bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationship of Species-Specific Filament Levels to Filamentous Bulking in Activated Sludge
Authors: Liao Jiangying , Lou Inchio , de los Reyes Francis L.
Published: April 2004

To examine the relationship between activated-sludge bulking and levels of specific filamentous bacteria, we developed a statistics-based quantification method for estimating the biomass levels of specific filaments using 16S rRNA-targeted fluorescent in situ hybridization (FISH) probes. The results of quantitative FISH for the filament
Sphaerotilus natans
were similar to the results of quantitative membrane hybridization in a sample from a full-scale wastewater treatment plant. Laboratory-scale reactors were operated under different flow conditions to develop bulking and nonbulking sludge and were bioaugmented with
S. natans
cells to stimulate bulking. Instead of
S. natans
, the filament Eikelboom type 1851 became dominant in the reactors. Levels of type 1851 filaments extending out of the flocs correlated strongly with the sludge volume index, and extended filament lengths of approximately 6 × 10
8
μm ml
−1
resulted in bulking in laboratory-scale and full-scale activated-sludge samples. Quantitative FISH showed that high levels of filaments occurred inside the flocs in nonbulking sludge, supporting the “substrate diffusion limitation” hypothesis for bulking. The approach will allow the monitoring of incremental improvements in bulking control methods and the delineation of the operational conditions that lead to bulking due to specific filaments.
Exploring Nitrilase Sequence Space for Enantioselective Catalysis
Authors: Robertson Dan E. , Chaplin Jennifer A. , DeSantis Grace , Podar Mircea , Madden Mark , Chi Ellen , Richardson Toby , Milan Aileen , Miller Mark , Weiner David P. , Wong Kelvin , McQuaid Jeff , Farwell Bob , Preston Lori A. , Tan Xuqiu , Snead Marjory A. , Keller Martin , Mathur Eric , Kretz Patricia L. , Burk Mark J. , Short Jay M.
Published: April 2004

Nitrilases are important in the biosphere as participants in synthesis and degradation pathways for naturally occurring, as well as xenobiotically derived, nitriles. Because of their inherent enantioselectivity, nitrilases are also attractive as mild, selective catalysts for setting chiral centers in fine chemical synthesis. Unfortunately, <20 nitrilases have been reported in the scientific and patent literature, and because of stability or specificity shortcomings, their utility has been largely unrealized. In this study, 137 unique nitrilases, discovered from screening of >600 biotope-specific environmental DNA (eDNA) libraries, were characterized. Using culture-independent means, phylogenetically diverse genomes were captured from entire biotopes, and their genes were expressed heterologously in a common cloning host. Nitrilase genes were targeted in a selection-based expression assay of clonal populations numbering 10
6
to 10
10
members per eDNA library. A phylogenetic analysis of the novel sequences discovered revealed the presence of at least five major sequence clades within the nitrilase subfamily. Using three nitrile substrates targeted for their potential in chiral pharmaceutical synthesis, the enzymes were characterized for substrate specificity and stereospecificity. A number of important correlations were found between sequence clades and the selective properties of these nitrilases. These enzymes, discovered using a high-throughput, culture-independent method, provide a catalytic toolbox for enantiospecific synthesis of a variety of carboxylic acid derivatives, as well as an intriguing library for evolutionary and structural analyses.
Genetically Modified Bacterial Strains and Novel Bacterial Artificial Chromosome Shuttle Vectors for Constructing Environmental Libraries and Detecting Heterologous Natural Products in Multiple Expression Hosts
Authors: Martinez Asuncion , Kolvek Steven J. , Yip Choi Lai Tiong , Hopke Joern , Brown Kara A. , MacNeil Ian A. , Osburne Marcia S.
Published: April 2004

The enormous diversity of uncultured microorganisms in soil and other environments provides a potentially rich source of novel natural products, which is critically important for drug discovery efforts. Our investigators reported previously on the creation and screening of an
Escherichia coli
library containing soil DNA cloned and expressed in a bacterial artificial chromosome (BAC) vector. In that initial study, our group identified novel enzyme activities and a family of antibacterial small molecules encoded by soil DNA cloned and expressed in
E. coli
. To continue our pilot study of the utility and feasibility of this approach to natural product drug discovery, we have expanded our technology to include
Streptomyces lividans
and
Pseudomonas putida
as additional hosts with different expression capabilities, and herein we describe the tools we developed for transferring environmental libraries into all three expression hosts and screening for novel activities. These tools include derivatives of
S. lividans
that contain complete and unmarked deletions of the
act
and
red
endogenous pigment gene clusters, a derivative of
P. putida
that can accept environmental DNA vectors and integrate the heterologous DNA into the chromosome, and new BAC shuttle vectors for transferring large fragments of environmental DNA from
E. coli
to both
S. lividans
and
P. putida
by high-throughput conjugation. Finally, we used these tools to confirm that the three hosts have different expression capabilities for some known gene clusters.
Phylogeny and Strain Typing ofEscherichiacoli, Inferred from Variation at Mononucleotide RepeatLoci
Authors: Diamant Eran , Palti Yniv , Gur-Arie Riva , Cohen Helit , Hallerman Eric M. , Kashi Yechezkel
Published: April 2004

Multilocus sequencing of housekeeping genes has been used previously for bacterial strain typing and for inferring evolutionary relationships among strains ofEscherichia coli. In this study, we used shorter intergenic sequences that contained simple sequence repeats (SSRs) of repeating mononucleotide motifs (mononucleotide repeats [MNRs]) to infer the phylogeny of pathogenic and commensalE. colistrains. Seven noncoding loci (four MNRs and three non-SSRs) were sequenced in 27 strains, including enterohemorrhagic (six isolates of O157:H7), enteropathogenic, enterotoxigenic, B, and K-12 strains. The four MNRs were also sequenced in 20 representative strains of theE. colireference (ECOR) collection. Sequence polymorphism was significantly higher at the MNR loci, including the flanking sequences, indicating a higher mutation rate in the sequences flanking the MNR tracts. The four MNR loci were amplifiable by PCR in the standard ECOR A, B1, and D groups, but only one (yaiN) in the B2 group was amplified, which is consistent with previous studies that suggested that B2 is the most ancient group. High sequence compatibility was found between the four MNR loci, indicating that they are in the same clonal frame. The phylogenetic trees that were constructed from the sequence data were in good agreement with those of previous studies that used multilocus enzyme electrophoresis. The results demonstrate that MNR loci are useful for inferring phylogenetic relationships and provide much higher sequence variation than housekeeping genes. Therefore, the use of MNR loci for multilocus sequence typing should prove efficient for clinical diagnostics, epidemiology, and evolutionary study of bacteria.
Method for Collecting Air-Water Interface Microbes Suitable for Subsequent Microscopy and Molecular Analysis in both Research and Teaching Laboratories
Authors: Henk Margaret C.
Published: April 2004

A method has been developed for collecting air-water interface (AWI) microbes and biofilms that enables analysis of the same sample with various combinations of bright-field and fluorescence light microscopy optics, scanning and transmission electron microscopy (TEM), and atomic force microscopy. The identical sample is then subjected to molecular analysis. The sampling tool consists of a microscope slide supporting appropriate substrates, TEM grids, for example, that are removable for the desired protocols. The slide with its substrates is then coated with a collodion polymer membrane to which in situ AWI organisms adhere upon contact. This sampling device effectively separates the captured AWI bacterial community from the bulk water community immediately subtending. Preliminary data indicate that the AWI community differs significantly from the water column community from the same sample site when both are evaluated with microscopy and with 16S ribosomal DNA sequence-based culture-independent comparisons. This microbe collection method can be used at many levels in research and teaching.
Chlorophenol Production by Anaerobic Microorganisms: Transformation of a Biogenic Chlorinated Hydroquinone Metabolite
Authors: Milliken C. E. , Meier G. P. , Sowers K. R. , May H. D.
Published: April 2004

Chlorinated hydroquinones of biological origin are fully dechlorinated to 1,4-dihydroquinone by anaerobic bacteria such as
Desulfitobacterium
spp. (C. E. Milliken, G. P. Meier, J. E. M. Watts, K. R. Sowers, and H. D. May, Appl. Environ. Microbiol.
70:
385-392, 2004). In the present study, mixed microbial communities from Baltimore Harbor sediment and a pure culture of
Desulfitobacterium
sp. strain PCE1 were discovered to demethylate, reductively dehydroxylate, and dechlorinate chlorinated hydroquinones into chlorophenols. Mixed microbial cultures from a freshwater source and several other desulfitobacteria in pure culture did not perform these reactions.
Desulfitobacterium
sp. strain PCE1 degraded 2,3,5,6-tetrachloro-4-methoxyphenol, a metabolite of basidiomycete fungi, to 2,3,5,6-tetrachlorophenol and 2,3,5-trichlorophenol, recalcitrant compounds that are primarily synthesized anthropogenically.
Fate of
Salmonella enterica
Serovar Typhimurium on Carrots and Radishes Grown in Fields Treated with Contaminated Manure Composts or Irrigation Water
Authors: Islam Mahbub , Morgan Jennie , Doyle Michael P. , Phatak Sharad C. , Millner Patricia , Jiang Xiuping
Published: April 2004

Three different types of compost, PM-5 (poultry manure compost), 338 (dairy cattle manure compost), and NVIRO-4 (alkaline-pH-stabilized dairy cattle manure compost), and irrigation water were inoculated with an avirulent strain of
Salmonella enterica
serovar Typhimurium at 10
7
CFU g
−1
and 10
5
CFU ml
−1
, respectively, to determine the persistence of salmonellae in soils containing these composts, in irrigation water, and also on carrots and radishes grown in these contaminated soils. A split-plot block design plan was used for each crop, with five treatments (one without compost, three with each of the three composts, and one without compost but with contaminated water applied) and five replicates for a total of 25 plots for each crop, with each plot measuring 1.8 × 4.6 m. Salmonellae persisted for an extended period of time, with the bacteria surviving in soil samples for 203 to 231 days, and were detected after seeds were sown for 84 and 203 days on radishes and carrots, respectively.
Salmonella
survival was greatest in soil amended with poultry compost and least in soil containing alkaline-pH-stabilized dairy cattle manure compost. Survival profiles of
Salmonella
on vegetables and soil samples contaminated by irrigation water were similar to those observed when contamination occurred through compost. Hence, both contaminated manure compost and irrigation water can play an important role in contaminating soil and root vegetables with salmonellae for several months.
Frequency and Distribution of Tetracycline Resistance Genes in Genetically Diverse, Nonselected, and Nonclinical
Escherichia coli
Strains Isolated from Diverse Human and Animal Sources
Authors: Bryan Andrew , Shapir Nir , Sadowsky Michael J.
Published: April 2004

Nonselected and natural populations of
Escherichia coli
from 12 animal sources and humans were examined for the presence and types of 14 tetracycline resistance determinants. Of 1,263 unique
E. coli
isolates from humans, pigs, chickens, turkeys, sheep, cows, goats, cats, dogs, horses, geese, ducks, and deer, 31% were highly resistant to tetracycline. More than 78, 47, and 41% of the
E. coli
isolates from pigs, chickens, and turkeys were resistant or highly resistant to tetracycline, respectively. Tetracycline MICs for 61, 29, and 29% of
E. coli
isolates from pig, chickens, and turkeys, respectively, were ≥233 μg/ml. Muliplex PCR analyses indicated that 97% of these strains contained at least 1 of 14 tetracycline resistance genes [
tetA
,
tetB
,
tetC
,
tetD
,
tetE
,
tetG
,
tetK
,
tetL
,
tetM
,
tetO
,
tetS
,
tetA(P)
,
tetQ
, and
tetX
] examined. While the most common genes found in these isolates were
tetB
(63%) and
tetA
(35%),
tetC
,
tetD
, and
tetM
were also found.
E. coli
isolates from pigs and chickens were the only strains to have
tetM
. To our knowledge, this represents the first report of
tetM
in
E. coli
.
Growth and Sporulation of
Bacillus cereus
ATCC 14579 under Defined Conditions: Temporal Expression of Genes for Key Sigma Factors
Authors: de Vries Ynte P. , Hornstra Luc M. , de Vos Willem M. , Abee Tjakko
Published: April 2004

An airlift fermentor system allowing precise regulation of pH and aeration combined with a chemically defined medium was used to study growth and sporulation of
Bacillus cereus
ATCC 14579. Sporulation was complete and synchronous. Expression of
sigA
,
sigB
,
sigF
, and
sigG
was monitored with real-time reverse transcription-PCR, and the pattern qualitatively resembled that of
Bacillus subtilis
. This method allows reproducible production of stable spores, while the synchronous growth and defined conditions are excellently suitable for further gene expression studies of cellular differentiation of
B. cereus
.
Geobacter sulfurreducens
Can Grow with Oxygen as a Terminal Electron Acceptor
Authors: Lin W. C. , Coppi M. V. , Lovley D. R.
Published: April 2004

Geobacter sulfurreducens
, previously classified as a strict anaerobe, tolerated exposure to atmospheric oxygen for at least 24 h and grew with oxygen as the sole electron acceptor at concentrations of 10% or less in the headspace. These results help explain how
Geobacter
species may survive in oxic subsurface environments, being poised to rapidly take advantage of the development of anoxic conditions.
ω-Amino Acid:Pyruvate Transaminase from
Alcaligenes denitrificans
Y2k-2: a New Catalyst for Kinetic Resolution of β-Amino Acids and Amines
Authors: Yun Hyungdon , Lim Seongyop , Cho Byung-Kwan , Kim Byung-Gee
Published: April 2004

Alcaligenes denitrificans
Y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed ω-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic β-amino acid, and the corresponding structural gene (
aptA
) was cloned. The gene was functionally expressed in
Escherichia coli
BL21 by using an isopropyl-β-
d
-thiogalactopyranoside (IPTG)-inducible pET expression system (9.6 U/mg), and the recombinant AptA was purified to show a specific activity of 77.2 U/mg for
l
-β-amino-
n
-butyric acid (
l
-β-ABA). The enzyme converts various β-amino acids and amines to the corresponding β-keto acids and ketones by using pyruvate as an amine acceptor. The apparent

K
m

and
V
max
for
l
-β-ABA were 56 mM and 500 U/mg, respectively, in the presence of 10 mM pyruvate. In the presence of 10 mM
l
-β-ABA, the apparent

K
m

and
V
max
for pyruvate were 11 mM and 370 U/mg, respectively. The enzyme exhibits high stereoselectivity (E > 80) in the kinetic resolution of 50 mM
d,l
-β-ABA, producing optically pure
d
-β-ABA (99% enantiomeric excess) with 53% conversion.
Killing of
Bacillus subtilis
Spores by a Modified Fenton Reagent Containing CuCl
2
and Ascorbic Acid
Authors: Shapiro Michael P. , Setlow Barbara , Setlow Peter
Published: April 2004

Bacillus subtilis
spores were killed by CuCl
2
-ascorbic acid, chloride ions were essential for killing of spores, and spores with defective coats were killed more rapidly. CuCl
2
-ascorbic acid did not damage spore DNA, and spores killed by this reagent initiated germination. However, spores killed by CuCl
2
-ascorbic acid may have damage to their inner membrane.
Comparisons of Protocols for Decontamination of Environmental Ice Samples for Biological and Molecular Examinations
Authors: Rogers S. O. , Theraisnathan V. , Ma L. J. , Zhao Y. , Zhang G. , Shin S.-G. , Castello J. D. , Starmer W. T.
Published: April 2004

Drilling and laboratory manipulations of glacial ice cores introduce contemporary microbes and biomolecules onto the cores. We report herein a systematic comparative study of several decontamination protocols. Only treatment with 5% sodium hypochlorite eliminated all external contaminating microbes and nucleic acids while maintaining the integrity of those within the cores.
Development and Evaluation of a Reflective Solar Disinfection Pouch for Treatment of Drinking Water
Authors: Walker D. Carey , Len Soo-Voon , Sheehan Brita
Published: April 2004

A second-generation solar disinfection (SODIS) system (pouch) was constructed from food-grade, commercially available packaging materials selected to fully transmit and amplify the antimicrobial properties of sunlight. Depending upon the season, water source, and challenge organism, culturable bacteria were reduced between 3.5 and 5.5 log cycles. The system was also capable of reducing the background presumptive coliform population in nonsterile river water below the level of detection. Similar experiments conducted with a model virus, the F-specific RNA bacteriophage MS2, indicated that the pouch was slightly less efficient, reducing viable plaques by 3.5 log units in comparison to a 5.0 log reduction of enterotoxigenic
Escherichia coli
O18:H11 within the same time period. These results suggest that water of poor microbiological quality can be improved by using a freely available resource (sunlight) and a specifically designed plastic pouch constructed of food-grade packaging materials.
Serotyping,
stx
2
Subtyping, and Characterization of the Locus of Enterocyte Effacement Island of Shiga Toxin-Producing
Escherichia coli
and
E. coli
O157:H7 Strains Isolated from the Environment in France
Authors: Vernozy-Rozand C. , Montet M. P. , Bertin Y. , Trably F. , Girardeau J. P. , Martin C. , Livrelli V. , Beutin L.
Published: April 2004

Twenty-seven Shiga toxin-producing
Escherichia coli
(STEC) strains were isolated from 207
stx
-positive French environmental samples. Ten of these strains were positive for
stx
1
, and 24 were positive for
stx
2
(10 were positive for
stx
2vh-a
or
stx
2vh-b
, 19 were positive for
stx
2d
, and 15 were positive for
stx
2e
). One strain belonged to serotype O157:H7, and the others belonged to serogroups O2, O8, O11, O26, O76, O103, O113, O121, O141, O166, and O174. The environment is a reservoir in which new clones of STEC that are pathogenic for humans can emerge.
Antibiotic Production by a
Roseobacter
Clade-Affiliated Species from the German Wadden Sea and Its Antagonistic Effects on Indigenous Isolates
Authors: Brinkhoff Thorsten , Bach Gabriela , Heidorn Thorsten , Liang Lanfang , Schlingloff Andrea , Simon Meinhard
Published: April 2004

A strain affiliated with the
Roseobacter
clade and producing a new antibiotic named tropodithietic acid (L. Liang, Ph.D. thesis, University of Göttingen, Göttingen, Germany, 2003) was isolated from the German Wadden Sea. The compound showed strong inhibiting properties with respect to marine bacteria of various taxa and marine algae. Antibiotic production was found to occur during the complete growth phase. Strain mutants without antagonistic properties appeared several times spontaneously.
Assessment of the Epidemic Potential of a New Strain of Rotavirus Associated with the Novel G9 Serotype Which Caused an Outbreak in the United States for the First Time in the 1995-1996 Season
Authors: Clark H. Fred , Lawley Diane A. , Schaffer Alyssa , Patacsil Janice M. , Marcello Amy E. , Glass Roger I. , Jain Vivek , Gentsch Jon
Published: April 2004

Rotavirus causes severe morbidity in developed countries and frequent deaths (≥500,000 per year) in less-developed countries. Historically, four serotypes—G1, G2, G3, and G4—have predominated; they are distinguished by one of two surface neutralization antigens (VP7). However, in 1983 and 1984 we described a new rotavirus serotype, designated G9, in five children hospitalized for diarrhea in Philadelphia, Pa. G9 rotavirus was not identified again in the Western Hemisphere until it caused ca. 50% of the rotavirus disease detected in Philadelphia in the 1995-1996 season. This outbreak allowed us to question whether a rotavirus strain completely new to a well-studied community would target either very young infants or older children, cause especially severe disease, or completely displace previously extant serotypes. We observed a significant excess of G9 infections in younger infants (especially in those <6 months old) that might be attributed to the lack of G9-specific antibodies in mothers. Of further note, six of the seven oldest patients with rotavirus diarrhea were infected with the G9 strains (not significant). However, the age distribution of children with rotavirus did not differ over a 5-year study period regardless of the infecting serotype. Patients with diarrhea associated with G9 strains did not have disease more severe than that caused by the G1, G2, or G3 serotype. G9 strains did not displace the other serotypes but were virtually completely replaced by G1 or G2 serotypes in the three subsequent rotavirus seasons. We conclude that the abrupt appearance of this novel rotavirus serotype did not present a special threat to public health in the community.
Validation of Clinical Application of Cytomegalovirus Plasma DNA Load Measurement and Definition of Treatment Criteria by Analysis of Correlation to Antigen Detection
Authors: Kalpoe Jayant S. , Kroes Aloys C. M. , de Jong Menno D. , Schinkel Janke , de Brouwer Caroline S. , Beersma Matthias F. C. , Claas Eric C. J.
Published: April 2004

Successful preemptive cytomegalovirus (CMV) therapy in transplant patients depends on the availability of sensitive, specific, and timely diagnostic tests for CMV infections. The pp65 antigenemia assay has been used for this purpose with considerable success. Quantification of CMV DNA is currently regarded to be an alternative diagnostic approach. The precise relationship between these two methods has still to be defined, but is essential to compare diagnostic results. This study compared the results of both assays with a large series of transplant recipients in different categories. An internally controlled quantitative real-time CMV DNA PCR was used to test 409 plasma samples from solid organ transplant (SOT) and stem cell transplant (SCT) patients. Levels of CMV DNA in plasma correlated well with classified outcomes of the pp65 antigenemia test. Despite this correlation, the quantitative CMV PCR values in a class of antigen test results were within a wide range, and the definition of an optimal cutoff value for initiating treatment required further analysis by a receiver-operating characteristic curve analysis. This is essential for reactivating infections in particular. For the SCT patients the optimal cutoff value of CMV DNA load defining relevant viral reactivation (in this assay, 10,000 copies/ml) was slightly higher than that for the SOT patients (6,300 copies/ml). Based on a comparison with the established pp65 antigenemia assay, quantification of CMV DNA in plasma appeared to be capable of guiding the clinical management of transplant recipients. This approach may have important advantages, which include a superior reproducibility and sensitivity, allowing the inclusion of kinetic criteria in clinical guidelines.
Molecular Epidemiology of
Mycobacterium avium
subsp.
paratuberculosis
Isolates Recovered from Wild Animal Species
Authors: Motiwala Alifiya S. , Amonsin Alongkorn , Strother Megan , Manning Elizabeth J. B. , Kapur Vivek , Sreevatsan Srinand
Published: April 2004

Mycobacterial isolates were obtained by radiometric culture from 33 different species of captive or free-ranging animals (
n
= 106) and environmental sources (
n
= 3) from six geographic zones within the United States. The identities of all 109 isolates were confirmed by using mycobactin J dependence and characterization of five well-defined molecular markers, including two integration loci of IS
900
(loci L1 and L9), one
Mycobacterium avium
subsp.
paratuberculosis
(
M. paratuberculosis
)-specific sequence (locus 251), and one
M. avium
subsp.
avium
-specific marker (IS
1245
), as well as
hsp65
and IS
1311
restriction endonuclease analyses. Seventy-six acid-fast isolates were identified as
M. paratuberculosis
, 15 were identified as belonging to the
M. avium-M. intracellulare
complex (but not
M. paratuberculosis
), and the remaining 18 were identified as mycobacteria outside the
M. avium
-
M. intracellulare
complex. Fingerprinting by multiplex PCR for IS
900
integration loci clustered 67 of the 76
M. paratuberculosis
strains into a single clade (designated clade A18) and had a Simpson's diversity index (
D
) of 0.53. In contrast, sequence-based characterization of a recently identified
M. paratuberculosis
short sequence repeat (SSR) region enabled the differentiation of the
M. paratuberculosis
isolates in clade A18 into seven distinct alleles (
D
= 0.75). The analysis revealed eight subtypes among the 33 species of animals, suggesting the interspecies transmission of specific strains. Taken together, the results of our analyses demonstrate that SSR analysis enables the genetic characterization of
M. paratuberculosis
isolates from different host species and provide evidence for the host specificity of some
M. paratuberculosis
strains as well as sharing of strains between wild and domesticated animal species.
Evaluation of
porB
PCR-Amplicon Restriction Endonuclease Analysis as a Method To Determine
porB
Variable-Region Sequences in Nonserotypeable Meningococci
Authors: Dyet Kristin H. , Simmonds Robin S. , Martin Diana R.
Published: April 2004

porB
PCR-amplicon restriction endonuclease analysis is a rapid, simple method developed to assess
porB
variation in nonserotypeable meningococci isolated during New Zealand's epidemic of meningococcal disease. Most nonserotypeable meningococci isolated between 1990 and 1999 inclusively either were type 4 (40.5%) or contained the
porB
variable region 1 (VR1)-19, VR2-D, VR3-7, and VR4-14a sequences (45.1%).
Detection of Inducible Clindamycin Resistance of Staphylococci in Conjunction with Performance of Automated Broth Susceptibility Testing
Authors: Jorgensen J. H. , Crawford S. A. , McElmeel M. L. , Fiebelkorn K. R.
Published: April 2004

This study has shown that inducible clindamycin resistance in staphylococci can be detected by disk testing on sheep blood agar inoculum purity plates used with the bioMerieux VITEK 2. Tests of 150 erythromycin-resistant isolates correlated with standard D-zone tests on Mueller-Hinton agar and with PCR for
erm
(A),
erm
(C), and
msr
(A).
Problems in Identification of
Francisella philomiragia
Associated with Fatal Bacteremia in a Patient with Chronic Granulomatous Disease
Authors: Friis-Møller A. , Lemming L. E. , Valerius N. H. , Bruun B.
Published: April 2004

Francisella philomiragia
is a rare gram-negative, halophilic coccobacillus with bizarre spherical forms on primary isolation. A case of
F. philomiragia
bacteremia in a 24-year-old patient with chronic granulomatous disease is reported. Identification of
F. philomiragia
was problematic with conventional tests but was done correctly and rapidly by kit 16S ribosomal DNA sequencing.
Culture-Negative Endocarditis Due to Houston Complex
Bartonella henselae
Acquired in Noumea, New Caledonia
Authors: Rodrick Dani , Dillon Belinda , Dexter Mark , Nicholson Ian , Marcel Sebastien , Dickeson David , Iredell Jon
Published: April 2004

A 44-year-old man with a bioprosthetic aortic valve suffered destructive endocarditis with severe embolic disease due to
Bartonella henselae
infection. Multilocus sequence typing was successfully performed with crude preparations of operative tissue as templates, and the infecting organism was determined to be typical of the Houston clonal group, although it was never cultured from blood or tissue. This is the first report of
B. henselae
infection in the South Pacific, and it reminds one that
B. henselae
is a cause of potentially lethal culture-negative endocarditis which may respond poorly to conventional empirical therapy. Nothing is known of the epidemiology of the infection in this region, but it is likely to be common and to contain representatives of both major clonal complexes. This study emphasizes the ease with which multilocus sequence typing can be used directly with tissue, which is important because of suggestions of strain-dependent clinical outcomes.
Improving surveillance for injuries associated with potential motor vehicle safety defects
Authors: Whitfield R A , Whitfield A K
Published: April 2004

Objective:To improve surveillance for deaths and injuries associated with potential motor vehicle safety defects.

Design:Vehicles in fatal crashes can be studied for indications of potential defects using an “early warning” surveillance statistic previously suggested for screening reports of adverse drug reactions. This statistic is illustrated with time series data for fatal, tire related and fire related crashes. Geographic analyses are used to augment the tire related statistics.

Results:A statistical criterion based on the Poisson distribution that tests the likelihood of an expected number of events, given the number of events that actually occurred, is a promising method that can be readily adapted for use in injury surveillance.

Conclusions:Use of the demonstrated techniques could have helped to avert a well known injury surveillance failure. This method is adaptable to aid in the direction of engineering and statistical reviews to prevent deaths and injuries associated with potential motor vehicle safety defects using available databases.
Reality check: using newspapers, police reports, and court records to assess defensive gun use
Authors: Denton J F , Fabricius W V
Published: April 2004

Objective:To identify legitimate defensive gun uses (DGUs), and provide a reality check on previous estimates of the rate of DGUs by using a novel approach based on newspaper reports and police and court records. Previous estimates have relied on self report, differ by a factor of 10 or more, and are viewed as highly controversial.

Design and setting:The reported uses of firearms in a newspaper covering roughly the Phoenix metropolitan area over almost a 3.5 month period were examined, supplemented where necessary by police and court records.

Results:Two DGUs involving killing assailants and one involving firing at an assailant were found. The three DGUs stemmed from cases of “mutual combat” or exposed bystanders to gunfire.

Conclusions:These findings cast doubt on rates of DGUs reported in an influential study by Kleck and Gertz, which predict that the police should have known about 98 DGU killings or woundings and 236 DGU firings at adversaries during the time the newspaper was surveyed. The findings reported here were closer to predictions based on the National Crime Victimization Survey, which suggest that the police should have known about eight DGU killings or woundings and 19 DGU firings at adversaries.
Community paediatricians’ counseling patterns and knowledge of recommendations relating to child restraint use in motor vehicles
Authors: Rothenstein J , Howard A , Parkin P , Khambalia A , Macarthur C
Published: April 2004

Background:Road traffic injury is the leading cause of death among Canadian children and youth. Transport Canada recommends four types of child restraint depending on the size of the child, and recent studies have demonstrated the effectiveness of recommended restraint use.

Objectives:To determine community paediatricians’ knowledge of Transport Canada recommendations for child restraint use in vehicles, and to examine paediatricians’ counseling patterns in relation to child passenger safety.

Methods:A mailed questionnaire survey of all community paediatricians affiliated with the Hospital for Sick Children, Toronto was conducted. A 16 item questionnaire gathered information on knowledge of Transport Canada recommendations for child restraint use, general counseling patterns in relation to child passenger safety, and demographic information.

Results:In total, 60 community paediatricians in active practice were identified. Of these, 48 (80%) responded to the mailed questionnaire. Almost all paediatricians (92%) correctly identified the recommended weight for transition to a forward-facing car seat, whereas fewer paediatricians (63%) correctly identified the recommended weight for transition to a booster seat from a forward-facing car seat, and only one third of paediatricians correctly identified the recommended weight for transition from a booster seat to a seat belt.

Conclusion:Community paediatricians’ knowledge of Transport Canada recommendations for child restraint use in vehicles is incomplete. There is a need for such recommendations to be better disseminated to paediatricians and parents so that information on child restraint use is delivered in a clear and consistent manner.
Review of the role of alcohol in drowning associated with recreational aquatic activity
Authors: Driscoll T R , Harrison J A , Steenkamp M
Published: April 2004

Objective and design:To assess the role of alcohol in drowning associated with recreational aquatic activity by reviewing the English language literature published up to October 2003.

Results:Alcohol is widely used in association with recreational aquatic activity in the United States, but there is minimal information regarding the extent of use elsewhere. A priori and anecdotal evidence suggests that alcohol is an important risk factor for drowning associated with recreational aquatic activity. Specific studies provide good evidence supporting this, but the extent of increased risk associated with alcohol use, and the attributable risk due to alcohol use, is not well characterised. Drowning appears to be the overwhelming cause of death associated with recreational aquatic activity with alcohol detected in the blood in 30%–70% of persons who drown while involved in this activity. The few relevant studies on degree of increased risk suggest persons with a blood alcohol level of 0.10 g/100 ml have about 10 times the risk of death associated with recreational boating compared with persons who have not been drinking, but that even small amounts of alcohol can increase this risk. The population attributable risk seems to be in the range of about 10%–30%.

Conclusions:Alcohol consumption significantly increases the likelihood of immersions resulting in drowning during aquatic activities. However, more information is required if appropriate prevention activities are to be planned, initiated, and evaluated. This includes better information on alcohol use, and attitudes to alcohol use, in association with recreational aquatic activity, and the nature and extent of increased risk associated with alcohol use. Evaluation of interventions is also needed.
Downhill skiing injury fatalities among children
Authors: Xiang H , Stallones L , Smith G A
Published: April 2004

Objective:Young skiers are at increased risk for injury, however, epidemiological data on skiing related fatal injuries among child skiers are scarce. This study aimed to provide information needed to develop injury control and prevention programs.

Design and setting:Study subjects came from Colorado, USA and were identified using a death certificate based surveillance system. Fatal injuries were limited to events that occurred at established commercial ski resorts in Colorado, and subjects were classified as child skiers (0–17 years) or adult skiers (⩾18 years).

Main outcome measure:Type and external cause, time, and week day of injury, gender and residency of the decedents.

Results:During the study period from 1980–2001, 149 fatal injuries associated with downhill skiing were identified; 21 (14.1%) occurred among child skiers aged ⩽17 years. The age of the youngest decedent was 7 years. In females the proportion of fatal injuries among child skiers was nearly three times that of adults. Traumatic brain injuries were the leading cause of death (67% of all deaths) among children, while multiple internal injuries and traumatic brain injuries accounted for almost equal proportions of fatal injuries among adults. Collision was the leading external mechanism of fatal injuries, accounting for more than two thirds of fatal injuries in both child and adult skiers.

Conclusions:Traumatic brain injury was the leading cause and collision was the leading external injury mechanism of fatal injuries associated with downhill skiing among child skiers. This underscores the importance of brain injury prevention strategies, including the use of ski helmets and prevention of collisions on ski slopes.
Epidemiology of electrical and lightning related deaths and injuries among Canadian children and youth
Authors: Nguyen B H , MacKay M , Bailey B , Klassen T P
Published: April 2004

Among burn injuries, electrical injuries constitute a small but devastating fraction. To describe the epidemiology of electrical injuries in Canadian children, data on deaths and emergency department visits related to electrical injuries, including lightning strikes, were obtained from provincial coroners’ offices and the Canadian Hospitals Injury Reporting and Prevention Program (CHIRPP) respectively, for the years 1991–96. Twenty one deaths and 606 emergency visits highlight that electrical related deaths, more frequent among school age children, are more likely the result of high voltage and lightning strike, while emergency department visits, more frequent among younger children, are more likely the result of low voltage. While the introduction of legislated standards for child safe outlets and educational programs for parents, children, and youth are recommended strategies toward reducing the frequency of these incidents, these strategies require further evaluation before their effectiveness can be estimated.
Effects of predatorprey interactions and adaptive change on sustainable yield
Authors: Matsuda Hiroyuki , Abrams Peter A
Published: April 2004

We explore the effects on population size and yield of different levels of harvesting of a predator in a predatorprey system. We consider the consequences of adaptive change in the predator's foraging time (or effort) and feedback control of fishing effort. The predator may increase in population size with increasing fishing effort, either when the prey is characterized by a positive effect of its own population size on its own growth rate or when the prey is overexploited by the predator. The predator abundance at which the sustainable yield is maximized can be larger than the abundance without fishing. The effort that achieves maximum sustainable yield and the effort that maximizes predator abundance can both be close to the effort at which the stock collapses. Feedback control in the response to predator abundance may fail to achieve the desired abundance of the target stock or its prey even if the fishing effort is well controlled. These results suggest that developing policies for exploiting adaptive predator species in potentially cycling systems cannot be based on the stable single-species models often used in fisheries management.
Effects of sex, stock, and environment on the shape of known-age Atlantic cod (Gadus morhua) otoliths
Authors: Cardinale M , Doering-Arjes P , Kastowsky M , Mosegaard H
Published: April 2004

The effects of sex, stock, and environment on the shape of known-age Atlantic cod (Gadus morhua) otoliths from the Faroe Islands were investigated. Moreover, the feasibility of otolith shape analysis for stock identification was evaluated. The shape was described by using several normalized Fourier descriptors and morphometric variables. There were no consistent differences between the left and right otoliths and between sexes within different age classes, stocks, and environments. With our experimental design, we could evaluate the relative importance of genetic and environmental conditions (water temperature and diet regime) on otolith shape and morphometrics. Using otolith shape, cod individuals were significantly separated into Bank and Plateau stocks. Total classification success was between 79% and 85% between stocks and between 85% and 96% between environments for the different age classes. The significant differences in otolith shape between Faroe Bank and Faroe Plateau cod stocks provided a phenotypic basis for stock separation. Stock and environmental influences were substantial in determining the shape of cod otoliths.
Transferability of habitat preference criteria for larval European grayling (Thymallus thymallus)
Authors: Nykänen M , Huusko A
Published: April 2004

We examined the transferability of habitat preference criteria for larval European grayling (Thymallus thymallus) to two rivers in Finland by testing whether there were significant positive rank correlations between local fish densities (shoals per square metre) and preference indices for depth, velocity, substrate, and vegetation cover or selected combinations. Two sets of preference curves, one obtained from literature for the River Pollon, France, and another for the River Kuusinkijoki, Finland, were tested. All transferability tests for water velocity criteria were successful, correlation coefficients between local fish densities and preference indices ranging from 0.83 to 0.92. Criteria for depth and substrate transferred inconsistently, and criteria for vegetation cover failed to transfer to either target site. Combined indices predicted fish microdistributions inconsistently and they never performed better than the best univariate index for each site. Our results suggest that universal preference criteria for water velocity may exist for larval grayling and that it may be best to use these criteria alone in habitat hydraulic modelling when predicting habitat suitability to larval grayling.
Detecting persistent change in the habitat of salmon-bearing streams in the Pacific Northwest
Authors: Larsen David P , Kaufmann Philip R , Kincaid Thomas M , Urquhart N Scott
Published: April 2004

In the northwestern United States, there is considerable interest in the recovery of Pacific salmon (Oncorhynchus spp.) populations listed as threatened or endangered. A critical component of any salmon recovery effort is the improvement of stream habitat that supports various life stages. Two factors in concert control our ability to detect consistent change in habitat conditions that could result from significant expenditures on habitat improvement: the magnitude of spatial and temporal variation and the design of the monitoring network. We summarize the important components of variation that affect trend detection and explain how well-designed networks of 3050 sites monitored consistently over years can detect underlying changes of 12% per year in a variety of key habitat characteristics within 1020 years, or sooner, if such trends are present. We emphasize the importance of the duration of surveys for trend detection sensitivity because the power to detect trends improves substantially with the passage of years.
The effects of adult length and arrival date on individual reproductive success in wild steelhead trout (Oncorhynchus mykiss)
Authors: Seamons Todd R , Bentzen Paul , Quinn Thomas P
Published: April 2004

To determine the relative importance of adult size and arrival date for reproductive success in a natural setting, we first genetically determined relationships between all spawning adult steelhead (Oncorhynchus mykiss) and juvenile offspring in four brood years and then tested hypothesized relationships between parents' phenotypes and the number and size of their juvenile offspring. Patterns of reproductive success varied among years, but in all cases, a few adults of each sex produced most of the offspring. The number of offspring showed a weak, positive relationship to the mother's size but not to her arrival date. Paternal reproductive success varied considerably but was only weakly associated with size in 1998 and weakly related to arrival date in 2000. In 1997, 1998, and 1999, the offspring of early-spawning females were larger at the end of their first and second summers in the stream; however, in 2000, both arrival date and length were positively related to offspring size. There was no general trend in offspring size in relation to paternal size or arrival date; however, paternal length affected offspring size in 1998 and male arrival date affected offspring size in 2000.
Drifters versus residents: assessing size and age differences in Atlantic salmon (Salmo salar) fry
Authors: Bujold Valérie , Cunjak Richard A , Dietrich Jason P , Courtemanche David A
Published: April 2004

Some young-of-the-year Atlantic salmon (Salmo salar) have a tendency to drift soon after emergence from the gravel, whereas others, called resident fry, set up and defend territories. Little is known about the mechanisms regulating this strong tendency to drift soon after emergence, a phenomenon that can greatly influence survival within a population. This study was carried out in the Western Brook system, Gros Morne National Park, Newfoundland, Canada. The objective was to assess differences, through biometric characteristics, between drifting and resident Atlantic salmon fry by examining both groups of fish caught simultaneously in the same riverine habitat. Resident salmon fry can be up to 4.8% longer and 20.4% heavier compared with drifting fry of similar age (measured in days since emergence). Therefore, it seems that competition, more than prior residence effect, could be part of the driving forces behind this active movement and that differences between subpopulations of Atlantic salmon fry can have major repercussions on life history patterns.
An integrated model for growth incorporating tagrecapture, lengthfrequency, and direct aging data
Authors: Eveson J Paige , Laslett Geoff M , Polacheck Tom
Published: April 2004

A maximum likelihood method for modelling fish growth is presented that integrates data from three key sources of growth information: tagrecapture studies, lengthfrequency samples from commercial catches, and direct aging data from hard-parts analyses. Previous studies have almost exclusively modelled growth using only one of these sources of information. Different data sources are often most informative about different portions of the life cycle. The development of an integrated approach allows for the different data sources to complement each other and provide more comprehensive and robust estimates of growth parameters. The integrated method is applied to data sets from southern bluefin tuna (Thunnus maccoyii) using the von Bertalanffy growth curve as well as a more sophisticated growth curve that makes a smooth transition between two von Bertalanffy curves with different growth rate parameters. The latter is found to provide a significantly better fit and supports previous findings that southern bluefin tuna experience a transition in growth during the juvenile stage of life. Many species exhibit a seasonal growth pattern, including southern bluefin tuna for which growth is fastest during the austral summer. A method for incorporating an annual seasonal component into the analysis is described and applied.