bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutational and Functional Analysis of the β-Carotene Ketolase Involved in the Production of Canthaxanthin and Astaxanthin
Authors: Ye Rick W. , Stead Kristen J. , Yao Henry , He Hongxian 
Published: September 2006

ABSTRACT

Biosynthesis of the commercial carotenoids canthaxanthin and astaxanthin requires β-carotene ketolase. The functional importance of the conserved amino acid residues of this enzyme from
Paracoccus
sp. strain N81106 (formerly classified as
Agrobacterium aurantiacum
) was analyzed by alanine-scanning mutagenesis. Mutations in the three highly conserved histidine motifs involved in iron coordination abolished its ability to catalyze the formation of ketocarotenoids. This supports the hypothesis that the CrtW ketolase belongs to the family of iron-dependent integral membrane proteins. Most of the mutations generated at other highly conserved residues resulted in partial activity. All partially active mutants showed a higher amount of adonixanthin accumulation than did the wild type when expressed in
Escherichia coli
cells harboring the zeaxanthin biosynthetic gene cluster. Some of the partially active mutants also produced a significant amount of echinenone when expressed in cells producing β-carotene. In fact, expression of a mutant carrying D117A resulted in the accumulation of echinenone as the predominant carotenoid. These observations indicate that partial inactivation of the CrtW ketolase can often lead to the production of monoketolated intermediates. In order to improve the conversion rate of astaxanthin catalyzed by the CrtW ketolase, a color screening system was developed. Three randomly generated mutants, carrying L175M, M99V, and M99I, were identified to have improved activity. These mutants are potentially useful in pathway engineering for the production of astaxanthin.
Detection of
Cryptosporidium
Oocysts in Water: Effect of the Number of Samples and Analytic Replicates on Test Results
Authors: Xiao Lihua , Alderisio Kerri A. , Jiang Jianlin 
Published: September 2006

ABSTRACT

Due to the small number of
Cryptosporidium
oocysts in water, the number of samples taken and the analyses performed can affect the results of detection. In this study, 42 water samples were collected from one watershed during 20 storm events over 1 year, including duplicate or quadruplicate samples from 16 storm events. Ten samples from four events had three to eight subsamples. They were processed by EPA method 1623, and
Cryptosporidium
oocysts present were detected by immunofluorescent microscopy or PCR. Altogether, 24 of 39 samples (47 of 67 samples and subsamples) analyzed by microscopy were positive for
Cryptosporidium
. In contrast, 36 of 42 samples (62 of 76 samples and subsamples) were positive by PCR, including 10 microscopy-negative samples (13 microscopy-negative samples and subsamples). Six of the 24 microscopy-positive samples were negative by PCR, and all samples had one or less oocyst in a 0.5-ml packed pellet volume calculated. Discordant results were obtained by microscopy and PCR from six and three of the storm events, respectively, with multiple samples. Discordant microscopy or PCR results were also obtained among subsamples. Most of the 14
Cryptosporidium
genotypes were found over a brief period.
Cryptosporidium
-positive samples had a mean of 1.9 genotypes per sample, with 39 of the 62 positive samples/subsamples having more than one genotype. Samples/subsamples with more than one genotype had an overall PCR-positive rate of 73%, compared to 34% for those with one genotype. The PCR amplification rate of samples was affected by the volume of DNA used in PCR.
Microbial Population Dynamics Associated with Crude-Oil Biodegradation in Diverse Soils
Authors: Hamamura Natsuko , Olson Sarah H. , Ward David M. , Inskeep William P. 
Published: September 2006

ABSTRACT

Soil bacterial population dynamics were examined in several crude-oil-contaminated soils to identify those organisms associated with alkane degradation and to assess patterns in microbial response across disparate soils. Seven soil types obtained from six geographically distinct areas of the United States (Arizona, Oregon, Indiana, Virginia, Oklahoma, and Montana) were used in controlled contamination experiments containing 2% (wt/wt) crude oil spiked with [1-
14
C]hexadecane. Microbial populations present during hydrocarbon degradation were analyzed using both 16S rRNA gene sequence analysis and by traditional methods for cultivating hydrocarbon-oxidizing bacteria. After a 50-day incubation, all seven soils showed comparable hydrocarbon depletion, where >80% of added crude oil was depleted and approximately 40 to 70% of added [
14
C]hexadecane was converted to
14
CO
2
. However, the initial rates of hydrocarbon depletion differed up to 10-fold, and preferential utilization of shorter-chain-length
n
-alkanes relative to longer-chain-length
n-
alkanes was observed in some soils. Distinct microbial populations developed, concomitant with crude-oil depletion. Phylogenetically diverse bacterial populations were selected across different soils, many of which were identical to hydrocarbon-degrading isolates obtained from the same systems (e.g.,
Nocardioides albus
,
Collimonas
sp., and
Rhodococcus coprophilus
). In several cases, soil type was shown to be an important determinant, defining specific microorganisms responding to hydrocarbon contamination. However, similar
Rhodococcus erythropolis
-like populations were observed in four of the seven soils and were the most common hydrocarbon-degrading organisms identified via cultivation.
Contraselectable Streptomycin Susceptibility Determinant for Genetic Manipulation and Analysis of
Helicobacter pylori
Authors: Dailidiene Daiva , Dailide Giedrius , Kersulyte Dangeruta , Berg Douglas E. 
Published: September 2006

ABSTRACT

Many
Helicobacter pylori
genetic studies would benefit from an ability to move DNA sequences easily between strains by transformation and homologous recombination, without needing to leave a conventional drug resistance determinant at the targeted locus. Presented here is a two-gene cassette that can be selected both (i) against, due to a
Campylobacter jejuni rpsL
gene (dominant streptomycin susceptibility in cells also carrying an
rpsL
-
str

r

allele), and (ii) for, due to an
erm
gene (erythromycin resistance). This
rpsL,erm
cassette's utility was assessed by using it to replace four gene loci (
mdaB
,
frxA
,
fur
, and
nikR
) in four streptomycin-resistant [Str
r
] strain backgrounds (derivatives of 26695, SS1, X47, and G27MA). The resultant 16 strains (phenotypically erythromycin resistant [Erm
r
] and Str
s
) were each transformed with wild-type genomic DNAs, and Str
r
derivatives were selected. The desired Erm
s
Str
r
isolates were obtained at frequencies that ranged from 17 to 96% among Str
r
transformants, with the Erm
s
yield apparently depending on the strain background and genome location of the targeted locus. The ease of isolating unmarked transformants described here should be valuable for many
H. pylori
molecular genetic and evolutionary analyses.
Enzymatic Activation of Lysine 2,3-Aminomutase from
Porphyromonas gingivalis
Authors: Brazeau Brian J. , Gort Steven J. , Jessen Holly J. , Andrew Amy J. , Liao Hans H. 
Published: September 2006

ABSTRACT

The development of lysine 2,3-aminomutase as a robust biocatalyst hinges on the development of an in vivo activation system to trigger catalysis. This is the first report to show that, in the absence of chemical reductants, lysine 2,3-aminomutase activity is dependent upon the presence of flavodoxin, ferredoxin, or flavodoxin-NADP
+
reductase.
Assay of Poly(3-Hydroxybutyrate) Depolymerase Activity and Product Determination
Authors: Gebauer Birgit , Jendrossek Dieter 
Published: September 2006

ABSTRACTTwo methods for accurate poly(3-hydroxybutyrate) (PHB) depolymerase activity determination and quantitative and qualitative hydrolysis product determination are described. The first method is based on online determination of NaOH consumption rates necessary to neutralize 3-hydroxybutyric acid (3HB) and/or 3HB oligomers produced during the hydrolysis reaction and requires a pH-stat apparatus equipped with a software-controlled microliter pump for rapid and accurate titration. The method is universally suitable for hydrolysis of any type of polyhydroxyalkanoate or other molecules with hydrolyzable ester bonds, allows the determination of hydrolysis rates of as low as 1 nmol/min, and has a dynamic capacity of at least 6 orders of magnitude. By applying this method, specific hydrolysis rates of native PHB granules isolated fromRalstonia eutrophaH16 were determined for the first time. The second method was developed for hydrolysis product identification and is based on the derivatization of 3HB oligomers into bromophenacyl derivates and separation by high-performance liquid chromatography. The method allows the separation and quantification of 3HB and 3HB oligomers up to the octamer. The two methods were applied to investigate the hydrolysis of different types of PHB by selected PHB depolymerases.
Complementation of a
Clostridium perfringens spo0A
Mutant with Wild-Type
spo0A
from Other
Clostridium
Species
Authors: Huang I-Hsiu , Sarker Mahfuzur R. 
Published: September 2006

ABSTRACT

To evaluate whether
C. perfringens
can be used as a model organism for studying the sporulation process in other clostridia,
C. perfringens spo0A
mutant IH101 was complemented with wild-type
spo0A
from four different
Clostridium
species. Wild-type
spo0A
from
C. acetobutylicum
or
C. tetani
, but not from
C. botulinum
or
C. difficile
, restored sporulation and enterotoxin production in IH101. The ability of
spo0A
from
C. botulinum
or
C. difficile
to complement the lack of spore formation in IH101 might be due, at least in part, to the low levels of
spo0A
transcription and Spo0A production.
Integrated Analysis of Established and Novel Microbial and Chemical Methods for Microbial Source Tracking
Authors: Blanch Anicet R. , Belanche-Muñoz Lluís , Bonjoch Xavier , Ebdon James , Gantzer Christophe , Lucena Francisco , Ottoson Jakob , Kourtis Christos , Iversen Aina , Kühn Inger , Mocé Laura , Muniesa Maite , Schwartzbrod Janine , Skraber Sylvain , Papageorgiou Georgios T. , Taylor Huw , Wallis Jessica , Jofre Joan 
Published: September 2006

ABSTRACT

Several microbes and chemicals have been considered as potential tracers to identify fecal sources in the environment. However, to date, no one approach has been shown to accurately identify the origins of fecal pollution in aquatic environments. In this multilaboratory study, different microbial and chemical indicators were analyzed in order to distinguish human fecal sources from nonhuman fecal sources using wastewaters and slurries from diverse geographical areas within Europe. Twenty-six parameters, which were later combined to form derived variables for statistical analyses, were obtained by performing methods that were achievable in all the participant laboratories: enumeration of fecal coliform bacteria, enterococci, clostridia, somatic coliphages, F-specific RNA phages, bacteriophages infecting
Bacteroides fragilis
RYC2056 and
Bacteroides thetaiotaomicron
GA17, and total and sorbitol-fermenting bifidobacteria; genotyping of F-specific RNA phages; biochemical phenotyping of fecal coliform bacteria and enterococci using miniaturized tests; specific detection of
Bifidobacterium adolescentis
and
Bifidobacterium dentium
; and measurement of four fecal sterols. A number of potentially useful source indicators were detected (bacteriophages infecting
B. thetaiotaomicron
, certain genotypes of F-specific bacteriophages, sorbitol-fermenting bifidobacteria, 24-ethylcoprostanol, and epycoprostanol), although no one source identifier alone provided 100% correct classification of the fecal source. Subsequently, 38 variables (both single and derived) were defined from the measured microbial and chemical parameters in order to find the best subset of variables to develop predictive models using the lowest possible number of measured parameters. To this end, several statistical or machine learning methods were evaluated and provided two successful predictive models based on just two variables, giving 100% correct classification: the ratio of the densities of somatic coliphages and phages infecting
Bacteroides thetaiotaomicron
to the density of somatic coliphages and the ratio of the densities of fecal coliform bacteria and phages infecting
Bacteroides thetaiotaomicron
to the density of fecal coliform bacteria. Other models with high rates of correct classification were developed, but in these cases, higher numbers of variables were required.
Visible-Light-Induced Bactericidal Activity of a Nitrogen-Doped Titanium Photocatalyst against Human Pathogens
Authors: Wong Ming-Show , Chu Wen-Chen , Sun Der-Shan , Huang Hsuan-Shun , Chen Jiann-Hwa , Tsai Pei-Jane , Lin Nien-Tsung , Yu Mei-Shiuan , Hsu Shang-Feng , Wang Shih-Lien , Chang Hsin-Hou 
Published: September 2006

ABSTRACT

The antibacterial activity of photocatalytic titanium dioxide (TiO
2
) substrates is induced primarily by UV light irradiation. Recently, nitrogen- and carbon-doped TiO
2
substrates were shown to exhibit photocatalytic activities under visible-light illumination. Their antibacterial activity, however, remains to be quantified. In this study, we demonstrated that nitrogen-doped TiO
2
substrates have superior visible-light-induced bactericidal activity against
Escherichia coli
compared to pure TiO
2
and carbon-doped TiO
2
substrates. We also found that protein- and light-absorbing contaminants partially reduce the bactericidal activity of nitrogen-doped TiO
2
substrates due to their light-shielding effects. In the pathogen-killing experiment, a significantly higher proportion of all tested pathogens, including
Shigella flexneri
,
Listeria monocytogenes
,
Vibrio parahaemolyticus
,
Staphylococcus aureus
,
Streptococcus pyogenes
, and
Acinetobacter baumannii
, were killed by visible-light-illuminated nitrogen-doped TiO
2
substrates than by pure TiO
2
substrates. These findings suggest that nitrogen-doped TiO
2
has potential application in the development of alternative disinfectants for environmental and medical usages.
Identification and Differentiation of
Legionella pneumophila
and
Legionella
spp. with Real-Time PCR Targeting the 16S rRNA Gene and Species Identification by
mip
Sequencing
Authors: Stølhaug Anne , Bergh Kåre 
Published: September 2006

ABSTRACT

Fluorescent resonance energy transfer probes targeting the 16S rRNA gene were constructed for a sensitive and specific real-time PCR for identification and differentiation of
Legionella pneumophila
from other
Legionella
spp. For identification of non-
L. pneumophila
spp. by direct amplicon sequencing, two conventional PCR assays targeting the
mip
gene were established.
Copper Resistance in
Enterococcus faecium
, Mediated by the
tcrB
Gene, Is Selected by Supplementation of Pig Feed with Copper Sulfate
Authors: Hasman Henrik , Kempf Isabelle , Chidaine Bérangère , Cariolet Roland , Ersbøll Annette Kjær , Houe Hans , Bruun Hansen Hans Christian , Aarestrup Frank Møller 
Published: September 2006

ABSTRACT

The
tcr
gene cluster mediates in vitro copper resistance in
Enterococcus faecium
. Here we describe the selection of
tcr
-mediated copper resistance in
E. faecium
in an animal feeding experiment with young pigs fed 175 mg copper/kg feed (ppm), which is the concentration commonly used for piglets in European pig production.
tcr
-mediated copper resistance was not selected for in a control group fed low levels of copper (6 ppm). We also show coselection of macrolide- and glycopeptide-resistant
E. faecium
in the animal group fed the high level of copper. Finally, we identify the
tcr
genes in the enterococcal species
E. mundtii
,
E. casseliflavus
, and
E. gallinarum
for the first time.
Microbial Community Diversity Associated with Carbon and Nitrogen Cycling in Permeable Shelf Sediments
Authors: Hunter Evan M. , Mills Heath J. , Kostka Joel E. 
Published: September 2006

ABSTRACT

Though a large fraction of primary production and organic matter cycling in the oceans occurs on continental shelves dominated by sandy deposits, the microbial communities associated with permeable shelf sediments remain poorly characterized. Therefore, in this study, we provide the first detailed characterization of microbial diversity in marine sands of the South Atlantic Bight through parallel analyses of small-subunit (SSU) rRNA gene (
Bacteria
),
nosZ
(denitrifying bacteria), and
amoA
(ammonia-oxidizing bacteria) sequences. Communities were analyzed by parallel DNA extractions and clone library construction from both sediment core material and manipulated sediment within column experiments designed for geochemical rate determinations. Rapid organic-matter degradation and coupled nitrification-denitrification were observed in column experiments at flow rates resembling in situ conditions over a range of oxygen concentrations. Numerous SSU rRNA phylotypes were affiliated with the phyla
Proteobacteria
(classes
Alpha
-,
Delta
-, and
Gammaproteobacteria
),
Planctomycetes
,
Cyanobacteria
,
Chloroflexi
, and
Bacteroidetes
. Detectable sequence diversity of
nosZ
and SSU rRNA genes increased in stratified redox-stabilized columns compared to in situ sediments, with the
Alphaproteobacteria
comprising the most frequently detected group. Alternatively, nitrifier communities showed a relatively low and stable diversity that did not covary with the other gene targets. Our results elucidate predominant phylotypes that are likely to catalyze carbon and nitrogen cycling in marine sands. Although overall diversity increased in response to redox stabilization and stratification in column experiments, the major phylotypes remained the same in all of our libraries, indicating that the columns sufficiently mimic in situ conditions.
Isolation and Characterization of a New T-Even Bacteriophage, CEV1, and Determination of Its Potential To Reduce
Escherichia coli
O157:H7 Levels in Sheep
Authors: Raya Raul R. , Varey Peter , Oot Rebecca A. , Dyen Michael R. , Callaway Todd R. , Edrington Tom S. , Kutter Elizabeth M. , Brabban Andrew D. 
Published: September 2006

ABSTRACT

Bacteriophage CEV1 was isolated from sheep resistant to
Escherichia coli
O157:H7 colonization. In vitro, CEV1 efficiently infected
E.
coli
O157:H7 grown both aerobically and anaerobically. In vivo,
sheep receiving a single oral dose of CEV1 showed a 2-log-unit
reduction in intestinal
E. coli
O157:H7 levels within 2 days
compared to levels in the
controls.
Survival of Environmental Mycobacteria in
Acanthamoeba polyphaga
Authors: Adékambi Toïdi , Ben Salah Skandar , Khlif Mohamed , Raoult Didier , Drancourt Michel 
Published: September 2006

ABSTRACT

Free-living amoebae in water are hosts to many bacterial species living in such an environment. Such an association enables bacteria to select virulence factors and survive in adverse conditions. Waterborne mycobacteria (WBM) are important sources of community- and hospital-acquired outbreaks of nontuberculosis mycobacterial infections. However, the interactions between WBM and free-living amoebae in water have been demonstrated for only few
Mycobacterium
spp. We investigated the ability of a number (
n
= 26) of
Mycobacterium
spp. to survive in the trophozoites and cysts of
Acanthamoeba polyphaga
. All the species tested entered the trophozoites of
A. polyphaga
and survived at this location over a period of 5 days. Moreover, all
Mycobacterium
spp. survived inside cysts for a period of 15 days. Intracellular
Mycobacterium
spp. within amoeba cysts survived when exposed to free chlorine (15 mg/liter) for 24 h. These data document the interactions between free-living amoebae and the majority of waterborne
Mycobacterium
spp. Further studies are required to examine the effects of various germicidal agents on the survival of WBM in an aquatic environment.
A pilot study on the effects of pre-event manipulation on jump height and running velocity
Authors: Shrier I , Macdonald D , Uchacz G 
Published: September 2006

Purpose:To compare changes in jump height and running velocity with and without pre-event high-velocity, low-amplitude manipulation (HVLA).Methods:A crossover study design with elite healthy athletes was used. After a 15 min warm-up, the subjects were tested for countermovement jump height (CMJ) and flying 40 m sprint time (SPRINT). A sport chiropractor then evaluated each subject. Subjects were randomised to either HVLA (applied to joints based on examination) or placebo (simulated performance-enhancement stickers). They then rested for 60 min, performed another 15 min warm-up, and were retested. The protocol was repeated 48 h later with the alternative intervention. The mean of two sprints and three jumps were analysed, as well as peak performances. The sample size was based on prior results from the effects of stretching.Results:19 subjects involved in sprint sports were enrolled; two were too sore to participate on day 2, and one could only participate in the jump (all had HVLA on day 1). Of the 17 participants analysed, seven were female, age range was 19–35, and 17 were national or world-class athletes. The ranges for baseline measures were: SPRINT 4.1–5.5 s; CMJ 47.4–92.7 cm. Overall, the greater than expected variability in this pilot study led to the study being underpowered. Subjects tended to perform better after HVLA for both CMJ and SPRINT (both mean and peak results), but none of the results were statistically significant (p  =  0.30–0.61).Conclusion:Although the larger than expected variability in the pilot study means that the observed clinically relevant differences were not statistically significant, the direction and magnitude of the changes associated with HVLA suggest that it may be beneficial. That said, the increased soreness after HVLA suggests that it may be detrimental. HVLA warrants further study.
SILICON FIBRE TECHNOLOGY DEVELOPMENT FOR WEARABLE AND AMBIENT ELECTRONICS APPLICATIONS
Authors: HEALY THOMAS , DONNELLY JULIE , O'NEILL BRENDAN , ALDERMAN JOHN , MATHEWSON ALAN 
Published: September 2006

The concept of silicon fibre technology follows the aspiration of making whole computers recede into textile format, which can be used in a wearable or ambient environment. The integration of IC technology into fibre format is an important development for a wide range of emerging scientific applications from wearable vital sign health monitoring systems [1] to Ambient Intelligence Microsystems. This concept is achieved by building a device in silicon on insulator (SOI) [2] material and under-cutting the sacrificial SiO 2 layer by a combination of isotropic and anisotropic etch processes, to leave a freestanding functional fibre. A demonstration of functionality based on this technology was produced in the form of a PN diode on a fibre [3]. After demonstrating the feasibility of the concept, subsequent active device circuits were designed and fabricated as a more complex demonstration of functionality. One of the primary considerations involved with this technology is the interconnection of these flexible silicon structures to each other and to the outside environment. A novel interconnection protocol has been developed and a prototype demonstration of a flexible LED circuit has been fabricated.