bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and Molecular Characterization of Class 1 Integrons in Multiresistant Escherichia coli Isolates from Poultry Litter
Authors: Ponce-Rivas Elizabeth , Muñoz-Márquez María-Enriqueta , Khan Ashraf A. 
Published: May 2012

ABSTRACT

This study describes the prevalence of arrays of class 1 integron cassettes and Qnr determinants (A, B, and S) in 19 fluoroquinolone-resistant
Escherichia coli
isolates from chicken litter.
qnrS
and
qnrA
were the predominant genes in these fluoroquinolone-resistant isolates, and an uncommon array of
aacA4
-
catB3
-
dfrA1
gene cassettes from a class1 integron was found. Additionally,
aadA1
and
dfrA1
gene cassettes, encoding resistance to streptomycin and trimethoprim, constituted the most common genes identified and was located on megaplasmids as well on the chromosome. Antibiotic resistance, pulsed-field gel electrophoresis (PFGE), and plasmid data suggest a genetically diverse origin of poultry
E. coli
isolates.
Reclamation of Ampicillin Sensitivity for the Genetic Manipulation of Legionella pneumophila
Authors: Sutherland Molly C. , Vogel Joseph P. 
Published: May 2012

ABSTRACT

Research on
Legionella pneumophila
, the causative agent of Legionnaires' disease, has been hampered due to the lack of selectable markers for genetic manipulation. We report the construction of a mutant strain of
L. pneumophila
lacking
loxA
, a chromosomally encoded β-lactamase, that has enhanced sensitivity to ampicillin. Also described are a method for converting
Legionella
strains to ampicillin sensitivity and conditions for utilizing
bla
as a selectable marker.
Involvement of a Putative Cyclic AMP Receptor Protein (CRP)-Like Binding Sequence and a CRP-Like Protein in Glucose-Mediated Catabolite Repression of
thn
Genes in Rhodococcus sp. Strain TFB
Authors: Tomás-Gallardo Laura , Santero Eduardo , Floriano Belén 
Published: May 2012

ABSTRACT

Glucose catabolite repression of tetralin catabolic genes in
Rhodococcus
sp. strain TFB was shown to be exerted by a protein homologous to transcriptional regulators of the cyclic AMP receptor (CRP)-FNR family. The protein was detected bound to putative CRP-like boxes localized at the promoters of the
thnA1
and
thnS
genes.
Real-Time PCR Methodology for Selective Detection of Viable Escherichia coli O157:H7 Cells by Targeting Z3276 as a Genetic Marker
Authors: Li Baoguang , Chen Jin-Qiang 
Published: May 2012

ABSTRACT

The goal of this study was to develop a sensitive, specific, and accurate method for the selective detection of viable
Escherichia coli
O157:H7 cells in foods. A unique open reading frame (ORF), Z3276, was identified as a specific genetic marker for the detection of
E. coli
O157:H7. We developed a real-time PCR assay with primers and probe targeting ORF Z3276 and confirmed that this assay was sensitive and specific for
E. coli
O157:H7 strains (
n
= 298). Using this assay, we can detect amounts of genomic DNA of
E. coli
O157:H7 as low as a few CFU equivalents. Moreover, we have developed a new propidium monoazide (PMA)–real-time PCR protocol that allows for the clear differentiation of viable from dead cells. In addition, the protocol was adapted to a 96-well plate format for easy and consistent handling of a large number of samples. Amplification of DNA from PMA-treated dead cells was almost completely inhibited, in contrast to the virtually unaffected amplification of DNA from PMA-treated viable cells. With beef spiked simultaneously with 8 × 10
7
dead cells/g and 80 CFU viable cells/g, we were able to selectively detect viable
E. coli
O157:H7 cells with an 8-h enrichment. In conclusion, this PMA–real-time PCR assay offers a sensitive and specific means to selectively detect viable
E. coli
O157:H7 cells in spiked beef. It also has the potential for high-throughput selective detection of viable
E. coli
O157:H7 cells in other food matrices and, thus, will have an impact on the accurate microbiological and epidemiological monitoring of food safety and environmental sources.
A Conserved Two-Component Signal Transduction System Controls the Response to Phosphate Starvation in Bifidobacterium breve UCC2003
Authors: Alvarez-Martin Pablo , Fernández Matilde , O'Connell-Motherway Mary , O'Connell Kerry Joan , Sauvageot Nicolas , Fitzgerald Gerald F. , MacSharry John , Zomer Aldert , van Sinderen Douwe 
Published: May 2012

ABSTRACT

This work reports on the identification and molecular characterization of the two-component regulatory system (2CRS) PhoRP, which controls the response to inorganic phosphate (P
i
) starvation in
Bifidobacterium breve
UCC2003. The response regulator PhoP was shown to bind to the promoter region of
pstSCAB
, specifying a predicted P
i
transporter system, as well as that of
phoU
, which encodes a putative P
i
-responsive regulatory protein. This interaction is assumed to cause transcriptional modulation under conditions of P
i
limitation. Our data suggest that the
phoRP
genes are subject to positive autoregulation and, together with
pstSCAB
and presumably
phoU
, represent the complete regulon controlled by the
phoRP
-encoded 2CRS in
B. breve
UCC2003. Determination of the minimal PhoP binding region combined with bioinformatic analysis revealed the probable recognition sequence of PhoP, designated here as the PHO box, which together with
phoRP
is conserved among many high-GC-content Gram-positive bacteria. The importance of the
phoRP
2CRS in the response of
B. breve
to P
i
starvation conditions was confirmed by analysis of a
B. breve
phoP
insertion mutant which exhibited decreased growth under phosphate-limiting conditions compared to its parent strain UCC2003.
Effects of Subinhibitory Concentrations of Menthol on Adaptation, Morphological, and Gene Expression Changes in Enterohemorrhagic Escherichia coli
Authors: Landau Elad , Shapira Roni 
Published: May 2012

ABSTRACT

Menthol (C
10
H
20
O) possesses antibacterial activity; nevertheless, bacterial adaptation to this compound has never been studied. Here we report that precultivation of enterohemorrhagic
Escherichia coli
(EHEC) strains in increasing subinhibitory (SI) concentrations of menthol significantly elevates (4- to 16-fold) their resistance to menthol. Concomitant morphological alterations included the appearance of mucoid colonies and reduced biofilm production. Scanning electron microscopy (SEM) examination revealed suppressed curli formation in menthol-adapted cells. Expression of the gene
cpsB10
(encoding one of the enzymes responsible for colanic acid production) was elevated in response to SI concentrations of menthol in a laboratory
E. coli
strain, whereas expression in an
rcsC
null mutant was reduced, implicating a partial role for the Rcs phosphorelay system in mediating the menthol signal. Adaptation to menthol also reduced expression of the locus of enterocyte effacement-encoded regulator (Ler). This reduction, together with reduced curli and biofilm formation and elevated mucoidity, suggests a general reduction in bacterial virulence following adaptation to menthol. Our results thus suggest menthol as a potential lead in the recently emerging alternative strategy of targeting bacterial virulence factors to develop new types of anti-infective agents.
Modeling of Phenoxy Acid Herbicide Mineralization and Growth of Microbial Degraders in 15 Soils Monitored by Quantitative Real-Time PCR of the Functional
tfdA
Gene
Authors: Bælum Jacob , Prestat Emmanuel , David Maude M. , Strobel Bjarne W. , Jacobsen Carsten S. 
Published: May 2012

ABSTRACT

Mineralization potentials, rates, and kinetics of the three phenoxy acid (PA) herbicides, 2,4-dichlorophenoxyacetic acid (2,4-D), 4-chloro-2-methylphenoxyacetic acid (MCPA), and 2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP), were investigated and compared in 15 soils collected from five continents. The mineralization patterns were fitted by zero/linear or exponential growth forms of the three-half-order models and by logarithmic (log), first-order, or zero-order kinetic models. Prior and subsequent to the mineralization event,
tfdA
genes were quantified using real-time PCR to estimate the genetic potential for degrading PA in the soils. In 25 of the 45 mineralization scenarios, ∼60% mineralization was observed within 118 days. Elevated concentrations of
tfdA
in the range 1 × 10
5
to 5 × 10
7
gene copies g
−1
of soil were observed in soils where mineralization could be described by using growth-linked kinetic models. A clear trend was observed that the mineralization rates of the three PAs occurred in the order 2,4-D > MCPA > MCPP, and a correlation was observed between rapid mineralization and soils exposed to PA previously. Finally, for 2,4-D mineralization, all seven mineralization patterns which were best fitted by the exponential model yielded a higher
tfdA
gene potential after mineralization had occurred than the three mineralization patterns best fitted by the Lin model.
Microbiological and Physicochemical Characterization of Small-Scale Cocoa Fermentations and Screening of Yeast and Bacterial Strains To Develop a Defined Starter Culture
Authors: Pereira Gilberto Vinícius de Melo , Miguel Maria Gabriela da Cruz Pedrozo , Ramos Cíntia Lacerda , Schwan Rosane Freitas 
Published: May 2012

ABSTRACT

Spontaneous cocoa bean fermentations performed under bench- and pilot-scale conditions were studied using an integrated microbiological approach with culture-dependent and culture-independent techniques, as well as analyses of target metabolites from both cocoa pulp and cotyledons. Both fermentation ecosystems reached equilibrium through a two-phase process, starting with the simultaneous growth of the yeasts (with
Saccharomyces cerevisiae
as the dominant species) and lactic acid bacteria (LAB) (
Lactobacillus fermentum
and
Lactobacillus plantarum
were the dominant species), which were gradually replaced by the acetic acid bacteria (AAB) (
Acetobacter tropicalis
was the dominant species). In both processes, a sequence of substrate consumption (sucrose, glucose, fructose, and citric acid) and metabolite production kinetics (ethanol, lactic acid, and acetic acid) similar to that of previous, larger-scale fermentation experiments was observed. The technological potential of yeast, LAB, and AAB isolates was evaluated using a polyphasic study that included the measurement of stress-tolerant growth and fermentation kinetic parameters in cocoa pulp media. Overall, strains
L. fermentum
UFLA CHBE8.12 (citric acid fermenting, lactic acid producing, and tolerant to heat, acid, lactic acid, and ethanol),
S. cerevisiae
UFLA CHYC7.04 (ethanol producing and tolerant to acid, heat, and ethanol), and
Acetobacter tropicalis
UFLA CHBE16.01 (ethanol and lactic acid oxidizing, acetic acid producing, and tolerant to acid, heat, acetic acid, and ethanol) were selected to form a cocktail starter culture that should lead to better-controlled and more-reliable cocoa bean fermentation processes.
Upregulation of Plasmid Genes during Stationary Phase in Synechocystis sp. Strain PCC 6803, a Cyanobacterium
Authors: Berla Bertram M. , Pakrasi Himadri B. 
Published: May 2012

ABSTRACTWe analyzed DNA microarrays to identify highly expressed genes during stationary-phase growth ofSynechocystissp. PCC 6803. Many identified genes are on endogenous plasmids, with copy numbers between 0.4 and 7 per chromosome. The promoters of such genes will be useful for synthetic biology applications with this phototrophic host.
O
-Demethylation and Successive Oxidative Dechlorination of Methoxychlor by Bradyrhizobium sp. Strain 17-4, Isolated from River Sediment
Authors: Satsuma Koji , Masuda Minoru , Sato Kiyoshi 
Published: May 2012

ABSTRACT

O
-Demethylation of insecticide methoxychlor is well known as a phase I metabolic reaction in various eukaryotic organisms. Regarding prokaryotic organisms, however, no individual species involved in such reaction have been specified and characterized so far. Here we successfully isolated a bacterium that mediates oxidative transformation of methoxychlor, including
O
-demethylation and dechlorination, from river sediment. The isolate was found to be closely related to
Bradyrhizobium elkanii
at the 16S rRNA gene sequence level (100% identical). However, based on some differences in the physiological properties of this bacterium, we determined that it was actually a different species,
Bradyrhizobium
sp. strain 17-4. The isolate mediated
O
-demethylation of methoxychlor to yield a monophenolic derivative [Mono-OH; 1,1,1-trichloro-2-(4-hydroxyphenyl)-2-(4-methoxyphenyl)ethane] as the primary degradation product. The chiral high-performance liquid chromatography (HPLC) analysis revealed that the isolate possesses high enantioselectivity favoring the formation of (
S
)-Mono-OH (nearly 100%). Accompanied by the sequential
O
-demethylation to form the bis-phenolic derivative Bis-OH [1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane], oxidative dechlorination of the side chain proceeded, and monophenolic carboxylic acid accumulated, followed by the formation of multiple unidentified polar degradation products. The breakdown proceeded more rapidly when reductively dechlorinated (dichloro-form) methoxychlor was applied as the initial substrate. The resultant carboxylic acids and polar degradation products are likely further biodegraded by ubiquitous bacteria. The isolate possibly plays an important role for complete degradation (mineralization) of methoxychlor by providing the readily biodegradable substrates.
Archaeal Tetrathionate Hydrolase Goes Viral: Secretion of a Sulfur Metabolism Enzyme in the Form of Virus-Like Particles
Authors: Krupovic Mart , Peixeiro Nuno , Bettstetter Marcus , Rachel Reinhard , Prangishvili David 
Published: May 2012

ABSTRACT

In the course of screening for virus-host systems in extreme thermal environments, we have isolated a strain of the hyperthermophilic archaeaon
Acidianus hospitalis
producing unusual filamentous particles with a zipper-like appearance. The particles were shown to represent a secreted form of a genuine cellular enzyme, tetrathionate hydrolase, involved in sulfur metabolism.
Genome Sequence and Mutational Analysis of Plant-Growth-Promoting Bacterium Agrobacterium tumefaciens CCNWGS0286 Isolated from a Zinc-Lead Mine Tailing
Authors: Hao Xiuli , Xie Pin , Johnstone Laurel , Miller Susan J. , Rensing Christopher , Wei Gehong 
Published: May 2012

ABSTRACT

The plant-growth-promoting bacterium
Agrobacterium tumefaciens
CCNWGS0286, isolated from the nodules of
Robinia pseudoacacia
growing in zinc-lead mine tailings, both displayed high metal resistance and enhanced the growth of
Robinia
plants in a metal-contaminated environment. Our goal was to determine whether bacterial metal resistance or the capacity to produce phytohormones had a larger impact on the growth of host plants under zinc stress. Eight zinc-sensitive mutants and one zinc-sensitive mutant with reduced indole-3-acetic acid (IAA) production were obtained by transposon mutagenesis. Analysis of the genome sequence and of transcription via reverse transcriptase PCR (RT-PCR) combined with transposon gene disruptions revealed that ZntA-4200 and the transcriptional regulator ZntR1 played important roles in the zinc homeostasis of
A. tumefaciens
CCNWGS0286. In addition, interruption of a putative oligoketide cyclase/lipid transport protein reduced IAA synthesis and also showed reduced zinc and cadmium resistance but had no influence on copper resistance. In greenhouse studies,
R. pseudoacacia
inoculated with
A. tumefaciens
CCNWGS0286 displayed a significant increase in biomass production over that without inoculation, even in a zinc-contaminated environment. Interestingly, the differences in plant biomass improvement among
A. tumefaciens
CCNWGS0286,
A. tumefaciens
C58, and zinc-sensitive mutants 12-2 (
zntA
::Tn
5
) and 15-6 (low IAA production) revealed that phytohormones, rather than genes encoding zinc resistance determinants, were the dominant factor in enhancing plant growth in contaminated soil.
Predominance of a Versatile-Peroxidase-Encoding Gene,
mnp4
, as Demonstrated by Gene Replacement via a Gene Targeting System for Pleurotus ostreatus
Authors: Salame Tomer M. , Knop Doriv , Tal Dana , Levinson Dana , Yarden Oded , Hadar Yitzhak 
Published: May 2012

ABSTRACT

Pleurotus ostreatus
(the oyster mushroom) and other white rot filamentous basidiomycetes are key players in the global carbon cycle.
P. ostreatus
is also a commercially important edible fungus with medicinal properties and is important for biotechnological and environmental applications. Efficient gene targeting via homologous recombination (HR) is a fundamental tool for facilitating comprehensive gene function studies. Since the natural HR frequency in
Pleurotus
transformations is low (2.3%), transformed DNA is predominantly integrated ectopically. To overcome this limitation, a general gene targeting system was developed by producing a
P. ostreatus
PC9 homokaryon Δ
ku80
strain, using carboxin resistance complemented by the development of a protocol for hygromycin B resistance protoplast-based DNA transformation and homokaryon isolation. The Δ
ku80
strain exhibited exclusive (100%) HR in the integration of transforming DNA, providing a high efficiency of gene targeting. Furthermore, the Δ
ku80
strains produced showed a phenotype similar to that of the wild-type PC9 strain, with similar growth fitness, ligninolytic functionality, and capability of mating with the incompatible strain PC15 to produce a dikaryon which retained its resistance to the corresponding selection and was capable of producing typical fruiting bodies. The applicability of this system is demonstrated by inactivation of the versatile peroxidase (VP) encoded by
mnp4
. This enzyme is part of the ligninolytic system of
P. ostreatus
, being one of the nine members of the manganese-peroxidase (MnP) gene family, and is the predominantly expressed VP in Mn
2+
-deficient media.
mnp4
inactivation provided a direct proof that
mnp4
encodes a key VP responsible for the Mn
2+
-dependent and Mn
2+
-independent peroxidase activity under Mn
2+
-deficient culture conditions.
The Bacterial Surface Layer Provides Protection against Antimicrobial Peptides
Authors: de la Fuente-Núñez César , Mertens Jan , Smit John , Hancock Robert E. W. 
Published: May 2012

ABSTRACT
This report describes a previously unrecognized role for bacterial surface layers as barriers that confer protection against antimicrobial peptides. As antimicrobial peptides exist in natural environments, S-layers may provide a bacterial survival mechanism that has been selected for through evolution.
Characterization of Geographically Distinct Bacterial Communities Associated with Coral Mucus Produced by Acropora spp. and Porites spp
Authors: McKew B. A. , Dumbrell A. J. , Daud S. D. , Hepburn L. , Thorpe E. , Mogensen L. , Whitby C. 
Published: May 2012

ABSTRACT

Acropora
and
Porites
corals are important reef builders in the Indo-Pacific and Caribbean. Bacteria associated with mucus produced by
Porites
spp. and
Acropora
spp. from Caribbean (Punta Maroma, Mexico) and Indo-Pacific (Hoga and Sampela, Indonesia) reefs were determined. Analysis of pyrosequencing libraries showed that bacterial communities from Caribbean corals were significantly more diverse (H′, 3.18 to 4.25) than their Indonesian counterparts (H′, 2.54 to 3.25). Dominant taxa were
Gammaproteobacteria
,
Alphaproteobacteria
,
Firmicutes
, and
Cyanobacteria
, which varied in relative abundance between coral genera and region. Distinct coral host-specific communities were also found; for example,
Clostridiales
were dominant on
Acropora
spp. (at Hoga and the Mexican Caribbean) compared to
Porites
spp. and seawater. Within the
Gammproteobacteria
,
Halomonas
spp. dominated sequence libraries from
Porites
spp. (49%) and
Acropora
spp. (5.6%) from the Mexican Caribbean, compared to the corresponding Indonesian coral libraries (<2%). Interestingly, with the exception of
Porites
spp. from the Mexican Caribbean, there was also a ubiquity of
Psychrobacter
spp., which dominated
Acropora
and
Porites
libraries from Indonesia and
Acropora
libraries from the Caribbean. In conclusion, there was a dominance of
Halomonas
spp. (associated with
Acropora
and
Porites
[Mexican Caribbean]),
Firmicutes
(associated with
Acropora
[Mexican Caribbean] and with
Acropora
and
Porites
[Hoga]), and
Cyanobacteria
(associated with
Acropora
and
Porites
[Hoga] and
Porites
[Sampela]). This is also the first report describing geographically distinct
Psychrobacter
spp. associated with coral mucus. In addition, the predominance of
Clostridiales
associated with
Acropora
spp. provided additional evidence for coral host-specific microorganisms.
Patterns of [FeFe] Hydrogenase Diversity in the Gut Microbial Communities of Lignocellulose-Feeding Higher Termites
Authors: Ballor Nicholas R. , Leadbetter Jared R. 
Published: May 2012

ABSTRACTHydrogen is the central free intermediate in the degradation of wood by termite gut microbes and can reach concentrations exceeding those measured for any other biological system. Degenerate primers targeting the largest family of [FeFe] hydrogenases observed in a termite gut metagenome have been used to explore the evolution and representation of these enzymes in termites. Sequences were cloned from the guts of the higher termitesAmitermessp. strain Cost010,Amitermessp. strain JT2,Gnathamitermessp. strain JT5,Microcerotermessp. strain Cost008,Nasutitermessp. strain Cost003, andRhyncotermessp. strain Cost004. Each gut sample harbored a more rich and evenly distributed population of hydrogenase sequences than observed previously in the guts of lower termites andCryptocercus punctulatus.This accentuates the physiological importance of hydrogen for higher termite gut ecosystems and may reflect an increased metabolic burden, or metabolic opportunity, created by a lack of gut protozoa. The sequences were phylogenetically distinct from previously sequenced [FeFe] hydrogenases. Phylogenetic and UniFrac comparisons revealed congruence between host phylogeny and hydrogenase sequence library clustering patterns. This may reflect the combined influences of the stable intimate relationship of gut microbes with their host and environmental alterations in the gut that have occurred over the course of termite evolution. These results accentuate the physiological importance of hydrogen to termite gut ecosystems.
Role of Fig1, a Component of the Low-Affinity Calcium Uptake System, in Growth and Sexual Development of Filamentous Fungi
Authors: Cavinder Brad , Trail Frances 
Published: May 2012

ABSTRACTThe function of Fig1, a transmembrane protein of the low-affinity calcium uptake system (LACS) in fungi, was examined for its role in the growth and development of the plant pathogenFusarium graminearum. The Δfig1mutants failed to produce mature perithecia, and sexual development was halted prior to the formation of perithecium initials. The loss of Fig1 function also resulted in a reduced vegetative growth rate. Macroconidium production was reduced 70-fold in the Δfig1mutants compared to the wild type. The function of the high-affinity calcium uptake system (HACS), comprised of the Ca2+channels Mid1 and Cch1, was previously characterized forF. graminearum. To better understand the roles of the LACS and the HACS, Δfig1Δmid1, Δfig1Δcch1, and Δfig1Δmid1Δcch1double and triple mutants were generated, and the phenotypes of these mutants were more severe than those of the Δfig1mutants. Pathogenicity on wheat was unaffected for the Δfig1mutants, but the Δfig1Δmid1, Δfig1Δcch1, and Δfig1Δmid1Δcch1mutants, lacking both LACS and HACS functions, had reduced pathogenicity. Additionally, Δfig1mutants ofNeurospora crassawere examined and did not affect filamentous growth or female fertility in a Δfig1mating typeAstrain, but the Δfig1mating typeastrain failed to produce fertile fruiting bodies. These results are the first report of Fig1 function in filamentous ascomycetes and expand its role to include complex fruiting body and ascus development.