2005

A highly porous inorganic material (Anopore) was shown to be an effective support for culturing and imaging a wide range of microorganisms. An inert barrier grid was printed on the rigid surface of Anopore to create a “living chip” of 336 miniaturized compartments (200/cm
2
) with broad applications in microbial culture.
Rapid Detection of Subtype-Selective Nuclear Hormone Receptor Binding with Bacterial Genetic Selection
Authors: Skretas Georgios , Wood David W.
Published: December 2005

Subtype-selective nuclear hormone receptor modulators could potentially allow the development of valuable tissue-specific therapeutics. A simple biosensor that allows subtype-specific nuclear hormone receptor binding to be reflected by the growth phenotype of
Escherichia coli
cells has been constructed. This system will potentially enable the facile detection or evolution of subtype-selective hormone analogues.
Results from the ARTEMIS DISK Global AntifungalSurveillance Study: a 6.5-Year Analysis of Susceptibilitiesof
Candida
and Other Yeast Species to Fluconazole andVoriconazole by Standardized Disk Diffusion Testing
Authors: Pfaller M. A. , Diekema D. J. , Rinaldi M. G. , Barnes R. , Hu B. , Veselov A. V. , Tiraboschi N. , Nagy E. , Gibbs D. L.
Published: December 2005

Fluconazole
in vitro susceptibility test results for 140,767 yeasts were collected
from 127 participating investigators in 39 countries from June 1997
through December 2003. Data were collected on 79,343 yeast isolates
tested with voriconazole from 2001 through 2003. All investigators
tested clinical yeast isolates by the CLSI (formerly NCCLS) M44-A disk
diffusion method. Test plates were automatically read and results were
recorded with the BIOMIC Vision Image Analysis System. Species, drug,
zone diameter, susceptibility category, and quality control results
were collected quarterly via e-mail for analysis. Duplicate (the same
patient, same species, and same susceptible-resistant biotype profile
during any 7-day period) and uncontrolled test results were not
analyzed. The 10 most common species of yeasts all showed less
resistance to voriconazole than to fluconazole.
Candida krusei
showed the largest difference, with over 70% resistance to fluconazole
and less than 8% to voriconazole. All species of yeasts tested were
more susceptible to voriconazole than to fluconazole, assuming proposed
interpretive breakpoints of ≥17 mm (susceptible) and≤
13 mm (resistant) for voriconazole. MICs reported in this
study were determined from the zone diameter in millimeters from the
continuous agar gradient around each disk, which was calibrated with
MICs determined from the standard CLSI M27-A2 broth dilution method by
balanced-weight regression analysis. The results from this
investigation demonstrate the broad spectrum of the azoles for most of
the opportunistic yeast pathogens but also highlight several areas
where resistance may be progressing and/or where previously rare
species may be“
emerging.”
Use of Immunoglobulin G Avidity Assays for Differentiation of Primary from Previous Infections with West Nile Virus
Authors: Levett P. N. , Sonnenberg K. , Sidaway F. , Shead S. , Niedrig M. , Steinhagen K. , Horsman G. B. , Drebot M. A.
Published: December 2005

Since its introduction in 1999, West Nile virus (WNV) infections have spread rapidly across the North American continent. Diagnosis of acute WNV infection by detection of WNV-specific immunoglobulin M (IgM) is complicated by the persistence of detectable IgM for more than 1 year in some patients. IgG antibody avidity testing was assessed as a supplemental assay in the diagnosis of current infections. Three groups of serum samples were assayed in parallel by two different IgG avidity test systems (indirect immunofluorescence test [IIFT] and prototype enzyme-linked immunosorbent assay [ELISA]; EUROIMMUN, Luebeck, Germany). Group I (40 sera taken between 2 and 9 days after the onset of influenza-like symptoms) and group II (40 sera taken between 10 and 43 days after onset) were acute and convalescent specimens from patients with a positive anti-WNV IgM test (ELISA; Focus Diagnostics, Cypress, CA). Group III consisted of 43 patient sera collected between 6 and 12 months after infection. IgG antibodies specific for WNV were detected in 38% (ELISA) and 50% (IIFT) of group I sera, in 90% (ELISA and IIFT) of group II sera, and in 100% (ELISA and IIFT) of group III sera. Low-avidity IgG antibodies were demonstrated in 86% (ELISA) and 95% (IIFT) of IgG-positive patient samples taken between 2 and 43 days after the onset of symptoms (groups I and II). High-avidity IgG antibodies were detected in 100% of group III sera obtained 6 months or more after the onset of symptoms (ELISA and IIFT). IgG avidity tests for WNV infections are rapid and simple to perform. The determination of IgG avidity provides additional diagnostic certainty in differentiating between recently acquired and previous infections with WNV.
Genotyping of
Toxoplasma gondii
Strains from Immunocompromised Patients Reveals High Prevalence of Type I Strains
Authors: Khan A. , Su C. , German M. , Storch G. A. , Clifford D. B. , Sibley L. David
Published: December 2005

Toxoplasma gondii
is an important food- and waterborne opportunistic pathogen that causes severe disease in immunocompromised patients.
T. gondii
has an unusual clonal population structure consisting of three widespread lineages known as I, II, and III. To establish the genotypes of strains of
T. gondii
associated with human toxoplasmosis, we have developed a set of four highly sensitive and polymorphic nested PCR markers. Multiplex nested PCR analysis was used to genotype parasites in cerebral spinal fluid samples from 8 of 10 human immunodeficiency virus-positive patients. Remarkably, a majority of these patients had infections with type I strains or strains containing type I alleles, despite the fact that this lineage is normally uncommon in humans and animals. Multiplex analysis of these four unlinked makers was able to distinguish all three common genotypes and also detected two strains with mixed genotypes. Further analysis based on sequencing of a polymorphic intron revealed that one of these recombinant strains was an exotic lineage distinct from the archetypal clonal lineages. The multiplex nested PCR analysis described here will be useful for analyzing the contribution of parasite genotype to toxoplasmosis.
Use of Several Inducer and Substrate Antibiotic Combinations in a Disk Approximation Assay Format To Screen for AmpC Induction in Patient Isolates of
Pseudomonas aeruginosa
,
Enterobacter
spp.,
Citrobacter
spp., and
Serratia
spp
Authors: Dunne W. Michael , Hardin Daniel J.
Published: December 2005

Two-hundred consecutive, single patient isolates of
Enterobacter
spp.,
Serratia
spp.,
Citrobacter
spp., and
Pseudomonas aeruginosa
were evaluated for AmpC production using a variety of inducer-substrate antibiotic combinations in a disk approximation format. The combinations examined included cefoxitin-piperacillin, imipenem-cefotaxime, imipenem-ceftazidime, imipenem-piperacillin-tazobactam, and imipenem-cefoxitin. All isolates were also screened for the presence of extended-spectrum β-lactamase (ESBL) activity. In total, 85.5% of isolates were shown to be inducible for the production of AmpC by one or more inducer/substrate combinations and 11% of all isolates were stably derepressed for the expression of AmpC. Of all of the combinations, imipenem/piperacillin-tazobactam provided the greatest sensitivity (97.1%). All combinations were 100% specific when a positive test was observed. Given this background among these organisms in our institution, it is reasonable to develop an antibiotic reporting strategy that favors the selection of agents for therapy of these organisms that do not serve as labile substrates of AmpC.
Comparison of Two Human Immunodeficiency Virus (HIV) RNA Surrogate Assays to the Standard HIV RNA Assay
Authors: Jennings Cheryl , Fiscus Susan A. , Crowe Suzanne M. , Danilovic Aleksandra D. , Morack Ralph J. , Scianna Salvatore , Cachafeiro Ada , Brambilla Donald J. , Schupbach Jorg , Stevens Wendy , Respess Richard , Varnier Oliviero E. , Corrigan Gary E. , Gronowitz J. Simon , Ussery Michael A. , Bremer James W.
Published: December 2005

Human immunodeficiency virus (HIV) RNA testing is the gold standard for monitoring antiretroviral therapy in HIV-infected patients. However, equipment and reagent costs preclude widespread use of the assay in resource-limited settings. The Perkin-Elmer Ultrasensitive p24 assay and the Cavidi Exavir Load assay both offer potentially simpler, less costly technologies for monitoring viral load. These assays were compared to the Roche Amplicor HIV-1 Monitor Test, v1.5, using panels of clinical samples (subtype B) from HIV-positive subjects and HIV-spiked samples (subtypes A, C, D, CRF_01AE, CRF_02AG, and F). The Ultrasensitive p24 assay detected 100% of the spiked samples with virus loads of >250,000copies/ml and 61% of the clinical samples with virus loads of 219 to 288,850 copies/ml. Detection rates were improved substantially if an external lysis buffer was added to the procedure. The Cavidi assay detected 54 to 100% of spiked samples with virus loads >10,000 copies/ml and 68% of the clinical samples. These detection rates were also greatly improved with a newly implemented version of this kit. Coefficients of variation demonstrate good reproducibility for each of these kits. The results from the Cavidi v1.0, Cavidi v2.0, and Perkin-Elmer, and the Perkin-Elmer Plus external buffers all correlated well with the results from the Roche Monitor Test (
r
= 0.83 to 0.96,
r
= 0.84 to 0.99,
r
= 0.58 to 0.67, and
r
= 0.59 to 0.95, respectively). Thus, the use of these two assays for monitoring patients, together with less-frequent confirmation testing, offers a feasible alternative to frequent HIV RNA testing in resource-limited settings.
Analysis of Genomic Downsizing on the Basis of Region-of-Difference Polymorphism Profiling of
Mycobacterium tuberculosis
Patient Isolates Reveals Geographic Partitioning
Authors: Rao K. Rajender , Kauser Farhana , Srinivas Sriramula , Zanetti Stefania , Sechi Leonardo A. , Ahmed Niyaz , Hasnain Seyed E.
Published: December 2005

Mycobacterium tuberculosis
, the etiological agent of tuberculosis, has lost many coding and noncoding regions in its genome during the course of evolution. We performed region-of-difference (RD) analysis using PCR-based genotyping of 131
M. tuberculosis
clinical isolates obtained from four different countries, namely, India, Peru, Libya, and Angola. Our studies revealed that RD patterns are often distinct for strains circulating in specific geographical regions and can be used to trace the descent and spread of an isolate from its original reservoir. We describe our findings, which show that no single isolate from the four countries (
n
= 131) had all the 15 RDs either deleted or retained. Tuberculosis-specific deletion 1 (TbD1) was found to be conserved in 23% of the Indian isolates, indicating their possible ancient origin. RD9 was the most conserved region, RD11 was predominantly deleted, and RD6 was the most variable among the isolates in our collection irrespective of their geographic region. In contrast to earlier reports, our results demonstrate that the deletion of RD1 does not correlate with a decrease in the virulence potential of
M. tuberculosis
, as Indian isolates (
n
= 30) examined by us were from diseased individuals and yet had lost the RD1 region. Our results further illustrated that the intactness of the RD5 region may be associated with increased virulence of the organism. This study highlights that the RDs in
M. tuberculosis
genomes are geographically distributed and specific and may possibly be associated with virulence spectrum.
Multilocus Sequence Typing of
Neisseria meningitidis
Directly from Clinical Samples and Application of the Method to the Investigation of Meningococcal Disease Case Clusters
Authors: Birtles Andrew , Hardy Katie , Gray Stephen J. , Handford Suzanne , Kaczmarski Edward B. , Edwards-Jones Valerie , Fox Andrew J.
Published: December 2005

Infections associated with
Neisseria meningitidis
are a major public health problem in England, Wales, and Northern Ireland. Currently, over 40% of cases are confirmed directly from clinical specimens using PCR-based methodologies without an organism being isolated. A nested/seminested multilocus sequence typing (MLST) system was developed at the Health Protection Agency Meningococcal Reference Unit to allow strain characterization beyond the serogroup for cases confirmed by PCR only. This system was evaluated on a panel of 20 meningococcus-positive clinical specimens (3 cerebrospinal fluid and 17 blood samples) from different patients containing various concentrations of meningococcal DNA that had corresponding
N. meningitidis
isolates. In each case, the sequence type generated from the clinical specimens matched that produced from the corresponding
N. meningitidis
isolate; the sensitivity of the MLST system was determined to be less than 12 genome copies per PCR. The MLST system was then applied to 15 PCR meningococcus-positive specimens (2 cerebrospinal fluid and 13 blood samples), each from a different patient, involved in three case clusters (two serogroup B and one serogroup W135) for which no corresponding
N. meningitidis
organisms had been isolated. In each case, an MLST sequence type was generated, allowing the accurate assignment of individual cases within each of the case clusters. In summary, the adaptation of the
N. meningitidis
MLST to a sensitive nested/seminested format for strain characterization directly from clinical specimens provides an important tool for surveillance and management of meningococcal infection.
Molecular Fingerprinting of
Leishmania infantum
Strains following an Outbreak of Visceral Leishmaniasis in Central Israel
Authors: Nasereddin Abedelmajeed , Baneth Gad , Schönian Gabriele , Kanaan Moein , Jaffe Charles L.
Published: December 2005

Human and canine visceral leishmaniasis caused by
Leishmania infantum
emerged in central Israel after an absence of over 30 years. The origin of this outbreak was investigated by examining genetic polymorphisms in 37 strains isolated from dogs and patients with visceral leishmaniasis in the continuously active northern Israeli and West Bank foci and in a new Israeli focus using DNA fingerprinting with the human multilocus minisatellite probe 33.15. Analysis of the patterns obtained by DNA fingerprinting separated the strains geographically into northern (clade B) and central (clades A and C) genotypic groups. These results suggest that the emergence of visceral leishmaniasis in central Israel is due not to parasite spread from northern Israel to the new focus but rather to increased parasite transmission in central Israel and the West Bank coupled with changes in the ecoepidemiology of this region.
Bacterial Characteristics in Relation to Clinical Source of
Escherichia coli
Isolates from Women with Acute Cystitis or Pyelonephritis and Uninfected Women
Authors: Johnson James R. , Owens Krista , Gajewski Abby , Kuskowski Michael A.
Published: December 2005

Characteristics differentiating
Escherichia coli
strains that cause cystitis or pyelonephritis from fecal
E. coli
remain incompletely defined, particularly among adult women in the United States. Accordingly, phylogenetic group, O antigens, and virulence factors (VFs) were analyzed among 329
E. coli
isolates from the mid-to-late 1990s from women in the United States with acute pyelonephritis (
n
= 170), cystitis (
n
= 83), or no infection (fecal;
n
= 76). Compared with fecal and cystitis isolates, pyelonephritis isolates exhibited a greater prevalence of phylogenetic group B2, most virulence-associated O antigens, and most VFs and had higher VF scores. In contrast, cystitis and fecal isolates differed minimally. By stepwise multivariable logistic regression, significant (
P
≤ 0.015) predictors of cystitis and/or pyelonephritis (versus fecal) included
afa/dra
(Dr-binding adhesins),
ibeA
(invasion of brain endothelium),
iha
(putative adhesin-siderophore),
malX
(pathogenicity island marker), the O75 antigen,
papEF
(P fimbriae),
papG
allele II (P adhesin variant), group B2, and
sfa
/
foc
(S and F1C fimbriae). However, virulence profiles overlapped considerably among source groups and varied greatly within each group.
E. coli
“clonal group A” (CGA) and the O2:K5/K7:H1 and O75:K+ clonal groups were significantly associated with cystitis and/or pyelonephritis. These findings identify potential vaccine targets, suggest that urovirulence is multiply determined, and confirm the urovirulence of specific
E. coli
clonal groups, including recently recognized CGA.
Molecular Evolution of Human Influenza A/H3N2 Virus in Asia and Europe from 2001 to 2003
Authors: Chi X. Sherry , Bolar Trentice V. , Zhao Ping , Tam John S. , Rappaport Ruth , Cheng Sheau-Mei
Published: December 2005

Hemagglutinin sequences of 146 human influenza A/H3N2 strains identified in respiratory specimens from Asia and Europe during the 2001-2003 influenza seasons were analyzed by DNA sequencing. Our results suggest that four amino acid substitutions, L25I, H75Q, H155T, and Q156H, led to the antigenic conversion of the previously predominant A/Panama/2007/99-like strains to the more recent A/Fujian/411/2002-like strains.
Comparison of the Binax NOW Flu A Enzyme Immunochromatographic Assay and R-Mix Shell Vial Culture for the 2003-2004 Influenza Season
Authors: Fader Robert C.
Published: December 2005

The Binax NOW Flu A enzyme immunochromatographic assay was compared to viral culture with R-Mix shell vials for 455 nasal-wash or nasal-aspirate specimens. The overall sensitivity, specificity, positive predictive value, and negative predictive value of the assay were 64.9%, 98.4%, 89.3%, and 93.2%, respectively. However, the assay sensitivity decreased significantly with increasing patient age.
Development of a Triplex Real-Time PCR Assay for Detection of Panton-Valentine Leukocidin Toxin Genes in Clinical Isolates of Methicillin-Resistant
Staphylococcus aureus
Authors: McDonald Ryan R. , Antonishyn Nick A. , Hansen Toni , Snook Laelie A. , Nagle Evelyn , Mulvey Michael R. , Levett Paul N. , Horsman Greg B.
Published: December 2005

Community-associated methicillin-resistant
Staphylococcus aureus
harboring Panton-Valentine leukocidin (PVL) genes is an emerging pathogen. A novel real-time PCR assay for identification of MRSA isolates containing PVL was developed. The PVL assay was used in a triplex format allowing simultaneous amplification of
mecA
,
nuc
, and PVL genes in 614 clinical isolates. This assay facilitates the rapid identification of PVL-positive isolates of MRSA.
Detection and Serotyping of
Streptococcus pneumoniae
from Nasopharyngeal Samples by PCR-Based Multiplex Assay
Authors: Moreno Jaime , Hernández Elkin , Sanabria Olga , Castañeda Elizabeth
Published: December 2005

We developed a multiplex PCR-based methodology for nasopharyngeal samples maintained in egg thioglycolate antibiotic and skim milk-tryptone-glucose-glycerol media to identify and serotype the most important serotypes of
Streptococcus pneumoniae
that cause invasive disease in children. This technique can be used to study the epidemiology of pneumococcal colonization and the effect of conjugate vaccines.
Molecular Epidemiology of an Outbreak Caused by Methicillin-Resistant
Staphylococcus aureus
in a Health Care Ward and Associated Nursing Home
Authors: Kerttula Anne-Marie , Lyytikäinen Outi , Vuopio-Varkila Jaana , Ibrahem Salha , Agthe Niina , Broas Markku , Jägerroos Henrik , Virolainen Anni
Published: December 2005

Our point-prevalence survey followed an outbreak of methicillin-resistant
Staphylococcus aureus
(MRSA) in a long-term care facility and identified five MRSA strains, of which two possessed an outbreak genotype not encountered previously and three had another profile. All of them possessed SCC
mec
type V. Six methicillin-sensitive
S. aureus
strains were genotypically related to the epidemic strains.
Frequent Importation of Enterovirus 71 from Surrounding Countries into the Local Community of Yamagata, Japan, between 1998 and 2003
Authors: Mizuta K. , Abiko C. , Murata T. , Matsuzaki Y. , Itagaki T. , Sanjoh K. , Sakamoto M. , Hongo S. , Murayama S. , Hayasaka K.
Published: December 2005

Phylogenetic analysis of 45 enterovirus 71 (EV71) isolates for 6 years in Yamagata, Japan, clarified that the annual outbreak of hand-foot-and-mouth disease was due to four genetically distinct subgenogroups, including a novel “B5.” Our results suggest that the importation of EV71 from surrounding countries has had a major epidemiological impact on the local community used in our study.
Toscana Virus Central Nervous System Infections in Southern Italy
Authors: Di Nicuolo Giuseppe , Pagliano Pasquale , Battisti Sonia , Starace Maria , Mininni Vera , Attanasio Vittorio , Faella Francesco Saverio
Published: December 2005

Toscana virus was detected by reverse transcription-nested PCR in 5.6% of cerebrospinal fluid (CSF) samples from patients with meningitis and encephalitis during the summer in southern Italy. The central nervous system infections were associated with young adults and with a substantially benign clinical course. Presenting features and CSF findings are also discussed in the present report.
Analysis of sound radiation from the coupling effect of vibrating noise and moving-vehicle noise on bridges
Authors: Lee Yong-Seon , Kim Sang-Hyo , Jang Won-Suk
Published: December 2005

An acoustic finite element model of a bridge is developed to evaluate the noise generated by the traffic-induced vibration of the bridge. The dynamic response of a multi-girder bridge, modeled by a three-dimensional (3-D) frame element model, is analyzed with a 3-axle (8 degrees of freedom (DOF)) truck model and a 5-axle (13 DOF) tractor-trailer. The flat plate element is used to analyze the acoustic pressure due to the fluid–structure interactions between the vibrating surface and contiguous acoustic fluid medium. The radiation fields of noise with a specified distribution of vibrating velocity and pressure on the structural surface are also computed using the Kirchhoff–Helmholtz integral. Among the diverse parameters affecting the dynamic response of a bridge, vehicle velocity, vehicle weight, and spatial distribution of the road surface roughness are found to be the main factors that increase the level of vibration noise. In an attempt to illustrate the influence of the structural vibration noise of a bridge to total noise level around the bridge, the random function is used to generate the vehicle noise source including the engine noise and the rolling noise between the road and tire. The results show that the low-frequency noise produced by the vibrating bridge members amplifies the high-frequency vehicle noise by 4–7 dB. In addition, the amplification rate of noise increases with traveling speed and vehicle weight. Key words: acoustic pressure on surface, sound radiation, noise level, Kirchhoff–Helmholtz integrals, dynamic response, vehicle noise model, sound pressure level.
Assessing the impact of corrosion control measures on tap drinking water of the Greater Vancouver Regional District
Authors: Knox Gillian , Mavinic Don , Atwater Jim , MacQuarrie Doug
Published: December 2005

A study on the quality of water distributed within the Greater Vancouver Regional District (GVRD) was carried out to evaluate the effectiveness of previously implemented corrosion controls. In addition, the effect of temperature fluctuations was investigated to determine if it influenced the efficacy of the control measures. The GVRD was divided into four distribution areas. The Capilano water had no corrosion control treatment. Seymour, Coquitlam, and Newton waters were treated with soda ash, resulting in a pH of 6.8, 6.9, and 8.1, respectively. Standing cold water and running hot and cold water samples were collected from the four zones and analyzed for lead, copper, and zinc concentrations. The source water did not influence the amount of lead at the tap. The source water did influence the amount of copper and zinc at the tap. The highest copper and zinc concentrations were found in the water with the lowest pH (Capilano) and the lowest concentrations in the water with the highest pH (Newton). Seasonal temperature fluctuations of distributed GVRD water did not affect the metal concentrations in the water.Key words: corrosion control, GVRD drinking water, copper, lead, zinc, pH adjustment.
Gusset plate connections under monotonic and cyclic loading
Authors: Walbridge S S , Grondin G Y , Cheng J J.R
Published: December 2005

A numerical investigation of the monotonic and cyclic behaviour of steel gusset plate connections is conducted using a nonlinear finite element model. Successive versions of the model, which include the effects of framing member stiffness, nonlinear material behaviour, initial imperfections, and bolt slip, are formulated and validated by comparison with test results. A parametric study is then conducted to examine the effects of the load sequence and the interaction between the gusset plate and the brace member under cyclic loading. This investigation demonstrates that the cyclic behaviour of gusset plate connections can be modelled accurately using a simplified finite element model. Gusset plate – brace member subassemblies, wherein the gusset plate is designed as the weak element in compression rather than the brace member, are shown to have stable behaviour under cyclic loading and better energy absorption characteristics than similar subassemblies with the brace member designed as the weak element in compression.Key words: steel, connections, gusset plates, cyclic loading, concentric bracing, buckling.
Modeling incremental pavement roughness using functional network
Authors: Attoh-Okine Nii O
Published: December 2005

Incremental roughness prediction is a critical component of decision making of any pavement management systems, therefore, proper estimation is of paramount importance. This paper presents the application of functional equations and networks to incremental roughness prediction of flexible pavement. In the functional networks, neuron functions are multivariate and multiargumentative. Functional equations form the basis of functional networks, therefore, established theorem in functional equations are easily applicable in the analysis. The model is developed from validated set of incremental and interactive pavement distress functions in the highway design and maintenance standard models (HDM). The models proposed and developed are intended for use in infrastructure management (pavement) applications and as a performance model for pavement design. The paper presents a computational procedure of the functional network using the serial associative functional network. The functional equation and networks approach use the domain knowledge and data for developing the roughness models.Key words: pavement roughness, functional equation, functional networks, neural networks, pavement management.
A new transition curve with enhanced properties
Authors: Tari Ergin , Baykal Orhan
Published: December 2005

A new transition curve-3 (NTC-3), joining two straight lines by providing second-degree contact related to the properties of vehicle–road system without the necessity of a circular arc, is presented. The NTC-3 is offered by curvature and superelevation functions and is compared with the new generation transition curves-1 and -2 (NTC-1, NTC-2) and spiral curves. The properties of vehicle–road system, represented by function of lateral change of acceleration (LCA), are examined for these curves. Three criteria are taken into account to compare the curves. The NTC-3 and NTC-1 are compared in five-different motion models: model with constant velocity, model with positive acceleration, model with negative acceleration, model with negative acceleration – positive acceleration, and model with positive acceleration – negative acceleration. Examination of three criteria shows that NTC-3 is superior to the other curves on the basis of vehicle–road system.Key words: route design, transition curve, vehicle–road system, curvature, lateral change of acceleration, superelevation, motion model.
Structural basis for phosphorylation-dependent signaling in the DNA-damage response
Authors: Williams R Scott , Bernstein Nina , Lee Megan S , Rakovszky Melissa L , Cui Diana , Green Ruth , Weinfeld Michael , Glover J N. Mark
Published: December 2005

The response of eukaryotic cells to DNA damage requires a multitude of protein–protein interactions that mediate the ordered repair of the damage and the arrest of the cell cycle until repair is complete. Two conserved protein modules, BRCT and forkhead-associated (FHA) domains, play key roles in the DNA-damage response as recognition elements for nuclear Ser/Thr phosphorylation induced by DNA-damage-responsive kinases. BRCT domains, first identified at the C-terminus of BRCA1, often occur as multiple tandem repeats of individual BRCT modules. Our recent structural and functional work has revealed how BRCT repeats recognize phosphoserine protein targets. It has also revealed a secondary binding pocket at the interface between tandem repeats, which recognizes the amino-acid 3 residues C-terminal to the phosphoserine. We have also studied the molecular function of the FHA domain of the DNA repair enzyme, polynucleotide kinase (PNK). This domain interacts with threonine-phosphorylated XRCC1 and XRCC4, proteins responsible for the recruitment of PNK to sites of DNA-strand-break repair. Our studies have revealed a flexible mode of recognition that allows PNK to interact with numerous negatively charged substrates.Key words: BRCA1, BRCT, PNK, FHA, polynucleotide kinase, breast cancer, phosphopeptide-protein interactions, DNA damage response.
Screening of biosurfactants for crude oil contaminated soil washing
Authors: Urum Kingsley , Pekdemir Turgay , Çopur Mehmet
Published: December 2005

This study reports experimental measurements on the ability of aqueous biosurfactant solutions (aescin, lecithin, rhamnolipid, saponin, and tannin) at removing Ekofisk crude oil from a laboratory contaminated soil under varying washing conditions. The oil removal performance of the biosurfactants was evaluated against a synthetic anionic surfactant (sodium dodecyl sulphate, SDS) using distilled water as a base case. The washing parameters and ranges tested were temperature, time, shaking speed, volume/mass ratio, and surfactant concentrations. Results indicated that washing temperature was the most influential parameter on the oil removal whilst washing time was the least. It was possible to obtain more than 80% oil removal at 50 °C for all the surfactant solutions, except lecithin, which yielded less than 15% removal. However, saponin, lecithin, aescin, and tannin removed less than 50% crude oil when tested at a temperature of 20 °C and other parameters. Soil washing was found to have considerable potential in removing crude oil from the contaminated soil therefore, we suggest further testing be performed with weathered contaminated soils. Key words: soil washing, biosurfactants, crude oil, contaminated soil, oil removal, oil spill treatment.
A simple colorimetric method for analysis of aqueous phenylenediamines and aniline
Authors: Wang L , Biswas N , Bewtra J K , Taylor K E
Published: December 2005

A simple and accurate method has been developed for the field and laboratory analysis of four highly toxic substances found in certain industrial wastes in high concentrations. Trinitrobenzenesulfonic acid (TNBS) was used as a colorimetric reagent for 1,4-phenylenediamine (p-PD), 1,2-phenylenediamine (o-PD), 1,3-phenylenediamine (m-PD), and aniline in phosphate buffer of pH 7.4 to form relatively stable compounds that had high absorbance near 430 nm. With sodium sulfite present in the solution at 2 mmol·L–1 or above, higher extinction coefficients were attained and good linear relationships of absorbance with PDs and aniline concentrations were observed. Test times required to achieve maximum absorbance were 60 min for p-PD and m-PD, 30 min for aniline, and 200 min for o-PD. The reliable quantitation ranges were 2–20 µmol·L–1 for p-PD and m-PD and 2–40 µmol·L–1 for o-PD and aniline with the standard error of the estimates being less than 5% in these ranges. Key words: phenylenediamine, aniline, trinitrobenzenesulfonic acid, colorimetric test method.
Modeling soil thermal conductivities over a wide range of conditions
Authors: Balland Vincent , Arp Paul A
Published: December 2005

This paper presents a new method to seamlessly calculate thermal conductivity for various soil conditions, from loose to compact, organic to mineral, fine to coarse textured, frozen to unfrozen, and dry to wet. The soil is considered as a multi-phase system, containing air, water (liquid, ice), and particles finer (organic matter, minerals) and coarser (gravel) than 2 mm. The new method extends the general portability of the earlier Johansen (1975) method, and this generalization was fine-tuned empirically with data from soil, gravel, and peat drawn from recent and older literature, for frozen and unfrozen conditions from –30 to 30 °C, and for variable moisture and bulk density conditions from dry to saturated. Scatter plots between measured conductivity and best-fitted calculations consistently followed a straight 1:1 correspondence, with R2 values generally above 0.90. The new method was then used to re-interpret thermal conductivity data involving wettable and non-wettable soils, in situ field measurements, and snow. Key words: thermal conductivity, soil, quartz, ice, water, air, density, snow.
A technique to determine nitrogen removal rates in systems performing simultaneous nitrification and denitrification
Authors: Mavinic Donald S , Oldham William K , Koch Frederic A
Published: December 2005

This paper reports on a possible technique to determine specific nitrification and denitrification rates (SNR and SDNR) in an oxidation-reduction potential (ORP) controlled, intermittent aeration (IA) tank, in which simultaneous nitrification and denitrification (SND) occurred. In addition, SNRs in a three-stage Bardenpho aerobic zone and SDNRs in its anoxic zone were determined. This research was done at bench scale. The technique involves a steady-state run and two additional transient-state tests (created by either ammonia or nitrate shock loading). The rates obtained, using this technique, are the maximum rates possible in a continuous process under certain, improvised conditions. The technique is extremely flexible and generates data relating the rate to substrate concentration in one steady-state run. Data analysis was performed using the integral method; an excellent agreement between predicted and experimental data was found. Zero-order kinetics could describe nitrification in an ammonia concentration range of 1–30 mg/L and denitrification in a nitrate concentration range of 10–30 mg/L. The SNRs in the intermittently aerated, complete-mix (IACM) tank (0.39–1.69 mg g–1 h–1) were considerably lower than those in the 3-stage Bardenpho aerobic zone (3.4–3.81 mg g–1 h–1) due mainly to imposed dissolved oxygen limitations. The SDNRs in the IACM tank were in a range of 0.16–1.26 mg g–1 h–1, which were also considerably lower than that in the 3-stage Bardenpho anoxic zone (2.0–2.5 mg g–1 h–1). Key words: acetate, denitrification, intermittent aeration, kinetics, methanol, nitrification, ORP control, simultaneous nitrification and denitrification.