bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Application of a Blastocystis Subtype-Specific PCR Assay Reveals that Mixed-Subtype Infections Are Common in a Healthy Human Population
Authors: Scanlan Pauline D. , Stensvold Christen Rune , Cotter Paul D. 
Published: April 2015

ABSTRACT

The human gut is host to a diversity of microorganisms, including the single-celled microbial eukaryote
Blastocystis.
Research has shown that most carriers host a single
Blastocystis
subtype (ST), which is unusual given the considerable within-host species diversity observed for other microbial genera in this ecosystem. However, our limited knowledge of both the incidence and biological significance of
Blastocystis
diversity within hosts (i.e., so-called mixed infections) is likely due to problems with existing methodologies. Here, we developed and applied
Blastocystis
ST-specific PCRs for the investigation of the most common subtypes of
Blastocystis
(ST1 to ST4) to a healthy human cohort (
n
= 50). We detected mixed infections in 22% of the cases, all of which had been identified as single-ST infections in a previous study using state-of-the-art methods. Our results show that certain STs occur predominantly as either single (ST3 and 4) or mixed (ST1) infections, which may reflect
inter alia
transient colonization patterns and/or cooperative or competitive interactions between different STs. Comparative analyses with other primers that have been used extensively for ST-specific analysis found them unsuitable for detection of mixed- and, in some cases, single-ST infections. Collectively, our data shed new light on the diversity of
Blastocystis
within and between human hosts. Moreover, the development of these PCR assays will facilitate future work on the molecular epidemiology and significance of mixed infections in groups of interest, including health and disease cohorts, and also help identify sources of
Blastocystis
transmission to humans, including identifying potential animal and environmental reservoirs.
The Impact of Gamma Radiation on Sediment Microbial Processes
Authors: Brown Ashley R. , Boothman Christopher , Pimblott Simon M. , Lloyd Jonathan R. 
Published: April 2015

ABSTRACT

Microbial communities have the potential to control the biogeochemical fate of some radionuclides in contaminated land scenarios or in the vicinity of a geological repository for radioactive waste. However, there have been few studies of ionizing radiation effects on microbial communities in sediment systems. Here, acetate and lactate amended sediment microcosms irradiated with gamma radiation at 0.5 or 30 Gy h
−1
for 8 weeks all displayed NO
3
−
and Fe(III) reduction, although the rate of Fe(III) reduction was decreased in 30-Gy h
−1
treatments. These systems were dominated by fermentation processes. Pyrosequencing indicated that the 30-Gy h
−1
treatment resulted in a community dominated by two Clostridial species. In systems containing no added electron donor, irradiation at either dose rate did not restrict NO
3
−
, Fe(III), or SO
4
2−
reduction. Rather, Fe(III) reduction was stimulated in the 0.5-Gy h
−1
-treated systems. In irradiated systems, there was a relative increase in the proportion of bacteria capable of Fe(III) reduction, with
Geothrix fermentans
and
Geobacter
sp. identified in the 0.5-Gy h
−1
and 30-Gy h
−1
treatments, respectively. These results indicate that biogeochemical processes will likely not be restricted by dose rates in such environments, and electron accepting processes may even be stimulated by radiation.
Two-Component-System Histidine Kinases Involved in Growth of Listeria monocytogenes EGD-e at Low Temperatures
Authors: Pöntinen Anna , Markkula Annukka , Lindström Miia , Korkeala Hannu 
Published: April 2015

ABSTRACT

Two-component systems (TCSs) aid bacteria in adapting to a wide variety of stress conditions. While the role of TCS response regulators in the cold tolerance of the psychrotrophic foodborne pathogen
Listeria monocytogenes
has been demonstrated previously, no comprehensive studies showing the role of TCS histidine kinases of
L. monocytogenes
at low temperature have been performed. We compared the expression levels of each histidine kinase-encoding gene of
L. monocytogenes
EGD-e in logarithmic growth phase at 3°C and 37°C, as well as the expression levels 30 min, 3 h, and 7 h after cold shock at 5°C and preceding cold shock (at 37°C). We constructed a deletion mutation in each TCS histidine kinase gene, monitored the growth of the EGD-e wild-type and mutant strains at 3°C and 37°C, and measured the minimum growth temperature of each strain. Two genes,
yycG
and
lisK
, proved significant in regard to induced relative expression levels under cold conditions and cold-sensitive mutant phenotypes. Moreover, the Δ
resE
mutant showed a lower growth rate than that of wild-type EGD-e at 3°C. Eleven other genes showed upregulated gene expression but revealed no cold-sensitive phenotypes. The results show that the histidine kinases encoded by
yycG
and
lisK
are important for the growth and adaptation of
L. monocytogenes
EGD-e at low temperature.
Interactions between Human Norovirus Surrogates and Acanthamoeba spp
Authors: Hsueh Tun-Yun , Gibson Kristen E. 
Published: April 2015

ABSTRACT

Human noroviruses (HuNoVs) are the most common cause of food-borne disease outbreaks, as well as virus-related waterborne disease outbreaks in the United States. Here, we hypothesize that common free-living amoebae (FLA)—ubiquitous in the environment, known to interact with pathogens, and frequently isolated from water and fresh produce—could potentially act as reservoirs of HuNoV and facilitate the environmental transmission of HuNoVs. To investigate FLA as reservoirs for HuNoV, the interactions between two
Acanthamoeba
species,
A. castellanii
and
A. polyphaga
, as well as two HuNoV surrogates, murine norovirus type 1 (MNV-1) and feline calicivirus (FCV), were evaluated. The results showed that after 1 h of amoeba-virus incubation at 25°C, 490 and 337 PFU of MNV-1/ml were recovered from
A. castellanii
and
A. polyphaga
, respectively, while only few or no FCVs were detected. In addition, prolonged interaction of MNV-1 with amoebae was investigated for a period of 8 days, and MNV-1 was demonstrated to remain stable at around 200 PFU/ml from day 2 to day 8 after virus inoculation in
A. castellanii
. Moreover, after a complete amoeba life cycle (i.e., encystment and excystment), infectious viruses could still be detected. To determine the location of virus associated with amoebae, immunofluorescence experiments were performed and showed MNV-1 transitioning from the amoeba surface to inside the amoeba over a 24-h period. These results are significant to the understanding of how HuNoVs may interact with other microorganisms in the environment in order to aid in its persistence and survival, as well as potential transmission in water and to vulnerable food products such as fresh produce.
σ
54
-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111
Authors: Lardi Martina , Aguilar Claudio , Pedrioli Alessandro , Omasits Ulrich , Suppiger Angela , Cárcamo-Oyarce Gerardo , Schmid Nadine , Ahrens Christian H. , Eberl Leo , Pessi Gabriella 
Published: April 2015

ABSTRACT

Members of the genus
Burkholderia
are versatile bacteria capable of colonizing highly diverse environmental niches. In this study, we investigated the global response of the opportunistic pathogen
Burkholderia cenocepacia
H111 to nitrogen limitation at the transcript and protein expression levels. In addition to a classical response to nitrogen starvation, including the activation of glutamine synthetase, PII proteins, and the two-component regulatory system NtrBC,
B. cenocepacia
H111 also upregulated polyhydroxybutyrate (PHB) accumulation and exopolysaccharide (EPS) production in response to nitrogen shortage. A search for consensus sequences in promoter regions of nitrogen-responsive genes identified a σ
54
consensus sequence. The mapping of the σ
54
regulon as well as the characterization of a σ
54
mutant suggests an important role of σ
54
not only in control of nitrogen metabolism but also in the virulence of this organism.
Enhancing the Detection of Giardia duodenalis Cysts in Foods by Inertial Microfluidic Separation
Authors: Ganz Kyle R. , Clime Liviu , Farber Jeffrey M. , Corneau Nathalie , Veres Teodor , Dixon Brent R. 
Published: April 2015

ABSTRACT

The sensitivity and specificity of current
Giardia
cyst detection methods for foods are largely determined by the effectiveness of the elution, separation, and concentration methods used. The aim of these methods is to produce a final suspension with an adequate concentration of
Giardia
cysts for detection and a low concentration of interfering food debris. In the present study, a microfluidic device, which makes use of inertial separation, was designed and fabricated for the separation of
Giardia
cysts. A cyclical pumping platform and protocol was developed to concentrate 10-ml suspensions down to less than 1 ml. Tests involving
Giardia duodenalis
cysts and 1.90-μm microbeads in pure suspensions demonstrated the specificity of the microfluidic chip for cysts over smaller nonspecific particles. As the suspension cycled through the chip, a large number of beads were removed (70%) and the majority of the cysts were concentrated (82%). Subsequently, the microfluidic inertial separation chip was integrated into a method for the detection of
G. duodenalis
cysts from lettuce samples. The method greatly reduced the concentration of background debris in the final suspensions (10-fold reduction) in comparison to that obtained by a conventional method. The method also recovered an average of 68.4% of cysts from 25-g lettuce samples and had a limit of detection (LOD) of 38 cysts. While the recovery of cysts by inertial separation was slightly lower, and the LOD slightly higher, than with the conventional method, the sample analysis time was greatly reduced, as there were far fewer background food particles interfering with the detection of cysts by immunofluorescence microscopy.
Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types
Authors: Reavy Brian , Swanson Maud M. , Cock Peter J. A. , Dawson Lorna , Freitag Thomas E. , Singh Brajesh K. , Torrance Lesley , Mushegian Arcady R. , Taliansky Michael 
Published: April 2015

ABSTRACT

The potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the family
Microviridae
(icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis of
Microviridae
major coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamily
Gokushovirinae
, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar family
Circoviridae
in BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in the
Circoviridae
showed that they are a novel clade of
Circoviridae
-related CRESS-DNA viruses distinct from known
Circoviridae
genera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors.
Evaluation of Lactococcus lactis Isolates from Nondairy Sources with Potential Dairy Applications Reveals Extensive Phenotype-Genotype Disparity and Implications for a Revised Species
Authors: Cavanagh Daniel , Casey Aidan , Altermann Eric , Cotter Paul D. , Fitzgerald Gerald F. , McAuliffe Olivia 
Published: April 2015

ABSTRACT

Lactococcus lactis
is predominantly associated with dairy fermentations, but evidence suggests that the domesticated organism originated from a plant niche.
L. lactis
possesses an unusual taxonomic structure whereby strain phenotypes and genotypes often do not correlate, which in turn has led to confusion in
L. lactis
classification. A bank of
L. lactis
strains was isolated from various nondairy niches (grass, vegetables, and bovine rumen) and was further characterized on the basis of key technological traits, including growth in milk and key enzyme activities. Phenotypic analysis revealed all strains from nondairy sources to possess an
L. lactis
subsp.
lactis
phenotype (
lactis
phenotype); however, seven of these strains possessed an
L. lactis
subsp.
cremoris
genotype (
cremoris
genotype), determined by two separate PCR assays. Multilocus sequence typing (MLST) showed that strains with
lactis
and
cremoris
genotypes clustered together regardless of habitat, but it highlighted the increased diversity that exists among “wild” strains. Calculation of average nucleotide identity (ANI) and tetranucleotide frequency correlation coefficients (TETRA), using the JSpecies software tool, revealed that
L. lactis
subsp.
cremoris
and
L. lactis
subsp.
lactis
differ in ANI values by ∼14%, below the threshold set for species circumscription. Further analysis of strain TIFN3 and strains from nonindustrial backgrounds revealed TETRA values of <0.99 in addition to ANI values of <95%, implicating that these two groups are separate species. These findings suggest the requirement for a revision of
L. lactis
taxonomy.
Public Health Investigation of Two Outbreaks of Shiga Toxin-Producing Escherichia coli O157 Associated with Consumption of Watercress
Authors: Jenkins Claire , Dallman Timothy J. , Launders Naomi , Willis Caroline , Byrne Lisa , Jorgensen Frieda , Eppinger Mark , Adak Goutam K. , Aird Heather , Elviss Nicola , Grant Kathie A. , Morgan Dilys , McLauchlin Jim 
Published: April 2015

ABSTRACT

An increase in the number of cases of Shiga toxin-producing
Escherichia coli
(STEC) O157 phage type 2 (PT2) in England in September 2013 was epidemiologically linked to watercress consumption. Whole-genome sequencing (WGS) identified a phylogenetically related cluster of 22 cases (outbreak 1). The isolates comprising this cluster were not closely related to any other United Kingdom strain in the Public Health England WGS database, suggesting a possible imported source. A second outbreak of STEC O157 PT2 (outbreak 2) was identified epidemiologically following the detection of outbreak 1. Isolates associated with outbreak 2 were phylogenetically distinct from those in outbreak 1. Epidemiologically unrelated isolates on the same branch as the outbreak 2 cluster included those from human cases in England with domestically acquired infection and United Kingdom domestic cattle. Environmental sampling using PCR resulted in the isolation of STEC O157 PT2 from irrigation water at one implicated watercress farm, and WGS showed this isolate belonged to the same phylogenetic cluster as outbreak 2 isolates. Cattle were in close proximity to the watercress bed and were potentially the source of the second outbreak. Transfer of STEC from the field to the watercress bed may have occurred through wildlife entering the watercress farm or via runoff water. During this complex outbreak investigation, epidemiological studies, comprehensive testing of environmental samples, and the use of novel molecular methods proved invaluable in demonstrating that two simultaneous outbreaks of STEC O157 PT2 were both linked to the consumption of watercress but were associated with different sources of contamination.
Next-Generation Pyrosequencing Analysis of Microbial Biofilm Communities on Granular Activated Carbon in Treatment of Oil Sands Process-Affected Water
Authors: Islam M. Shahinoor , Zhang Yanyan , McPhedran Kerry N. , Liu Yang , Gamal El-Din Mohamed 
Published: April 2015

ABSTRACT

The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum
Proteobacteria
was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of
Alpha
- and
Gammaproteobacteria
sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely,
Burkholderiales
,
Pseudomonadales
,
Bdellovibrionales
, and
Sphingomonadales
, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>10
9
gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O
3
/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds.
Eaf1 Links the NuA4 Histone Acetyltransferase Complex to Htz1 Incorporation and Regulation of Purine Biosynthesis
Authors: Cheng Xue , Auger Andréanne , Altaf Mohammed , Drouin Simon , Paquet Eric , Utley Rhea T. , Robert François , Côté Jacques 
Published: April 2015

ABSTRACT

Proper modulation of promoter chromatin architecture is crucial for gene regulation in order to precisely and efficiently orchestrate various cellular activities. Previous studies have identified the stimulatory effect of the histone-modifying complex NuA4 on the incorporation of the histone variant H2A.Z (Htz1) at the
PHO5
promoter (A. Auger, L. Galarneau, M. Altaf, A. Nourani, Y. Doyon, R. T. Utley, D. Cronier, S. Allard, and J. Côté, Mol Cell Biol 28:2257–2270, 2008,
http://dx.doi.org/10.1128/MCB.01755-07
).
In vitro
studies with a reconstituted system also indicated an intriguing cross talk between NuA4 and the H2A.Z-loading complex, SWR-C (M. Altaf, A. Auger, J. Monnet-Saksouk, J. Brodeur, S. Piquet, M. Cramet, N. Bouchard, N. Lacoste, R. T. Utley, L. Gaudreau, J. Côté, J Biol Chem 285:15966–15977, 2010,
http://dx.doi.org/10.1074/jbc.M110.117069
). In this work, we investigated the role of the NuA4 scaffold subunit Eaf1 in global gene expression and genome-wide incorporation of Htz1. We found that loss of Eaf1 affects Htz1 levels mostly at the promoters that are normally highly enriched in the histone variant. Analysis of
eaf1
mutant cells by expression array unveiled a relationship between NuA4 and the gene network implicated in the purine biosynthesis pathway, as
EAF1
deletion cripples induction of several
ADE
genes. NuA4 directly interacts with Bas1 activation domain, a key transcription factor of adenine genes. Chromatin immunoprecipitation (ChIP) experiments demonstrate that nucleosomes on the inactive
ADE17
promoter are acetylated already by NuA4 and enriched in Htz1. Upon derepression, these poised nucleosomes respond rapidly to activate
ADE
gene expression in a mechanism likely reminiscent of the
PHO5
promoter, leading to nucleosome disassembly. These detailed molecular events depict a specific case of cross talk between NuA4-dependent acetylation and incorporation of histone variant Htz1, presetting the chromatin structure over
ADE
promoters for subsequent chromatin remodeling and activated transcription.
Aspergillus nidulans Ambient pH Signaling Does Not Require Endocytosis
Authors: Lucena-Agell Daniel , Galindo Antonio , Arst Herbert N. , Peñalva Miguel A. 
Published: April 2015

ABSTRACT

Aspergillus nidulans
(Pal) ambient pH signaling takes place in cortical structures containing components of the ESCRT pathway, which are hijacked by the alkaline pH-activated, ubiquitin-modified version of the arrestin-like protein PalF and taken to the plasma membrane. There, ESCRTs scaffold the assembly of dedicated Pal proteins acting downstream. The molecular details of this pathway, which results in the two-step proteolytic processing of the transcription factor PacC, have received considerable attention due to the key role that it plays in fungal pathogenicity. While current evidence strongly indicates that the pH signaling role of ESCRT complexes is limited to plasma membrane-associated structures where PacC proteolysis would take place, the localization of the PalB protease, which almost certainly catalyzes the first and only pH-regulated proteolytic step, had not been investigated. In view of ESCRT participation, this formally leaves open the possibility that PalB activation requires endocytic internalization. As endocytosis is essential for hyphal growth, nonlethal endocytic mutations are predicted to cause an incomplete block. We used a SynA internalization assay to measure the extent to which any given mutation prevents endocytosis. We show that none of the tested mutations impairing endocytosis to different degrees, including
slaB1
, conditionally causing a complete block, have any effect on the activation of the pathway. We further show that PalB, like PalA and PalC, localizes to cortical structures in an alkaline pH-dependent manner. Therefore, signaling through the Pal pathway does not involve endocytosis.