bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the Intracellular Glutamate Decarboxylase System: Analysis of Its Function, Transcription, and Role in the Acid Resistance of Various Strains of Listeria monocytogenes
Authors: Karatzas Kimon-Andreas G. , Suur Laura , O'Byrne Conor P. 
Published: March 2012

ABSTRACT

The glutamate decarboxylase (GAD) system is important for the acid resistance of
Listeria monocytogenes
. We previously showed that under acidic conditions, glutamate (Glt)/γ-aminobutyrate (GABA) antiport is impaired in minimal media but not in rich ones, like brain heart infusion. Here we demonstrate that this behavior is more complex and it is subject to strain and medium variation. Despite the impaired Glt/GABA antiport, cells accumulate intracellular GABA (GABA
i
) as a standard response against acid in any medium, and this occurs in all strains tested. Since these systems can occur independently of one another, we refer to them as the extracellular (GAD
e
) and intracellular (GAD
i
) systems. We show here that GAD
i
contributes to acid resistance since in a Δ
gadD1D2
mutant, reduced GABA
i
accumulation coincided with a 3.2-log-unit reduction in survival at pH 3.0 compared to that of wild-type strain LO28. Among 20 different strains, the GAD
i
system was found to remove 23.11% ± 18.87% of the protons removed by the overall GAD system. Furthermore, the GAD
i
system is activated at milder pH values (4.5 to 5.0) than the GAD
e
system (pH 4.0 to 4.5), suggesting that GAD
i
is the more responsive of the two and the first line of defense against acid. Through functional genomics, we found a major role for GadD2 in the function of GAD
i
, while that of GadD1 was minor. Furthermore, the transcription of the
gad
genes in three common reference strains (10403S, LO28, and EGD-e) during an acid challenge correlated well with their relative acid sensitivity. No transcriptional upregulation of the
gadT2D2
operon, which is the most important component of the GAD system, was observed, while
gadD3
transcription was the highest among all
gad
genes in all strains. In this study, we present a revised model for the function of the GAD system and highlight the important role of GAD
i
in the acid resistance of
L. monocytogenes
.
Cloning, Overexpression in Escherichia coli, and Characterization of a Thermostable Fungal Acetylxylan Esterase from Talaromyces emersonii
Authors: Waters Deborah M. , Murray Patrick G. , Miki Yuta , Martínez Angel T. , Tuohy Maria G. , Faulds Craig B. 
Published: March 2012

ABSTRACT

The gene encoding an acetylxylan esterase (AXE1) from the thermophilic ascomycete
Talaromyces emersonii
was cloned, expressed in
Escherichia coli
, and characterized. This form of AXE1, rTeAXE1, exhibits increased thermostability and activity at a higher temperature than other known fungal acetyl esterases, thus having huge potential application in biomass bioconversion to high value chemicals or biofuels.
Characterization of Extended-Spectrum β-Lactamase Genes Found among Escherichia coli Isolates from Duck and Environmental Samples Obtained on a Duck Farm
Authors: Ma Junying , Liu Jian-Hua , Lv Luchao , Zong Zhiyong , Sun Yan , Zheng Hongqing , Chen ZhangLiu , Zeng Zhen-Ling 
Published: March 2012

ABSTRACT

In this study, we focused on evaluating the occurrence of extended-spectrum β-lactamase (ESBL)-producing
Escherichia coli
in fecal samples of healthy ducks and environmental samples from a duck farm in South China. Duck cloacal swabs and pond water samples were cultivated on MacConkey agar plates supplemented with ceftiofur. Individual colonies were examined for ESBL production. Bacteria identified as
E. coli
were screened for the presence of ESBL and plasmid-borne AmpC genes. The genetic relatedness, plasmid replicon type, and genetic background were determined. Of 245 samples analyzed, 123 had
E. coli
isolates with ceftiofur MICs higher than 8 μg/ml (116 [50.4%] from 230 duck samples and 7 [46.7%] from 15 water samples).
bla
CTX-M
,
bla
SHV-12
,
bla
CMY-2
, and
bla
DHA-1
were identified in 108, 5, 9, and 1 isolates, respectively. The most common
bla
CTX-M
genes were
bla
CTX-M-27
(
n
= 34),
bla
CTX-M-55
(
n
= 27),
bla
CTX-M-24e
(
n
= 22), and
bla
CTX-M-105
(
n
= 20), followed by
bla
CTX-M-14a
,
bla
CTX-M-14b
,
bla
CTX-M-24a
, and
bla
CTX-M-24b
. Although most of the CTX-M producers had distinct pulsotypes, clonal transmission between duck and water isolates was observed.
bla
CTX-M
genes were carried by transferable IncN, IncF, and untypeable plasmids. The novel CTX-M gene
bla
CTX-M-105
was flanked by two hypothetical protein sequences, partial IS
Ecp1
upstream and truncated IS
903D
,
iroN
,
orf1
, and a Tn
1721
-like element downstream. It is suggested that the horizontal transfer of
bla
CTX-M
genes mediated by mobile elements and the clonal spread of CTX-M-producing
E. coli
isolates contributed to the dissemination of
bla
CTX-M
in the duck farm. Our findings highlight the importance of ducks for the dissemination of transferable antibiotic resistance genes into the environment.
Isolation of Potentially Novel Brucella spp. from Frogs
Authors: Eisenberg Tobias , Hamann Hans-Peter , Kaim Ute , Schlez Karen , Seeger Helga , Schauerte Nicole , Melzer Falk , Tomaso Herbert , Scholz Holger C. , Koylass Mark S. , Whatmore Adrian M. , Zschöck Michael 
Published: March 2012

ABSTRACT

Bacterial isolates from frogs were phenotypically identified as
Ochrobactrum anthropi
, but 16S rRNA sequencing showed up to 100% identity with
Brucella inopinata
. Further analysis of
recA
,
omp2a
,
omp2b
,
bcsp31
, and IS
711
and multilocus sequence analysis (MLSA) verified a close relationship with
Brucella
, suggesting the isolates may actually represent novel members of this growing genus of zoonotic pathogens.
Genetic Analysis of the Upper Phenylacetate Catabolic Pathway in the Production of Tropodithietic Acid by Phaeobacter gallaeciensis
Authors: Berger Martine , Brock Nelson L. , Liesegang Heiko , Dogs Marco , Preuth Ines , Simon Meinhard , Dickschat Jeroen S. , Brinkhoff Thorsten 
Published: March 2012

ABSTRACTProduction of the antibiotic tropodithietic acid (TDA) depends on the central phenylacetate catabolic pathway, specifically on the oxygenase PaaABCDE, which catalyzes epoxidation of phenylacetyl-coenzyme A (CoA). Our study was focused on genes of the upper part of this pathway leading to phenylacetyl-CoA as precursor for TDA.Phaeobacter gallaeciensisDSM 17395 encodes two genes with homology to phenylacetyl-CoA ligases (paaK1andpaaK2), which were shown to be essential for phenylacetate catabolism but not for TDA biosynthesis and phenylalanine degradation. Thus, inP. gallaeciensisanother enzyme must produce phenylacetyl-CoA from phenylalanine. Using random transposon insertion mutagenesis of apaaK1-paaK2double mutant we identified a gene (ior1) with similarity toiorAandiorBin archaea, encoding an indolepyruvate:ferredoxin oxidoreductase (IOR). Theior1mutant was unable to grow on phenylalanine, and production of TDA was significantly reduced compared to the wild-type level (60%). Nuclear magnetic resonance (NMR) spectroscopic investigations using13C-labeled phenylalanine isotopomers demonstrated that phenylalanine is transformed into phenylacetyl-CoA by Ior1. Using quantitative real-time PCR, we could show that expression ofior1depends on the adjacent regulator IorR. Growth on phenylalanine promotes production of TDA, induces expression ofior1(27-fold) andpaaK1(61-fold), and regulates the production of TDA. Phylogenetic analysis showed that the aerobic type of IOR as found in many roseobacters is common within a number of different phylogenetic groups of aerobic bacteria such asBurkholderia,Cupriavidis, andRhizobia, where it may also contribute to the degradation of phenylalanine.
Influence of Seasonality on the Genetic Diversity of Vibrio parahaemolyticus in New Hampshire Shellfish Waters as Determined by Multilocus Sequence Analysis
Authors: Ellis Crystal N. , Schuster Brian M. , Striplin Megan J. , Jones Stephen H. , Whistler Cheryl A. , Cooper Vaughn S. 
Published: March 2012

ABSTRACT

Risk of gastric infection with
Vibrio parahaemolyticus
increases with favorable environmental conditions and population shifts that increase prevalence of infective strains. Genetic analysis of New Hampshire strains revealed a unique population with some isolates similar to outbreak-causing strains and high-level diversity that increased as waters warmed.
Functional Robustness of a Polycyclic Aromatic Hydrocarbon Metabolic Network Examined in a
nidA
Aromatic Ring-Hydroxylating Oxygenase Mutant of Mycobacterium vanbaalenii PYR-1
Authors: Kim Seong-Jae , Song Jaekyeong , Kweon Ohgew , Holland Ricky D. , Kim Dae-Wi , Kim Jongnam , Yu Li-Rong , Cerniglia Carl E. 
Published: March 2012

ABSTRACT

In this study, we obtained over 4,000 transposon mutants of
Mycobacterium vanbaalenii
PYR-1 and analyzed one of the mutants, 8F7, which appeared to lose its ability to degrade pyrene while still being able to degrade fluoranthene. This mutant was identified to be defective in
nidA
, encoding an aromatic ring-hydroxylating oxygenase (RHO), known to be involved in the initial oxidation step of pyrene degradation. When cultured with pyrene as a sole source of polycyclic aromatic hydrocarbon (PAH), high-pressure liquid chromatography analysis revealed that the
nidA
mutant showed a significant decrease in the rate of pyrene degradation compared to the wild-type PYR-1, although pyrene was still being degraded. However, when incubated with PAH mixtures including pyrene, phenanthrene, and fluoranthene, the pyrene degradation rate of the mutant was higher than that of the mutant previously incubated with pyrene as a sole source of PAH. There was no significant difference between wild-type PYR-1 and the mutant in the rates of phenanthrene and fluoranthene degradation. From the whole-cell proteome analysis of mutant 8F7 induced by pyrene, we identified expression of a number of RHO enzymes which are suspected to be responsible for pyrene degradation in the
nidA
mutant, which had no expression of NidA. Taken together, results in this study provide direct evidence for the
in vivo
functional role of
nidA
in pyrene degradation at the level of the ring-cleavage-process (RCP) functional module but also for the robustness of the PAH metabolic network (MN) to such a genetic perturbation.
Density of the Waterborne Parasite Ceratomyxa shasta and Its Biological Effects on Salmon
Authors: Hallett Sascha L. , Ray R. Adam , Hurst Charlene N. , Holt Richard A. , Buckles Gerri R. , Atkinson Stephen D. , Bartholomew Jerri L. 
Published: March 2012

ABSTRACT

The myxozoan parasite
Ceratomyxa shasta
is a significant pathogen of juvenile salmonids in the Pacific Northwest of North America and is limiting recovery of Chinook (
Oncorhynchus tshawytscha
) and coho (
O. kisutch
) salmon populations in the Klamath River. We conducted a 5-year monitoring program that comprised concurrent sentinel fish exposures and water sampling across 212 river kilometers of the Klamath River. We used percent mortality and degree-days to death to measure disease severity in fish. We analyzed water samples using quantitative PCR and Sanger sequencing, to determine total parasite density and relative abundance of
C. shasta
genotypes, which differ in their pathogenicity to salmonids. We detected the parasite throughout the study zone, but parasite density and genetic composition fluctuated spatially and temporally. Chinook and coho mortality increased with density of their specific parasite genotype, but mortality-density thresholds and time to death differed. A lethality threshold of 40% mortality was reached with 10 spores liter
−1
for Chinook but only 5 spores liter
−1
for coho. Parasite density did not affect degree-days to death for Chinook but was negatively correlated for coho, and there was wider variation among coho individuals. These differences likely reflect the different life histories and genetic heterogeneity of the salmon populations. Direct quantification of the density of host-specific parasite genotypes in water samples offers a management tool for predicting host population-level impacts.
Metabolome and Transcriptome of the Interaction between Ustilago maydis and Fusarium verticillioides
In Vitro
Authors: Jonkers Wilfried , Rodriguez Estrada Alma E. , Lee Keunsub , Breakspear Andrew , May Georgiana , Kistler H. Corby 
Published: March 2012

ABSTRACT

The metabolome and transcriptome of the maize-infecting fungi
Ustilago maydis
and
Fusarium verticillioides
were analyzed as the two fungi interact. Both fungi were grown for 7 days in liquid medium alone or together in order to study how this interaction changes their metabolomic and transcriptomic profiles. When grown together, decreased biomass accumulation occurs for both fungi after an initial acceleration of growth compared to the biomass changes that occur when grown alone. The biomass of
U. maydis
declined most severely over time and may be attributed to the action of
F. verticillioides
, which secretes toxic secondary metabolites and expresses genes encoding adhesive and cell wall-degrading proteins at higher levels than when grown alone.
U. maydis
responds to cocultivation by expressing siderophore biosynthetic genes and more highly expresses genes potentially involved in toxin biosynthesis. Also, higher expression was noted for clustered genes encoding secreted proteins that are unique to
U. maydis
and that may play a role during colonization of maize. Conversely, decreased gene expression was seen for
U. maydis
genes encoding the synthesis of ustilagic acid, mannosylerythritol D, and another uncharacterized metabolite. Ultimately,
U. maydis
is unable to react efficiently to the toxic response of
F. verticillioides
and proportionally loses more biomass. This
in vitro
study clarifies potential mechanisms of antagonism between these two fungi that also may occur in the soil or in maize, niches for both fungi where they likely interact in nature.
Role of the Lizard Teira dugesii as a Potential Host for Ixodes ricinus Tick-Borne Pathogens
Authors: De Sousa R. , de Carvalho I. Lopes , Santos A. S. , Bernardes C. , Milhano N. , Jesus J. , Menezes D. , Núncio M. S. 
Published: March 2012

ABSTRACT

PCR screening of ticks and tissue samples collected from 151
Teira dugesii
lizards seems to indicate a potential role of this lizard species in the maintenance and transmission cycle of some
Ixodes ricinus
tick-borne agents, such as
Rickettsia monacensis
,
Rickettsia helvetica
, and
Borrelia lusitaniae
, that are circulating on Madeira Island.
Histone H3 Variants in Trichomonas vaginalis
Authors: Zubáčová Zuzana , Hostomská Jitka , Tachezy Jan 
Published: March 2012

ABSTRACT

The parabasalid protist
Trichomonas vaginalis
is a widespread parasite that affects humans, frequently causing vaginitis in infected women. Trichomonad mitosis is marked by the persistence of the nuclear membrane and the presence of an asymmetric extranuclear spindle with no obvious direct connection to the chromosomes. No centromeric markers have been described in
T. vaginalis
, which has prevented a detailed analysis of mitotic events in this organism. In other eukaryotes, nucleosomes of centromeric chromatin contain the histone H3 variant CenH3. The principal aim of this work was to identify a CenH3 homolog in
T. vaginalis
. We performed a screen of the
T. vaginalis
genome to retrieve sequences of canonical and variant H3 histones. Three variant histone H3 proteins were identified, and the subcellular localization of their epitope-tagged variants was determined. The localization of the variant TVAG_185390 could not be distinguished from that of the canonical H3 histone. The sequence of the variant TVAG_087830 closely resembled that of histone H3. The tagged protein colocalized with sites of active transcription, indicating that the variant TVAG_087830 represented H3.3 in
T. vaginalis
. The third H3 variant (TVAG_224460) was localized to 6 or 12 distinct spots at the periphery of the nucleus, corresponding to the number of chromosomes in G
1
phase and G
2
phase, respectively. We propose that this variant represents the centromeric marker CenH3 and thus can be employed as a tool to study mitosis in
T. vaginalis
. Furthermore, we suggest that the peripheral distribution of CenH3 within the nucleus results from the association of centromeres with the nuclear envelope throughout the cell cycle.
Motor Protein Myo5p Is Required To Maintain the Regulatory Circuit Controlling
WOR1
Expression in Candida albicans
Authors: Kachurina Nadezda , Turcotte Bernard , Whiteway Malcolm 
Published: March 2012

ABSTRACT

The
Candida albicans MYO5
gene encodes myosin I, a protein required for the formation of germ tubes and true hyphae. Because the polarized growth of opaque-phase cells in response to pheromone results in mating projections that can resemble germ tubes, we examined the role of Myo5p in this process. We localized green fluorescent protein (GFP)-tagged Myo5p in opaque-phase cells of
C. albicans
during both bud and shmoo formation. In vegetatively growing opaque cells, Myo5p is found at sites of bud emergence and bud growth, while in pheromone-stimulated cells, Myo5p localizes at the growing tips of shmoos. Intriguingly, cells homozygous for
MTL
a
in which the
MYO5
gene was deleted failed to switch efficiently from the white phase to the opaque phase, although ectopic expression of
WOR1
from the
MET3
promoter can convert
myo5
mutants into mating-competent opaque cells. However, when
WOR1
expression was shut off, the
myo5
-defective cells rapidly lost both their opaque phenotype and mating competence, suggesting that Myo5p is involved in the maintenance of the opaque state. When
MYO5
is expressed conditionally in opaque cells, the opaque phenotype, as well as the mating ability of the cells, becomes unstable under repressive conditions, and quantitative real-time PCR demonstrated that the shutoff of
MYO5
expression correlates with a dramatic reduction in
WOR1
expression. It appears that while myosin I is not directly required for mating in
C. albicans
, it is involved in
WOR1
expression and the white-opaque transition and thus is indirectly implicated in mating.
The Arthroderma benhamiae Hydrophobin HypA Mediates Hydrophobicity and Influences Recognition by Human Immune Effector Cells
Authors: Heddergott Christoph , Bruns Sandra , Nietzsche Sandor , Leonhardt Ines , Kurzai Oliver , Kniemeyer Olaf , Brakhage Axel A. 
Published: March 2012

ABSTRACT

Dermatophytes are the most common cause of superficial mycoses in humans and animals. They can coexist with their hosts for many years without causing significant symptoms but also cause highly inflammatory diseases. To identify mechanisms involved in the modulation of the host response during infection caused by the zoophilic dermatophyte
Arthroderma benhamiae
, cell wall-associated surface proteins were studied. By two-dimensional gel electrophoresis, we found that a hydrophobin protein designated HypA was the dominant cell surface protein. HypA was also detected in the supernatant during the growth and conidiation of the fungus. The
A. benhamiae
genome harbors only a single hydrophobin gene, designated
hypA
. A
hypA
deletion mutant was generated, as was a complemented
hypA
mutant strain (
hypA
C
). In contrast to the wild type and the complemented strain, the
hypA
deletion mutant exhibited “easily wettable” mycelia and conidia, indicating the loss of surface hydrophobicity of both morphotypes. Compared with the wild type, the
hypA
deletion mutant triggered an increased activation of human neutrophil granulocytes and dendritic cells, characterized by an increased release of the immune mediators interleukin-6 (IL-6), IL-8, IL-10, and tumor necrosis factor alpha (TNF-α). For the first time, we observed the formation of neutrophil extracellular traps against dermatophytes, whose level of formation was increased by the Δ
hypA
mutant compared with the wild type. Furthermore, conidia of the Δ
hypA
strain were killed more effectively by neutrophils. Our data suggest that the recognition of
A. benhamiae
by the cellular immune defense system is notably influenced by the presence of the surface rodlet layer formed by the hydrophobin HypA.
The LovK-LovR Two-Component System Is a Regulator of the General Stress Pathway in Caulobacter crescentus
Authors: Foreman Robert , Fiebig Aretha , Crosson Sean 
Published: March 2012

ABSTRACT

A conserved set of regulators control the general stress response in
Caulobacter crescentus
, including σ
T
, its anti-σ factor NepR, the anti-anti-σ factor PhyR, and the transmembrane sensor kinase PhyK. We report that the soluble histidine kinase LovK and the single-domain response regulator LovR also function within the
C. crescentus
general stress pathway. Our genetic data support a model in which LovK-LovR functions upstream of σ
T
by controlling the phosphorylation state and thus anti-anti-σ activity of PhyR. Transcription of
lovK
and
lovR
is independently activated by stress through a mechanism that requires
sigT
and
phyR
. Conversely,
lovK
and
lovR
function together to repress transcription of the general stress regulon. Concordant with a functional role of the LovK-LovR two-component system as a negative regulator of the general stress pathway,
lovK
-
lovR
-null mutants exhibit increased cell survival after osmotic stress, while coordinate overexpression of
lovK
and
lovR
attenuates cell survival relative to that of the wild type. Notably,
lovK
can complement the transcriptional and cell survival defects of a
phyK
-null mutant when
lovR
is deleted. Moreover, in this same genetic background, σ
T
-dependent transcription is activated in response to osmotic stress. This result suggests that flavin-binding LOV (light, oxygen, or voltage) histidine kinases are competent to perceive cytoplasmic signals in addition to the environmental signal blue light. We conclude that the PhyK-PhyR and LovK-LovR two-component signaling systems coordinately regulate stress physiology in
C. crescentus
.
A retrospective analysis of cervical spine radiography in a specialist trauma unit for head injury
Authors: Baneke Alex Jan , Shafei Rachelle , Costello Jonathan 
Published: March 2012

ObjectivesThe performance of an adequate and complete series of cervical radiographs in the trauma patient is essential in order to ensure safe trauma management. Eastern Association for the Surgery of Trauma (EAST) has produced widely recognised guidelines with which trauma units should comply. The aim of the study is to ascertain the adequacy of cervical spine imaging of trauma patients in a specialist trauma unit (head injury) using EAST guidelines as gold standard. An additional assessment of institutional reporting accuracy is conducted.MethodsData were examined from 81 consecutive trauma patients requiring cervical spine radiography. EAST guidelines were applied retrospectively to this cohort in order to define guideline compliance. An additional cohort assessment was conducted addressing the accuracy and adequacy of the formal institutional reports associated with these radiographs.Results99% of patients undergoing a full cervical trauma series had at least one inadequate initial image. Of these, 85% had at least one inadequate lateral or peg view (of which 26% did not have repeat radiographs performed). Over one-third of all trauma patients left the emergency department with inadequate cervical spine imaging (incomplete cervical spine series or inadequate films). From the institutional reporting perspective, only 27% of all inadequate initial and repeat lateral or peg views were subsequently explicitly reported as being inadequate.DiscussionThese findings call into question current practice. Clearly, multiple confounders exist in the context of process variability in a heterogeneous population such as that attending an emergency department. This study offer solutions to address this problem.