bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT

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

ABSTRACTSole-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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

SUMMARY
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

SUMMARY
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

SUMMARYConjugative 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.