bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation of a Methanogen from Deep Marine Sediments That Contain Methane Hydrates, and Description of
Methanoculleus submarinus
sp. nov
Authors: Mikucki Jill A. , Liu Yitai , Delwiche Mark , Colwell Frederick S. , Boone David R.
Published: June 2003

We isolated a methanogen from deep in the sediments of the Nankai Trough off the eastern coast of Japan. At the sampling site, the water was 950 m deep and the sediment core was collected at 247 m below the sediment surface. The isolated methanogen was named Nankai-1. Cells of Nankai-1 were nonmotile and highly irregular coccoids (average diameter, 0.8 to 2 μm) and grew with hydrogen or formate as a catabolic substrate. Cells required acetate as a carbon source. Yeast extract and peptones were not required but increased the growth rate. The cells were mesophilic, growing most rapidly at 45°C (no growth at ≤10°C or ≥55°C). Cells grew with a maximum specific growth rate of 2.43 day
−1
at 45°C. Cells grew at pH values between 5.0 and 8.7 but did not grow at pH 4.7 or 9.0. Strain Nankai-1 grew in a wide range of salinities, from 0.1 to 1.5 M Na
+
. The described phenotypic characteristics of this novel isolate were consistent with the in situ environment of the Nankai Trough. This is the first report of a methanogenic isolate from methane hydrate-bearing sediments. Phylogenetic analysis of its 16S rRNA gene sequence indicated that it is most closely related to
Methanoculleus marisnigri
(99.1% sequence similarity), but DNA hybridization experiments indicated a DNA sequence similarity of only 49%. Strain Nankai-1 was also found to be phenotypically similar to
M. marisnigri
, but two major phenotypic differences were found: strain Nankai-1 does not require peptones, and it grows fastest at a much higher temperature. We propose a new species,
Methanoculleus submarinus
, with strain Nankai-1 as the type strain.
Fluorescent Heteroduplex Assay for Monitoring
Bacillus anthracis
and Close Relatives in Environmental Samples
Authors: Merrill Lori , Richardson Jennifer , Kuske Cheryl R. , Dunbar John
Published: June 2003

A fluorescent heteroduplex method was developed to assess the presence of 16S rRNA gene (rDNA) sequences from
Bacillus anthracis
and close relatives in PCR-amplified 16S rDNA sequence mixtures from environmental samples. The method uses a single-stranded, fluorescent DNA probe, 464 nucleotides in length, derived from a
B. anthracis
16S rRNA gene. The probe contains a unique, engineered deletion such that all probe-target duplexes are heteroduplexes with an unpaired G at position 343 (ΔG343). Heteroduplex profiles of sequences ≥85% similar to the probe were produced using an ABI 377 sequencer in less than 3 h. The method divides strains of the
Bacillus cereus
-
Bacillus thuringiensis
-
B. anthracis
group into two subgroups. Each subgroup is defined by a specific 16S rRNA gene sequence type. Sequence type A, containing one mismatch with the probe, occurs in
B. anthracis
and a small number of closely related clonal lineages represented mostly by food-borne pathogenic isolates of
B. cereus
and
B. thuringiensis
. Sequence type B, containing two mismatches with the probe, is found in the majority of
B. cereus
and
B. thuringiensis
strains examined to date. Sequence types A and B, when hybridized to the probe, generate two easily differentiated heteroduplexes. Thus, from heteroduplex profiles, the presence of
B. cereus
-
B. thuringiensis
-
B. anthracis
subgroups in environmental samples can be inferred unambiguously. The results show that fluorescent heteroduplex analysis is an effective profiling technique for detection and differentiation of sequences representing small phylogenetic or functional groups in environmental samples.
Identification and Manipulation of Soil Properties To Improve the Biological Control Performance of Phenazine-ProducingPseudomonas fluorescens
Authors: Ownley Bonnie H. , Duffy Brion K. , Weller David M.
Published: June 2003

Pseudomonas fluorescens2-79RN10protects wheat against take-all disease caused byGaeumannomyces graminisvar.tritici; however, the level of protection in the field varies from site to site. Identification of soil factors that exert the greatest influence on disease suppression is essential to improving biocontrol. In order to assess the relative importance of 28 soil properties on take-all suppression, seeds were treated with strain 2-79RN10(which produces phenazine-1-carboxylate [PCA+]) or a series of mutants with PCA+and PCA−phenotypes. Bacterized seeds were planted in 10 soils, representative of the wheat-growing region in the Pacific Northwest. Sixteen soil properties were correlated with disease suppression. Biocontrol activity of PCA+strains was positively correlated with ammonium-nitrogen, percent sand, soil pH, sodium (extractable and soluble), sulfate-sulfur, and zinc. In contrast, biocontrol was negatively correlated with cation-exchange capacity (CEC), exchangeable acidity, iron, manganese, percent clay, percent organic matter (OM), percent silt, total carbon, and total nitrogen. Principal component factor analysis of the 16 soil properties identified a three-component solution that accounted for 87 percent of the variance in disease rating (biocontrol). A model was identified with step-wise regression analysis (R2= 0.96; Cpstatistic = 6.17) that included six key soil properties: ammonium-nitrogen, CEC, iron, percent silt, soil pH, and zinc. As predicted by our regression model, the biocontrol activity of 2-79RN10was improved by amending a soil low in Zn with 50 μg of zinc-EDTA/g of soil. We then investigated the negative correlation of OM with disease suppression and found that addition of OM (as wheat straw) at rates typical of high-OM soils significantly reduced biocontrol activity of 2-79RN10.
A Stable Bioluminescent Construct of
Escherichia coli
O157:H7 for Hazard Assessments of Long-Term Survival in the Environment
Authors: Ritchie Jennifer M. , Campbell Graeme R. , Shepherd Jill , Beaton Yvonne , Jones Davey , Killham Ken , Artz Rebekka R. E.
Published: June 2003

A chromosomally
lux-
marked (Tn
5 luxCDABE
) strain of nontoxigenic
Escherichia coli
O157:H7 was constructed by transposon mutagenesis and shown to have retained the O157, H7, and intimin phenotypes
.
The survival characteristics of this strain in the experiments performed (soil at −5, −100, and −1,500 kPa matric potential and artificial groundwater) were indistinguishable from the wild-type strain. Evaluation of potential luminescence was found to be a rapid, cheap, and quantitative measure of viable
E. coli
O157:H7 Tn
5 luxCDABE
populations in environmental samples. In the survival studies, bioluminescence of the starved populations of
E. coli
O157:H7 Tn
5 luxCDABE
could be reactivated to the original levels of light emission, suggesting that these populations remain viable and potentially infective to humans. The attributes of the construct offer a cheap and low-risk substitute to the use of verocytotoxin-producing
E. coli
O157:H7 in long-term survival studies.
Development of a Thermally Regulated Broad-Spectrum Promoter System for Use in Pathogenic Gram-Positive Species
Authors: Schofield David A. , Westwater Caroline , Hoel Brian D. , Werner Phillip A. , Norris James S. , Schmidt Michael G.
Published: June 2003

Selectively regulating gene expression is an essential molecular tool that is lacking for many pathogenic gram-positive bacteria. In this report, we describe the evaluation of a series of promoters regulated by the bacteriophage P1 temperature-sensitive C1 repressor in
Enterococcus faecium
,
Enterococcus faecalis
, and
Staphylococcus aureus
. Using the
lacZ
gene to monitor gene expression, we examined the strength, basal expression, and induced expression of synthetic promoters carrying C1 operator sites. The promoters exhibited extremely low basal expression and, under inducing conditions, gave high levels of expression (100- to 1,000-fold induction). We demonstrate that the promoter system could be modulated by temperature and showed rapid induction and that the mechanism of regulation occurred at the level of transcription. Controlled expression with the same constructs was also demonstrated in the gram-negative bacterium
Escherichia coli
. However, low basal expression and the ability to achieve derepression were dependent on both the number of mismatches in the C1 operator sites and the promoter driving
c
1 expression. Since the promoters were designed to contain conserved promoter elements from gram-positive species and were constructed in a broad-host-range plasmid, this system will provide a new opportunity for controlled gene expression in a variety of gram-positive bacteria.
Giardia
Cysts in Wastewater Treatment Plants in Italy
Authors: Cacciò Simone M. , De Giacomo Marzia , Aulicino Francesca A. , Pozio Edoardo
Published: June 2003

Reductions in annual rainfall in some regions and increased human consumption have caused a shortage of water resources at the global level. The recycling of treated wastewaters has been suggested for certain domestic, industrial, and agricultural activities. The importance of microbiological and parasitological criteria for recycled water has been repeatedly emphasized. Among water-borne pathogens, protozoa of the genera
Giardia
and
Cryptosporidium
are known to be highly resistant to water treatment procedures and to cause outbreaks through contaminated raw or treated water. We conducted an investigation in four wastewater treatment plants in Italy by sampling wastewater at each stage of the treatment process over the course of 1 year. The presence of the parasites was assessed by immunofluorescence with monoclonal antibodies. While
Cryptosporidium
oocysts were rarely observed,
Giardia
cysts were detected in all samples throughout the year, with peaks observed in autumn and winter. The overall removal efficiency of cysts in the treatment plants ranged from 87.0 to 98.4%. The removal efficiency in the number of cysts was significantly higher when the secondary treatment consisted of active oxidation with O
2
and sedimentation instead of activated sludge and sedimentation (94.5% versus 72.1 to 88.0%;
P
= 0.05, analysis of variance). To characterize the cysts at the molecular level, the β
-
giardin gene was PCR amplified, and the products were sequenced or analyzed by restriction. Cysts were typed as assemblage A or B, both of which are human pathogens, stressing the potential risk associated with the reuse of wastewater.
Use of Antibiotic Resistance Analysis for Representativeness Testing of Multiwatershed Libraries
Authors: Wiggins Bruce A. , Cash Philip W. , Creamer Wes S. , Dart Scott E. , Garcia Preston P. , Gerecke Todd M. , Han Jennifer , Henry Brian L. , Hoover Kylie B. , Johnson Erika L. , Jones K. C. , McCarthy Jacquie G. , McDonough Justin A. , Mercer Sarah A. , Noto Michael J. , Park Haewon , Phillips Matthew S. , Purner Stephanie M. , Smith Brian M. , Stevens Erin N. , Varner Amy K.
Published: June 2003

The use of antibiotic resistance analysis (ARA) for microbial source tracking requires the generation of a library of isolates collected from known sources in the watershed. The size and composition of the library are critical in determining if it represents the diversity of patterns found in the watershed. This study was performed to determine the size that an ARA library needs to be to be representative of the watersheds for which it will be used and to determine if libraries from different watersheds can be merged to create multiwatershed libraries. Fecal samples from known human, domesticated, and wild animal sources were collected from six Virginia watersheds. From these samples, enterococci were isolated and tested by ARA. Based on cross-validation discriminant analysis, only the largest of the libraries (2,931 isolates) were found to be able to classify nonlibrary isolates as well as library isolates (i.e., were representative). Small libraries tended to have higher average rates of correct classification, but were much less able to correctly classify nonlibrary isolates. A merged multiwatershed library (6,587 isolates) was created and was found to be large enough to be representative of the isolates from the contributing watersheds. When isolates that were collected from the contributing watersheds approximately 1 year later were analyzed with the multiwatershed library, they were classified as well as the isolates in the library, suggesting that the resistance patterns are temporally stable for at least 1 year. The ability to obtain a representative, temporally stable library demonstrates that ARA can be used to identify sources of fecal pollution in natural waters.
Glucose Metabolism in
Lactococcus lactis
MG1363 under Different Aeration Conditions: Requirement of Acetate To Sustain Growth under Microaerobic Conditions
Authors: Nordkvist Mikkel , Jensen Niels Bang Siemsen , Villadsen John
Published: June 2003

Lactococcus lactis
subsp.
lactis
MG1363 was grown in batch cultures on a defined medium with glucose as the energy source under different aeration conditions, namely, anaerobic conditions, aerobic conditions, and microaerobic conditions with a dissolved oxygen tension of 5% (when saturation with air was used as the reference). The maximum specific growth rate was high (0.78 to 0.91 h
−1
) under all aeration conditions but decreased with increasing aeration, and more than 90% of the glucose was converted to lactate. However, a shift in by-product formation was observed. Increasing aeration resulted in acetate, CO
2
, and acetoin replacing formate and ethanol as end products. Under microaerobic conditions, growth came to a gradual halt, although more than 60% of the glucose was still left. A decline in growth was not observed during microaerobic cultivation when acetate was added to the medium. We hypothesize that the decline in growth was due to a lack of acetyl coenzyme A (acetyl-CoA) needed for fatty acid synthesis since acetyl-CoA can be synthesized from acetate by means of acetate kinase and phosphotransacetylase activities.
Rapid Detection of
Campylobacter coli
,
C. jejuni
, and
Salmonella enterica
on Poultry Carcasses by Using PCR-Enzyme-Linked Immunosorbent Assay
Authors: Hong Yang , Berrang Mark E. , Liu Tongrui , Hofacre Charles L. , Sanchez Susan , Wang Lihua , Maurer John J.
Published: June 2003

Contamination of retail poultry by
Campylobacter
spp. and
Salmonella enterica
is a significant source of human diarrheal disease. Isolation and identification of these microorganisms require a series of biochemical and serological tests. In this study,
Campylobacter ceuE
and
Salmonella invA
genes were used to design probes in PCR-enzyme-linked immunosorbent assay (ELISA), as an alternative to conventional bacteriological methodology, for the rapid detection of
Campylobacter jejuni
,
Campylobacter coli
, and
S. enterica
from poultry samples. With PCR-ELISA (40 cycles), the detection limits for
Salmonella
and
Campylobacter
were 2 × 10
2
and 4 × 10
1
CFU/ml, respectively. ELISA increased the sensitivity of the conventional PCR method by 100- to 1,000-fold. DNA was extracted from carcass rinses and tetrathionate enrichments and used in PCR-ELISA for the detection of
Campylobacter
and
S. enterica
, respectively. With PCR-ELISA,
Salmonella
was detected in 20 of 120 (17%) chicken carcass rinses examined, without the inclusion of an enrichment step. Significant correlation was observed between PCR-ELISA and cultural methods (kappa = 0.83; chi-square test,
P
< 0.001) with only one false negative (1.67%) and four false positives (6.67%) when PCR-ELISA was used to screen 60 tetrathionate enrichment cultures for
Salmonella
. With PCR-ELISA, we observed a positive correlation between the ELISA absorbance (optical density at 405 nm) and the campylobacter cell number in carcass rinse, as determined by standard culture methods. Overall, PCR-ELISA is a rapid and cost-effective approach for the detection and enumeration of
Salmonella
and
Campylobacter
bacteria on poultry.
Bacterial Colonization of Particles: Growth and Interactions
Authors: Grossart Hans-Peter , Kiørboe Thomas , Tang Kam , Ploug Helle
Published: June 2003

Marine particles in the ocean are exposed to diverse bacterial communities, and colonization and growth of attached bacteria are important processes in the degradation and transformation of the particles. In an earlier study, we showed that the initial colonization of model particles by individual bacterial strains isolated from marine aggregates was a function of attachment and detachment. In the present study, we have investigated how this colonization process was further affected by growth and interspecific interactions among the bacteria. Long-term incubation experiments showed that growth dominated over attachment and detachment after a few hours in controlling the bacterial population density on agar particles. In the absence of grazing mortality, this growth led to an equilibrium population density consistent with the theoretical limit due to oxygen diffusion. Interspecific interaction experiments showed that the presence of some bacterial strains (“residents”) on the agar particles either increased or decreased the colonization rate of other strains (“newcomers”). Comparison between an antibiotic-producing strain and its antibiotic-free mutant showed no inhibitory effect on the newcomers due to antibiotic production. On the contrary, hydrolytic activity of the antibiotic-producing strain appeared to benefit the newcomers and enhance their colonization rate. These results show that growth- and species-specific interactions have to be taken into account to adequately describe bacterial colonization of marine particles. Changes in colonization pattern due to such small-scale processes may have profound effects on the transformation and fluxes of particulate matter in the ocean.
Chemical and Biological Interactions during Nitrate and Goethite Reduction by
Shewanella putrefaciens
200
Authors: Cooper D. Craig , Picardal Flynn W. , Schimmelmann Arndt , Coby Aaron J.
Published: June 2003

Although previous research has demonstrated that NO
3
−
inhibits microbial Fe(III) reduction in laboratory cultures and natural sediments, the mechanisms of this inhibition have not been fully studied in an environmentally relevant medium that utilizes solid-phase, iron oxide minerals as a Fe(III) source. To study the dynamics of Fe and NO
3
−
biogeochemistry when ferric (hydr)oxides are used as the Fe(III) source,
Shewanella putrefaciens
200 was incubated under anoxic conditions in a low-ionic-strength, artificial groundwater medium with various amounts of NO
3
−
and synthetic, high-surface-area goethite. Results showed that the presence of NO
3
−
inhibited microbial goethite reduction more severely than it inhibited microbial reduction of the aqueous or microcrystalline sources of Fe(III) used in other studies. More interestingly, the presence of goethite also resulted in a twofold decrease in the rate of NO
3
−
reduction, a 10-fold decrease in the rate of NO
2
−
reduction, and a 20-fold increase in the amounts of N
2
O produced. Nitrogen stable isotope experiments that utilized δ
15
N values of N
2
O to distinguish between chemical and biological reduction of NO
2
−
revealed that the N
2
O produced during NO
2
−
or NO
3
−
reduction in the presence of goethite was primarily of abiotic origin. These results indicate that concomitant microbial Fe(III) and NO
3
−
reduction produces NO
2
−
and Fe(II), which then abiotically react to reduce NO
2
−
to N
2
O with the subsequent oxidation of Fe(II) to Fe(III).
Molecular Diversity of Denitrifying Genes in Continental Margin Sediments within the Oxygen-Deficient Zone off the Pacific Coast of Mexico
Authors: Liu Xueduan , Tiquia Sonia M. , Holguin Gina , Wu Liyou , Nold Stephen C. , Devol Allan H. , Luo Kuan , Palumbo Anthony V. , Tiedje James M. , Zhou Jizhong
Published: June 2003

To understand the composition and structure of denitrifying communities in the oxygen-deficient zone off the Pacific coast of Mexico, the molecular diversity of
nir
genes from sediments obtained at four stations was examined by using a PCR-based cloning approach. A total of 50 operational taxonomic units (OTUs) for
nirK
and 82 OTUs for
nirS
were obtained from all samples. Forty-four of the
nirS
clones and 31 of the
nirK
clones were sequenced; the levels of similarity of the
nirS
clones were 52 to 92%, and the levels of similarity of the
nirS
clones were 50 to 99%. The percentages of overlapping OTUs between stations were 18 to 30% for
nirS
and 5 to 8% for
nirK
. Sequence analysis revealed that 26% of the
nirS
clones were related to the
nirS
genes of
Alcaligenes faecalis
(80 to 94% similar) and
Pseudomonas stutzeri
(80 to 99%), whereas 3 to 31% of the
nirK
clones were closely related to the
nirK
genes of
Pseudomonas
sp. strain G-179 (98 to 99%),
Bradyrhizobium japonicum
(91%),
Blastobacter denitrificans
(83%), and
Alcaligenes xylosoxidans
(96%). The rest of the clones, however, were less than 80% similar to
nirS
and
nirK
sequences available in sequence databases. The results of a principal-component analysis (PCA) based on the percentage of OTUs and biogeochemical data indicated that the nitrate concentration and oxygen have an effect on the denitrifying communities. The communities at the stations in oxygen-deficient zones were more similar than the communities at the stations in the oxygenated zone. The denitrifying communities were more similar at the stations that were closer together and had similar nitrate levels. Also, the results of PCA based on biogeochemical properties suggest that geographic location and biogeochemical conditions, especially the nitrate and oxygen levels, appear to be the key factors that control the structure of denitrifying communities.
A Rapid Microtiter Plate Method To Measure Carbon Dioxide Evolved from Carbon Substrate Amendments so as To Determine the Physiological Profiles of Soil Microbial Communities by Using Whole Soil
Authors: Campbell Colin D. , Chapman Stephen J. , Cameron Clare M. , Davidson Mitchell S. , Potts Jacqueline M.
Published: June 2003

Sole-carbon-source tests (Biolog), designed to identify bacteria, have become very popular for metabolically fingerprinting soil microbial communities, despite disadvantages associated with the use of carbon source profiles that primarily select for fast-growing bacteria. In this paper we describe the use of an alternative method that combines the advantages of the Biolog community-level physiological profile (CLPP) method, in which microtiter-based detection plates are used, with the ability to measure carbon dioxide evolution from whole soil. This method facilitates measurement over short periods of time (4 to 6 h) and does not require the extraction and culturing of organisms. Deep-well microtiter plates are used as test wells into which soil is placed. The apparatus to fill the deep-well plates and interface it with a second removable detection plate is described. Two detection systems, a simple colorimetric reaction in absorbent alkali and scintillation counting with radioactive carbon sources, are described. The methods were compared to the Biolog-CLPP system by using soils under different vegetation types and soil treated with wastewater sludge. We aimed to test the hypothesis that using whole soil would have specific advantages over using extracts in that more immediate responses to substrates could be obtained that would reflect activity rather than growth. The whole-soil method was more rapid and gave earlier detection of C source use. Also, the metabolic fingerprints obtained could discriminate between sludge treatments.
Characterization of an Autotrophic Nitrogen-Removing Biofilm from a Highly Loaded Lab-Scale Rotating Biological Contactor
Authors: Pynaert Kris , Smets Barth F. , Wyffels Stijn , Beheydt Daan , Siciliano Steven D. , Verstraete Willy
Published: June 2003

In this study, a lab-scale rotating biological contactor (RBC) treating a synthetic NH
4
+
wastewater devoid of organic carbon and showing high N losses was examined for several important physiological and microbial characteristics. The RBC biofilm removed 89% ± 5% of the influent N at the highest surface load of approximately 8.3 g of N m
−2
day
−1
, with N
2
as the main end product. In batch tests, the RBC biomass showed good aerobic and anoxic ammonium oxidation (147.8 ± 7.6 and 76.5 ± 6.4 mg of NH
4
+
-N g of volatile suspended solids [VSS]
−1
day
−1
, respectively) and almost no nitrite oxidation (< 1 mg of N g of VSS
−1
day
−1
). The diversity of aerobic ammonia-oxidizing bacteria (AAOB) and planctomycetes in the biofilm was characterized by cloning and sequencing of PCR-amplified partial 16S rRNA genes. Phylogenetic analysis of the clones revealed that the AAOB community was fairly homogeneous and was dominated by
Nitrosomonas
-like species. Close relatives of the known anaerobic ammonia-oxidizing bacterium (AnAOB)
Kuenenia stuttgartiensis
dominated the planctomycete community and were most probably responsible for anoxic ammonium oxidation in the RBC. Use of a less specific planctomycete primer set, not amplifying the AnAOB, showed a high diversity among other planctomycetes, with representatives of all known groups present in the biofilm. The spatial organization of the biofilm was characterized using fluorescence in situ hybridization (FISH) with confocal scanning laser microscopy (CSLM). The latter showed that AAOB occurred side by side with putative AnAOB (cells hybridizing with probe PLA46 and AMX820/KST1275) throughout the biofilm, while other planctomycetes hybridizing with probe PLA886 (not detecting the known AnAOB) were present as very conspicuous spherical structures. This study reveals that long-term operation of a lab-scale RBC on a synthetic NH
4
+
wastewater devoid of organic carbon yields a stable biofilm in which two bacterial groups, thought to be jointly responsible for the high autotrophic N removal, occur side by side throughout the biofilm.
Microbial Reduction and Precipitation of Vanadium by
Shewanella oneidensis
Authors: Carpentier W. , Sandra K. , De Smet I. , Brigé A. , De Smet L. , Van Beeumen J.
Published: June 2003

Shewanella oneidensis
couples anaerobic oxidation of lactate, formate, and pyruvate to the reduction of vanadium pentoxide (V
V
). The bacterium reduces V
V
(vanadate ion) to V
IV
(vanadyl ion) in an anaerobic atmosphere. The resulting vanadyl ion precipitates as a V
IV
-containing solid.
Adhesion, Invasion, and Translocation Characteristics of
Listeria monocytogenes
Serotypes in Caco-2 Cell and Mouse Models
Authors: Jaradat Ziad W. , Bhunia Arun K.
Published: June 2003

Adhesion is a crucial first step in
Listeria monocytogenes
pathogenesis. In this study, we examined how the adhesion properties of serotypes correlate with their invasion efficiencies in a cell culture model (Caco-2) and in a mouse model. Adhesion characteristics of all 13 serotypes of
L. monocytogenes
(25 strains) were analyzed, which yielded three distinct groups (
P
< 0.05) with high-, medium-, and low-level-adhesion profiles. The efficiency of these strains in invading the Caco-2 cell line was analyzed, which produced two groups; however, the overall correlation (
R
2
) was only 0.1236. In the mouse bioassay, all selected strains, irrespective of their adhesion profiles, translocated to the liver and the spleen with almost equal frequencies that did not show any clear relationship with adhesion profiles. However, the serotypes with increased adhesion showed a slightly increased translocation to the brain (
R
2
= 0.3371). Collectively, these results indicate that an in vitro adhesion profile might not be an accurate assessment of a strain's ability to invade a cultured cell line or organs or tissues in a mouse model.
Alkylphenol Biotransformations Catalyzed by 4-Ethylphenol Methylenehydroxylase
Authors: Hopper David J. , Cottrell Lisa
Published: June 2003

4-Ethylphenol methylenehydroxylase from
Pseudomonas putida
JD1 acts by dehydrogenation of its substrate to give a quinone methide, which is then hydrated to an alcohol. It was shown to be active with a range of 4-alkylphenols as substrates. 4-
n
-Propylphenol, 4-
n
-butylphenol, chavicol, and 4-hydroxydiphenylmethane were hydroxylated on the methylene group next to the benzene ring and produced the corresponding chiral alcohol as the major product. The alcohols 1-(4′-hydroxyphenyl)propanol and 1-(4′-hydroxyphenyl)-2-propen-1-ol, produced by the biotransformation of 4-
n
-propylphenol and chavicol, respectively, were shown to be
R
(+) enantiomers. 5-Indanol, 6-hydroxytetralin, 4-isopropylphenol, and cyclohexylphenol, with cyclic or branched alkyl groups, gave the corresponding vinyl compounds as their major products.
Phylogeny and Characterization of Three
nifH
-Homologous Genes from
Paenibacillus azotofixans
Authors: Choo Quok-Cheong , Samian Mohd-Razip , Najimudin Nazalan
Published: June 2003

In this paper, we report the cloning and characterization of three
Paenibacillus azotofixans
DNA regions containing genes involved in nitrogen fixation. Sequencing analysis revealed the presence of
nifB1H1D1K1
gene organization in the 4,607-bp
Sac
I DNA fragment. This is the first report of linkage of a
nifB
open reading frame upstream of the structural
nif
genes. The second (
nifB2H2
) and third (
nifH3
)
nif
homologues are confined within the 6,350-bp
Hin
dIII and 2,840-bp
Eco
RI DNA fragments, respectively. Phylogenetic analysis demonstrated that NifH1 and NifH2 form a monophyletic group among cyanobacterial NifH proteins. NifH3, on the other hand, clusters among NifH proteins of the highly divergent methanogenic archaea.
Molecular Genetics of Kaposi's Sarcoma-Associated Herpesvirus (Human Herpesvirus 8) Epidemiology and Pathogenesis
Authors: Dourmishev Lyubomir A. , Dourmishev Assen L. , Palmeri Diana , Schwartz Robert A. , Lukac David M.
Published: June 2003

Kaposi's sarcoma had been recognized as unique human cancer for a century before it manifested as an AIDS-defining illness with a suspected infectious etiology. The discovery of Kaposi's sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus-8, in 1994 by using representational difference analysis, a subtractive method previously employed for cloning differences in human genomic DNA, was a fitting harbinger for the powerful bioinformatic approaches since employed to understand its pathogenesis in KS. Indeed, the discovery of KSHV was rapidly followed by publication of its complete sequence, which revealed that the virus had coopted a wide armamentarium of human genes; in the short time since then, the functions of many of these viral gene variants in cell growth control, signaling apoptosis, angiogenesis, and immunomodulation have been characterized. This critical literature review explores the pathogenic potential of these genes within the framework of current knowledge of the basic herpesvirology of KSHV, including the relationships between viral genotypic variation and the four clinicoepidemiologic forms of Kaposi's sarcoma, current viral detection methods and their utility, primary infection by KSHV, tissue culture and animal models of latent- and lytic-cycle gene expression and pathogenesis, and viral reactivation from latency. Recent advances in models of de novo endothelial infection, microarray analyses of the host response to infection, receptor identification, and cloning of full-length, infectious KSHV genomic DNA promise to reveal key molecular mechanisms of the candidate pathogeneic genes when expressed in the context of viral infection.
Prophage Genomics
Authors: Canchaya Carlos , Proux Caroline , Fournous Ghislain , Bruttin Anne , Brüssow Harald
Published: June 2003

The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and γ-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and γ-proteobacteria.
Conjugative Plasmid Transfer in Gram-Positive Bacteria
Authors: Grohmann Elisabeth , Muth Günther , Espinosa Manuel
Published: June 2003

Conjugative transfer of bacterial plasmids is the most efficient way of horizontal gene spread, and it is therefore considered one of the major reasons for the increase in the number of bacteria exhibiting multiple-antibiotic resistance. Thus, conjugation and spread of antibiotic resistance represents a severe problem in antibiotic treatment, especially of immunosuppressed patients and in intensive care units. While conjugation in gram-negative bacteria has been studied in great detail over the last decades, the transfer mechanisms of antibiotic resistance plasmids in gram-positive bacteria remained obscure. In the last few years, the entire nucleotide sequences of several large conjugative plasmids from gram-positive bacteria have been determined. Sequence analyses and data bank comparisons of their putative transfer (tra) regions have revealed significant similarities totraregions of plasmids from gram-negative bacteria with regard to the respective DNA relaxases and their targets, the origins of transfer (oriT), and putative nucleoside triphosphatases NTP-ases with homologies to type IV secretion systems. In contrast, a single gene encoding a septal DNA translocator protein is involved in plasmid transfer between micelle-forming streptomycetes. Based on these clues, we propose the existence of two fundamentally different plasmid-mediated conjugative mechanisms in gram-positive microorganisms, namely, the mechanism taking place in unicellular gram-positive bacteria, which is functionally similar to that in gram-negative bacteria, and a second type that occurs in multicellular gram-positive bacteria, which seems to be characterized by double-stranded DNA transfer.
Football incident analysis: a new video based method to describe injury mechanisms in professional football
Authors: Andersen T E , Larsen Ø , Tenga A , Engebretsen L , Bahr R
Published: June 2003

Objectives:To develop and test a new video based method for match analysis that combines football specific and medical information to achieve a better understanding of the injury mechanisms and events leading up to high risk situations.

Methods:Football incident analysis (FIA) is a video based method describing incidents that may result in an injury using 19 variables and categories modified from match analysis. Videos from 35 of 76 (46%) official Norwegian under 21 matches played from 1994 to 1998 were analysed. Two football experts classified each incident on the basis of predetermined criteria, and their results were compared using interobserver and intraobserver reliability tests.

Results:κ correlation coefficients for interobserver and intraobserver agreement were very good for 63% and 95% and good for 37% and 5% of the variables respectively. Fifty two incidents were recorded (1.6 incidents per team per match or 94 per 1000 player hours), and 16 (31%) led to injuries (0.5 injuries per match or 29 injuries per 1000 player hours). FIA results showed that 28 incidents occurred while attacking in midfield zone 2 or the attacking zone, and 24 took place while defending in the defensive zone or midfield zone 1. Midfielders were exposed in 67% of the incidents, mainly in breakdown attacks or during long attacks by the opposing team. Of the 28 incidents during offence, only one was classified as having great potential to score a goal. Most incidents (70%) were the result of tackling duels both in the offensive and defensive playing phases. Of the 21 offensive incidents resulting from tackling duels, in 19 cases the exposed player was unaware of the tackling (passive duellist).

Conclusions:This study shows that football incident analysis is a potentially valuable tool for understanding the events leading up to injuries in football.
The Football Association Medical Research Programme: an audit of injuries in professional football: an analysis of ankle sprains
Authors: Woods C , Hawkins R , Hulse M , Hodson A
Published: June 2003

Aim:To conduct a detailed analysis of ankle sprains sustained in English professional football over two competitive seasons.

Methods:Club medical staff at 91 professional football clubs annotated player injuries. A specific injury audit questionnaire was used together with a weekly form that documented each club’s current injury status.

Results:Completed injury records for the two competitive seasons were obtained from 87% and 76% of the participating clubs. Ankle ligament sprains accounted for 11% of the total injuries over the two seasons, with over three quarters (77%) of sprains involving the lateral ligament complex. A total of 12 138 days and 2033 matches were missed because of ankle sprains. More sprains were caused by contact mechanisms than non-contact mechanisms (59%v39%) except in goalkeepers who sustained more non-contact sprains (21%v79%, p<0.01). Ankle sprains were most often observed during tackles (54%). More ankle sprains were sustained in matches than in training (66%v33%), with nearly half (48%) observed during the last third of each half of matches. A total of 44% of sprains occurred during the first three months of the season. A high number of players (32%) who sustained ankle sprains were wearing some form of external support. The recurrence rate for ankle sprains was 9% (see methodology for definition of reinjury).

Conclusion:Ankle ligament sprains are common in football usually involving the lateral ligament complex. The high rate of occurrence and recurrence indicates that prevention is of paramount importance.
A pilot study of the prevalence of lumbar disc degeneration in elite athletes with lower back pain at the Sydney 2000 Olympic Games
Authors: Ong A , Anderson J , Roche J
Published: June 2003

Objectives:To observe the prevalence of lumbar intervertebral disc degeneration in elite athletes as compared with published literature of changes seen in non-athletes—that is, normal population.

Methods:The lumbar spines of 31 Olympic athletes who presented to the Olympic Polyclinic with low back pain and/or sciatica were examined using magnetic resonance imaging. Three criteria were looked at: (a) the loss of disc signal intensity; (b) the loss of disc height; (c) the presence of disc displacement. The results were then recorded and correlated with the lumbar levels.

Results:The disc signal intensity was progressively reduced the more caudal the disc space. It was most common at the L5/S1 level, and, of the abnormal group, 36% (n = 11) showed the most degenerative change. Disc height reduction was also found to be most common at the L5/S1 level. However, the most common height reduction was only mild. A similar trend of increased prevalence of disc herniation was noted with more caudal levels. At the L5/S1 level, 58% were found to have an element of disc displacement, most of which were disc bulges. Compared with changes seen in the normal population (non-athletes) as described in the literature, disc degeneration defined by the above criteria was found to be significantly more severe in these Olympic athletes.

Conclusions:Although the study was limited, the results suggest that elite athletes have a greater prevalence and greater degree of lumbar disc degeneration than the normal population. A more detailed follow up study should be considered to investigate which particular training activities have the most impact on the lumbar spine, and how to modify training methods so as to avoid the long term sequelae of degenerative disc disease of the lumbar spine.
Day to day variability in the transferrin receptor/ferritin index in female athletes
Authors: Stupnicki R , Malczewska J , Milde K , Hackney A C
Published: June 2003

Objective:To determine the within subject (day to day) variability for variables reflecting iron status (concentrations of ferritin and soluble transferrin receptor (sTfR), and the sTfR/logFerr index) in female athletes during a training camp, and in female control subjects.

Results:The error for ferritin concentration was nearly twice as high in athletes as in controls, that for sTfR concentration was identical in the two groups, and that for the sTfR/logFerr index was about 50% higher in athletes than in controls.

Conclusions:The within subject, day to day error for the sTfR/logFerr index computed from data recorded for untrained subjects cannot serve as a reference value for training athletes. When the sTfR/logFerr index is used to monitor iron stores in athletes, an error value of 0.20 should be used, because determination of the index after a few days of rest may not be feasible.
Bilateral radial head fractures in a martial arts athlete
Authors: Deshmukh N V , Shah M S
Published: June 2003

Isolated radial head fractures, which are rare, comprise about 2% of all fractures around the elbow. A case is reported of bilateral radial head fracture in an international female athlete. Early recognition and aggressive rehabilitation is essential if an abrupt end to a promising sporting career is to be prevented.
Lacrosse stick entrapment injury to the thumb: Figure 1
Authors: Livingston L A , Forbes S L
Published: June 2003

A case of injury to the left thumb following an errant stick check, and subsequent entrapment of the digit in the open sidewall of a lacrosse stick, is presented. A circumferential laceration, severe swelling, and bruising to the proximal phalanx resulted. This case report emphasises the need to limit the dimensions of openings in the sidewalls of lacrosse sticks to prevent the occurrence of this and other preventable injuries.
How to conduct research on burnout: advantages and disadvantages of a unidimensional approach in burnout research
Authors: Brenninkmeijer V , VanYperen N
Published: June 2003

When conducting research on burnout, it may be difficult to decide whether one should report results separately for each burnout dimension or whether one should combine the dimensions. Although the multidimensionality of the burnout concept is widely acknowledged, for research purposes it is sometimes convenient to regard burnout as a unidimensional construct. This article deals with the question of whether and when it may be appropriate to treat burnout as a unidimensional variable, and presents a decision rule to distinguish between people high and low in burnout. To develop a guideline for obtaining a dichotomous measure of burnout, the scores on the Utrecht Burnout Scale (UBOS) of 44 well functioning individuals were compared with the scores of 29 individuals diagnosed as suffering from burnout. Based on these data, the authors recommend the “exhaustion + 1” criterion for research in non-clinical populations. Following this criterion, individuals can be considered as burnt out when they report, compared to a norm group, high emotional exhaustion, in combination with high depersonalisation or low personal accomplishment. The criterion may be used to estimate the percentage in a sample of individuals in a state of burnout.
Fatigue, burnout, and chronic fatigue syndrome among employees on sick leave: do attributions make the difference?
Authors: Huibers M J H , Beurskens A J H M , Prins J B , Kant IJ , Bazelmans E , van Schayck C P , Knottnerus J A , Bleijenberg G
Published: June 2003

Background:Persistent fatigue among employees, burnout, and chronic fatigue syndrome (CFS) are three fatigue conditions that share some characteristics in theory. However, these conditions have not been compared in empirical research, despite conceptual similarities.

Methods:This cross sectional study aimed to investigate relations between persistent fatigue, burnout, and CFS by describing the clinical features of a sample of 151 fatigued employees on sick leave. Using validated instruments, subgroups based on research criteria for CFS and burnout within the sample of fatigued employees and a reference group of 97 diagnosed CFS patients were compared. Analyses of covariance were performed.

Results:A total of 66 (43.7%) fatigued employees met research criteria for CFS (except symptom criteria) and 76 (50.3%) met research criteria for burnout. “CFS-like employees” (fatigued employees who met CFS criteria) reported stronger somatic attributions than “non-CFS-like employees”. Burnt out CFS-like employees were more depressed and distressed than CFS-like employees who were not burnt out. Burnout cases among the non-CFS-like employees had stronger psychological attributions than fatigued employees who were not burnt out. Compared to diagnosed CFS patients, CFS-like employees merely had a shorter duration of fatigue complaints. Burnt out CFS-like employees had stronger psychological attributions and were more distressed than CFS patients.

Conclusions:Fatigued employees shared many important characteristics with CFS patients, regardless of burnout status, and many fatigued employees met CFS criteria and/or burnout criteria. Differences however concerned the causal attributions that were made. This raises questions about the role of causal attributions: are they modified by fatigue complaints or do they determine illness outcome?
Measurement quality and validity of the “need for recovery scale”
Authors: van Veldhoven M , Broersen S
Published: June 2003

The “need for recovery scale” is suggested as an operationalisation for the measurement of (early symptoms of) fatigue at work. Definition of and background on the concept of need for recovery are briefly discussed. Details about scale construction are summarised. Correlations with other relevant measurement scales on fatigue at work are presented to validate the operationalisation claim, as are early results on predictive validity.

A study is presented that further investigates the measurement quality and validity of the scale. The data used in this study were collected by Occupational Health Services for 68 775 workers during the period 1996–2000. Comparing the measurement quality of subgroups (Cronbach’s alpha) differing in terms of age class, sex, and education level, the general applicability of the scale was shown. The validity of the scale was studied by analysing its association with psychosocial risk factors. Multiple regression analyses of need for recovery were performed on individual and department level data, using 10 psychosocial job characteristics as independent variables. The two most important factors in the explanation of variance at the individual level were also dominant at the department level: pace and amount of work, and emotional workload. The percentage of explained variance was higher at the department level than at the individual level, and increased with department size.

Results suggest that the need for recovery scale is an adequate scale, both for applications at the individual and at the group (department/organisation) level.