bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA-Stable Isotope Probing Integrated with Metagenomics for Retrieval of Biphenyl Dioxygenase Genes from Polychlorinated Biphenyl-Contaminated River Sediment
Authors: Sul Woo Jun , Park Joonhong , Quensen John F. , Rodrigues Jorge L. M. , Seliger Laurie , Tsoi Tamara V. , Zylstra Gerben J. , Tiedje James M. 
Published: August 2009

ABSTRACT

Stable isotope probing with [
13
C]biphenyl was used to explore the genetic properties of indigenous bacteria able to grow on biphenyl in PCB-contaminated River Raisin sediment. A bacterial 16S rRNA gene clone library generated from [
13
C]DNA after a 14-day incubation with [
13
C]biphenyl revealed the dominant organisms to be members of the genera
Achromobacter
and
Pseudomonas
. A library built from PCR amplification of genes for aromatic-ring-hydroxylating dioxygenases from the [
13
C]DNA fraction revealed two sequence groups similar to
bphA
(encoding biphenyl dioxygenase) of
Comamonas testosteroni
strain B-356 and of
Rhodococcus
sp. RHA1. A library of 1,568 cosmid clones was produced from the [
13
C]DNA fraction. A 31.8-kb cosmid clone, detected by aromatic dioxygenase primers, contained genes of biphenyl dioxygenase subunits
bphAE
, while the rest of the clone's sequence was similar to that of an unknown member of the
Gammaproteobacteria
. A discrepancy in G+C content near the
bphAE
genes implies their recent acquisition, possibly by horizontal transfer. The biphenyl dioxygenase from the cosmid clone oxidized biphenyl and unsubstituted and
para
-only-substituted rings of polychlorinated biphenyl (PCB) congeners. A DNA-stable isotope probing-based cosmid library enabled the retrieval of functional genes from an uncultivated organism capable of PCB metabolism and suggest dispersed dioxygenase gene organization in nature.
Biofilm Formation and Cell Surface Properties among Pathogenic and Nonpathogenic Strains of the
Bacillus cereus
Group
Authors: Auger Sandrine , Ramarao Nalini , Faille Christine , Fouet Agnès , Aymerich Stéphane , Gohar Michel 
Published: August 2009

ABSTRACT

Biofilm formation by 102
Bacillus cereus
and
B. thuringiensis
strains was determined. Strains isolated from soil or involved in digestive tract infections were efficient biofilm formers, whereas strains isolated from other diseases were poor biofilm formers. Cell surface hydrophobicity, the presence of an S layer, and adhesion to epithelial cells were also examined.
Identification of
Brevibacteriaceae
by Multilocus Sequence Typing and Comparative Genomic Hybridization Analyses
Authors: Forquin Marie-Pierre , Duvergey Hugo , Proux Caroline , Loux Valentin , Mounier Jerome , Landaud Sophie , Coppée Jean-Yves , Gibrat Jean-François , Bonnarme Pascal , Martin-Verstraete Isabelle , Vallaeys Tatiana 
Published: August 2009

ABSTRACT

Multilocus sequence typing with nine selected genes is shown to be a promising new tool for accurate identifications of
Brevibacteriaceae
at the species level. A developed microarray also allows intraspecific diversity investigations of
Brevibacterium aurantiacum
showing that 13% to 15% of the genes of strain ATCC 9174 were absent or divergent in strain BL2 or ATCC 9175.
Implications of Limits of Detection of Various Methods for
Bacillus anthracis
in Computing Risks to Human Health
Authors: Herzog Amanda B. , McLennan S. Devin , Pandey Alok K. , Gerba Charles P. , Haas Charles N. , Rose Joan B. , Hashsham Syed A. 
Published: August 2009

ABSTRACT

Used for decades for biological warfare,
Bacillus anthracis
(category A agent) has proven to be highly stable and lethal. Quantitative risk assessment modeling requires descriptive statistics of the limit of detection to assist in defining the exposure. Furthermore, the sensitivities of various detection methods in environmental matrices are vital information for first responders. A literature review of peer-reviewed journal articles related to methods for detection of
B. anthracis
was undertaken. Articles focused on the development or evaluation of various detection approaches, such as PCR, real-time PCR, immunoassay, etc. Real-time PCR and PCR were the most sensitive methods for the detection of
B. anthracis
, with median instrument limits of detection of 430 and 440 cells/ml, respectively. There were very few peer-reviewed articles on the detection methods for
B. anthracis
in the environment. The most sensitive limits of detection for the environmental samples were 0.1 CFU/g for soil using PCR-enzyme-linked immunosorbent assay (ELISA), 17 CFU/liter for air using an ELISA-biochip system, 1 CFU/liter for water using cultivation, and 1 CFU/cm
2
for stainless steel fomites using cultivation. An exponential dose-response model for the inhalation of
B. anthracis
estimates of risk at concentrations equal to the environmental limit of detection determined the probability of death if untreated to be as high as 0.520. Though more data on the environmental limit of detection would improve the assumptions made for the risk assessment, this study's quantification of the risk posed by current limitations in the knowledge of detection methods should be considered when employing those methods in environmental monitoring and cleanup strategies.
Improved Detection of F-Specific RNA Coliphages in Fecal Material by Extraction and Polyethylene Glycol Precipitation
Authors: Jones Tineke H. , Johns Michael W. 
Published: August 2009

ABSTRACT
Male-specific RNA coliphages (F-RNA coliphages) have been proposed as a potential viral indicator of fecal contamination in water and foods because they are easy to culture and are a normal component of the mammalian gut flora. F-RNA coliphage plaque numbers are typically obtained by directly plating a 10-fold dilution of 1 g of fecal material, but the numbers of F-RNA coliphages shed by animals and humans may be too low for direct enumeration. Therefore, the sensitivity of detecting F-RNA coliphages in fecal material was improved by extracting and precipitating F-RNA coliphage from a 10-g fecal sample by use of polyethylene glycol (PEG). The highest recovery of F-RNA coliphage with 10% beef extract, pH 7.2, was obtained in the presence of 1 M NaCl and 10% PEG after 16 h of precipitation, but a pellet was not obtained after a short precipitation time of 2 h. There was no significant difference between eluant-to-fecal-material ratios of 4:1 and 9:1 or homogenization with a stomacher or pulsifier. F-RNA coliphage were detected in 64% (16 of 25 samples) of fecal samples from various sources when the sample size was 10 g but in 36% (9 of 25 samples) of samples when the sample size was 1 g. When F-RNA coliphage were detected in 1-g samples, they were also detected in 10-g samples. When F-RNA coliphage were detected in 10-g samples but not in 1-g samples, the levels were <100 PFU/g.
Estimating Risk from Small Inocula by Using Population Growth Parameters
Authors: Malakar P. K. , Barker G. C. 
Published: August 2009

ABSTRACT
Risk from an uncertain small inoculum depends on variability of single-cell lag times. However, quantifying single-cell variability is technically challenging. It is possible to estimate this variability using population growth parameters. We demonstrate this possibility using data from literature and show a Bayesian scheme for performing this task.
Novel and Unique Diagnostic Biomarkers forBacillus anthracisInfection
Authors: Sela-Abramovich Sagit , Chitlaru Theodor , Gat Orit , Grosfeld Haim , Cohen Ofer , Shafferman Avigdor 
Published: August 2009

ABSTRACTA search for bacterium-specific biomarkers in peripheral blood following infection withBacillus anthraciswas carried out with rabbits, using a battery of specific antibodies generated by DNA vaccination against 10 preselected highly immunogenic bacterial antigens which were identified previously by a genomic/proteomic/serologic screen of theB. anthracissecretome. Detection of infection biomarkers in the circulation of infected rabbits could be achieved only after removal of highly abundant serum proteins by chromatography using a random-ligand affinity column. Besides the toxin component protective antigen, the following three secreted proteins were detected in the circulation of infected animals: the chaperone and protease HtrA (BA3660), an NlpC/P60 endopeptidase (BA1952), and a protein of unknown function harboring two SH3 (Src homology 3) domains (BA0796). The three proteins could be detected in plasma samples from infected animals exhibiting 103to 105CFU/ml blood and also in standard blood cultures at 3 to 6 h post-bacterial inoculation at a bacteremic level as low as 103CFU/ml. Furthermore, the three biomarkers appear to be present only in the secretome ofB. anthracis, not in those of the related pathogensB. thuringiensisandB. cereus. To the best of our knowledge, this is the first report of direct detection ofB. anthracis-specific proteins, other than the toxin components, in the circulation of infected animals.
Antimicrobial Resistance-Conferring Plasmids with Similarity to Virulence Plasmids from Avian Pathogenic
Escherichia coli
Strains in
Salmonella enterica
Serovar Kentucky Isolates from Poultry
Authors: Fricke W. Florian , McDermott Patrick F. , Mammel Mark K. , Zhao Shaohua , Johnson Timothy J. , Rasko David A. , Fedorka-Cray Paula J. , Pedroso Adriana , Whichard Jean M. , LeClerc J. Eugene , White David G. , Cebula Thomas A. , Ravel Jacques 
Published: August 2009

ABSTRACT

Salmonella enterica
, a leading cause of food-borne gastroenteritis worldwide, may be found in any raw food of animal, vegetable, or fruit origin.
Salmonella
serovars differ in distribution, virulence, and host specificity.
S
almonella enterica
serovar Kentucky, though often found in the food supply, is less commonly isolated from ill humans. The multidrug-resistant isolate
S
. Kentucky CVM29188, isolated from a chicken breast sample in 2003, contains three plasmids (146,811 bp, 101,461 bp, and 46,121 bp), two of which carry resistance determinants (pCVM29188_146 [
strAB
and
tetRA
] and pCVM29188_101 [
bla
CMY-2
and
sugE
]). Both resistance plasmids were transferable by conjugation, alone or in combination, to
S.
Kentucky,
S
almonella enterica
serovar Newport, and
E
scherichia coli
recipients. pCVM29188_146 shares a highly conserved plasmid backbone of 106 kb (>90% nucleotide identity) with two virulence plasmids from
a
vian
p
athogenic
E
scherichia c
oli
strains (pAPEC-O1-ColBM and pAPEC-O2-ColV). Shared avian pathogenic
E. coli
(APEC) virulence factors include
iutA iucABCD
,
sitABCD
,
etsABC
,
iss
, and
iroBCDEN.
PCR analyses of recent (1997 to 2005)
S.
Kentucky isolates from food animal, retail meat, and human sources revealed that 172 (60%) contained similar APEC-like plasmid backbones. Notably, though rare in human- and cattle-derived isolates, this plasmid backbone was found at a high frequency (50 to 100%) among
S.
Kentucky isolates from chickens within the same time span. Ninety-four percent of the APEC-positive isolates showed resistance to tetracycline and streptomycin. Together, our findings of a resistance-conferring APEC virulence plasmid in a poultry-derived
S.
Kentucky isolate and of similar resistance/virulence plasmids in most recent
S.
Kentucky isolates from chickens and, to lesser degree, from humans and cattle highlight the need for additional research in order to examine the prevalence and spread of combined virulence and resistance plasmids in bacteria in agricultural, environmental, and clinical settings.
Competition of
Listeria monocytogenes
Serotype 1/2a and 4b Strains in Mixed-Culture Biofilms
Authors: Pan Youwen , Breidt Frederick , Kathariou Sophia 
Published: August 2009

ABSTRACT

The majority of
Listeria monocytogenes
isolates recovered from foods and the environment are strains of serogroup 1/2, especially serotypes 1/2a and 1/2b. However, serotype 4b strains cause the majority of human listeriosis outbreaks. Our investigation of
L. monocytogenes
biofilms used a simulated food-processing system that consisted of repeated cycles of growth, sanitation treatment, and starvation to determine the competitive fitness of strains of serotypes 1/2a and 4b in pure and mixed-culture biofilms. Selective enumeration of strains of a certain serotype in mixed-culture biofilms on stainless steel coupons was accomplished by using serotype-specific quantitative PCR and propidium monoazide treatment to prevent amplification of extracellular DNA or DNA from dead cells. The results showed that the serotype 1/2a strains tested were generally more efficient at forming biofilms and predominated in the mixed-culture biofilms. The growth and survival of strains of one serotype were not inhibited by strains of the other serotype in mixed-culture biofilms. However, we found that a cocktail of serotype 4b strains survived and grew significantly better in mixed-culture biofilms containing a specific strain of serotype 1/2a (strain SK1387), with final cell densities averaging 0.5 log
10
CFU/cm
2
higher than without the serotype 1/2a strain. The methodology used in this study contributed to our understanding of how environmental stresses and microbial competition influence the survival and growth of
L. monocytogenes
in pure and mixed-culture biofilms.
Glyphosate Resistance as a Novel Select-Agent-Compliant, Non-Antibiotic-Selectable Marker in Chromosomal Mutagenesis of the Essential Genes
asd
and
dapB
of
Burkholderia pseudomallei
Authors: Norris Michael H. , Kang Yun , Lu Diana , Wilcox Bruce A. , Hoang Tung T. 
Published: August 2009

ABSTRACT

Genetic manipulation of the category B select agents
Burkholderia pseudomallei
and
Burkholderia mallei
has been stifled due to the lack of compliant selectable markers. Hence, there is a need for additional select-agent-compliant selectable markers. We engineered a selectable marker based on the
gat
gene (encoding glyphosate acetyltransferase), which confers resistance to the common herbicide glyphosate (GS). To show the ability of GS to inhibit bacterial growth, we determined the effective concentrations of GS against
Escherichia coli
and several
Burkholderia
species. Plasmids based on
gat
, flanked by unique flip recombination target (
FRT
) sequences, were constructed for allelic-replacement. Both allelic-replacement approaches, one using the counterselectable marker
pheS
and the
gat-FRT
cassette and one using the DNA incubation method with the
gat-FRT
cassette, were successfully utilized to create deletions in the
asd
and
dapB
genes of wild-type
B. pseudomallei
strains. The
asd
and
dapB
genes encode an aspartate-semialdehyde dehydrogenase (BPSS1704, chromosome 2) and dihydrodipicolinate reductase (BPSL2941, chromosome 1), respectively. Mutants unable to grow on media without diaminopimelate (DAP) and other amino acids of this pathway were PCR verified. These mutants displayed cellular morphologies consistent with the inability to cross-link peptidoglycan in the absence of DAP. The
B. pseudomallei
1026b Δ
asd
::
gat-FRT
mutant was complemented with the
B. pseudomallei asd
gene on a site-specific transposon, mini-Tn
7
-
bar
, by selecting for the
bar
gene (encoding bialaphos/PPT resistance) with PPT. We conclude that the
gat
gene is one of very few appropriate, effective, and beneficial compliant markers available for
Burkholderia
select-agent species. Together with the
bar
gene, the
gat
cassette will facilitate various genetic manipulations of
Burkholderia
select-agent species.
Identification of the Polyhydroxyalkanoate (PHA)-Specific Acetoacetyl Coenzyme A Reductase among Multiple FabG Paralogs in
Haloarcula hispanica
and Reconstruction of the PHA Biosynthetic Pathway in
Haloferax volcanii
Authors: Han Jing , Lu Qiuhe , Zhou Ligang , Liu Hailong , Xiang Hua 
Published: August 2009

ABSTRACT

Genome-wide analysis has revealed abundant FabG (β-ketoacyl-ACP reductase) paralogs, with uncharacterized biological functions, in several halophilic archaea. In this study, we identified for the first time that the
fabG1
gene, but not the other five
fabG
paralogs, encodes the polyhydroxyalkanoate (PHA)-specific acetoacetyl coenzyme A (acetoacetyl-CoA) reductase in
Haloarcula hispanica
. Although all of the paralogous
fabG
genes were actively transcribed, only disruption or knockout of
fabG1
abolished PHA synthesis, and complementation of the Δ
fabG1
mutant with the
fabG1
gene restored both PHA synthesis capability and the NADPH-dependent acetoacetyl-CoA reductase activity. In addition, heterologous coexpression of the PHA synthase genes (
phaEC
) together with
fabG1
, but not its five paralogs, reconstructed the PHA biosynthetic pathway in
Haloferax volcanii
, a PHA-defective haloarchaeon. Taken together, our results indicate that FabG1 in
H. hispanica
, and possibly its counterpart in
Haloarcula marismortui
, has evolved the distinct function of supplying precursors for PHA biosynthesis, like PhaB in bacteria. Hence, we suggest the renaming of FabG1 in both genomes as PhaB, the PHA-specific acetoacetyl-CoA reductase of halophilic archaea.
Genetic Basis for Alkaline Activation of Germination in
Bacillus thuringiensis
subsp.
israelensis
Authors: Abdoarrahem M. M. , Gammon K. , Dancer B. N. , Berry C. 
Published: August 2009

ABSTRACT

Differences in activation between spores from strains of
Bacillus thuringiensis
subsp.
israelensis
with and without the toxin-encoding plasmid pBtoxis are demonstrated. Following alkaline activation, the strain bearing pBtoxis shows a significantly greater germination rate. Expression of just three genes constituting a previously identified, putative
ger
operon from this plasmid is sufficient to produce the same phenotype and characterizes this operon as a genetic determinant of alkaline activation.
Microbial Decomposer Communities Are Mainly Structured by Trophic Status in Circumneutral and Alkaline Streams
Authors: Duarte Sofia , Pascoal Cláudia , Garabétian Frédéric , Cássio Fernanda , Charcosset Jean-Yves 
Published: August 2009

ABSTRACTIn streams, the release of nitrogen and phosphorus is reported to affect microbial communities and the ecological processes they govern. Moreover, the type of inorganic nitrogen (NO3, NO2, or NH4) may differently impact microbial communities. We aimed to identify the environmental factors that structure aquatic microbial communities and drive leaf litter decomposition along a gradient of eutrophication. We selected five circumneutral (Portuguese) and five alkaline (French) streams differing in nutrient concentrations to monitor mass loss of alder leaves, bacterial and fungal diversity by PCR-denaturing gradient gel electrophoresis, fungal biomass and reproduction, and bacterial biomass during 11 weeks of leaf immersion. The concentrations of inorganic nutrients in the stream water ranged from 5 to 300 μg liter−1soluble reactive phosphorus, 0.30 to 5.50 mg liter−1NO3-N, 2 to 103 μg liter−1NO2-N, and <4 to 7,100 μg liter−1NH4-N. Species richness was maximum in moderately anthropized (eutrophic) streams but decreased in the most anthropized (hypertrophic) streams. Different species assemblages were found in subsets of streams with different trophic statuses. In both geographic areas, the limiting nutrient, either nitrate or phosphate, stimulated the microbial activity in streams of intermediate trophic status. In the hypertrophic streams, fungal biomass and reproduction were significantly lower, and bacterial biomass dramatically decreased at the site with the highest ammonium concentration. The limiting nutrients that defined the trophic status were the main factor structuring fungal and bacterial communities, whatever the geographic area. A very high ammonium concentration in stream water most probably has negative impacts on microbial decomposer communities.
The Response ofCampylobacter jejunito Low Temperature Differs from That ofEscherichia coli
Authors: Hughes Rebecca-Ayme , Hallett Kathy , Cogan Tristan , Enser Mike , Humphrey Tom 
Published: August 2009

ABSTRACTHuman infection withCampylobacter jejuniis often associated with the consumption of foods that have been exposed to both chilling and high temperatures. Despite the public health importance of this pathogen, little is known about the effects of cold exposure on its ability to survive a subsequent heat challenge. This work examined the effect of rapid exposure to chilling, as would occur in poultry processing, on the heat resistance at 56°C of twoC. jejunistrains, 11168 and 2097e48, and ofEscherichia coliK-12. UnlikeE. coliK-12, whose cold-exposed cells showed increased sensitivity to 56°C, such exposure had only a marginal effect on subsequent heat resistance inC. jejuni. This may be explained by the finding that during rapid chilling, unlikeE. colicells,C. jejunicells are unable to alter their fatty acid composition and do not adapt to cold exposure. However, their unaltered fatty acid composition is more suited to survival when cells are exposed to high temperatures. This hypothesis is supported by the fact that inC. jejuni, the ratio of unsaturated to saturated fatty acids was not significantly different after cold exposure, but it was inE. coli. The low-temperature response ofC. jejuniis very different from that of other food-borne pathogens, and this may contribute to its tolerance to further heat stresses.
Mobilization of a Tn
402
-Like Class 1 Integron with a Novel Cassette Array via Flanking Miniature Inverted-Repeat Transposable Element-Like Structures
Authors: Gillings Michael R. , Labbate Maurizio , Sajjad Ammara , Giguère Nellie J. , Holley Marita P. , Stokes H. W. 
Published: August 2009

ABSTRACT

A Tn
402
-like class 1 integron was recovered from a prawn-associated bacterium. One of its cassettes included methionine sulfoxide reductase genes, the first example of such genes being captured by an integron. The integron was flanked by direct repeats that resemble miniature inverted-repeat transposable element sequences. Excision of the integron by homologous recombination through these sequences was demonstrated.
Isolation, Diversity, and Antimicrobial Activity of Rare Actinobacteria from Medicinal Plants of Tropical Rain Forests in Xishuangbanna, China
Authors: Qin Sheng , Li Jie , Chen Hua-Hong , Zhao Guo-Zhen , Zhu Wen-Yong , Jiang Cheng-Lin , Xu Li-Hua , Li Wen-Jun 
Published: August 2009

ABSTRACT

Endophytic actinobacteria are relatively unexplored as potential sources of novel species and novel natural products for medical and commercial exploitation. Xishuangbanna is recognized throughout the world for its diverse flora, especially the rain forest plants, many of which have indigenous pharmaceutical histories. However, little is known about the endophytic actinobacteria of this tropical area. In this work, we studied the diversity of actinobacteria isolated from medicinal plants collected from tropical rain forests in Xishuangbanna. By the use of different selective isolation media and methods, a total of 2,174 actinobacteria were isolated. Forty-six isolates were selected on the basis of their morphologies on different media and were further characterized by 16S rRNA gene sequencing. The results showed an unexpected level of diversity, with 32 different genera. To our knowledge, this is the first report describing the isolation of
Saccharopolyspora
,
Dietzia
,
Blastococcus
,
Dactylosporangium
,
Promicromonospora
,
Oerskovia
,
Actinocorallia
, and
Jiangella
species from endophytic environments. At least 19 isolates are considered novel taxa by our current research. In addition, all 46 isolates were tested for antimicrobial activity and were screened for the presence of genes encoding polyketide synthetases and nonribosomal peptide synthetases. The results confirm that the medicinal plants of Xishuangbanna represent an extremely rich reservoir for the isolation of a significant diversity of actinobacteria, including novel species, that are potential sources for the discovery of biologically active compounds.