bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence of
In Vivo
Prophage Induction during Clostridium difficile Infection
Authors: Meessen-Pinard Mathieu , Sekulovic Ognjen , Fortier Louis-Charles 
Published: August 2012

ABSTRACT

Prophages contribute to the evolution and virulence of most bacterial pathogens, but their role in
Clostridium difficile
is unclear. Here we describe the isolation of four
Myoviridae
phages, ϕMMP01, ϕMMP02, ϕMMP03, and ϕMMP04, that were recovered as free viral particles in the filter-sterilized stool supernatants of patients suffering from
C. difficile
infection (CDI). Furthermore, identical prophages were found in the chromosomes of
C. difficile
isolated from the corresponding fecal samples. We therefore provide, for the first time, evidence of
in vivo
prophage induction during CDI. We completely sequenced the genomes of ϕMMP02 and ϕMMP04, and bioinformatics analyses did not reveal the presence of virulence factors but underlined the unique character of ϕMMP04. We also studied the mobility of ϕMMP02 and ϕMMP04 prophages
in vitro
. Both prophages were spontaneously induced, with 4 to 5 log PFU/ml detected in the culture supernatants of the corresponding lysogens. When lysogens were grown in the presence of subinhibitory concentrations of ciprofloxacin, moxifloxacin, levofloxacin, or mitomycin C, the phage titers further increased, reaching 8 to 9 log PFU/ml in the case of ϕMMP04. In summary, our study highlights the extensive genetic diversity and mobility of
C. difficile
prophages. Moreover, antibiotics known to represent risk factors for CDI, such as quinolones, can stimulate prophage mobility
in vitro
and probably
in vivo
as well, which underscores their potential impact on phage-mediated horizontal gene transfer events and the evolution of
C. difficile
.
Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution
Authors: Judelson Howard S. 
Published: August 2012

ABSTRACT
The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens.
The Three Clades of the Telomere-Associated
TLO
Gene Family of Candida albicans Have Different Splicing, Localization, and Expression Features
Authors: Anderson Matthew Z. , Baller Joshua A. , Dulmage Keely , Wigen Lauren , Berman Judith 
Published: August 2012

ABSTRACT

Candida albicans
grows within a wide range of host niches, and this adaptability enhances its success as a commensal and as a pathogen. The telomere-associated
TLO
gene family underwent a recent expansion from one or two copies in other CUG clade members to 14 expressed copies in
C. albicans
. This correlates with increased virulence and clinical prevalence relative to those of other
Candida
clade species. The 14 expressed
TLO
gene family members have a conserved Med2 domain at the N terminus, suggesting a role in general transcription. The C-terminal half is more divergent, distinguishing three clades: clade α and clade β have no introns and encode proteins that localize primarily to the nucleus; clade γ sometimes undergoes splicing, and the gene products localize within the mitochondria as well as the nuclei. Additionally,
TLO
α genes are generally expressed at much higher levels than are
TLO
γ genes. We propose that expansion of the
TLO
gene family and the predicted role of Tlo proteins in transcription regulation provide
C. albicans
with the ability to adapt rapidly to the broad range of different environmental niches within the human host.
Functional Characterization of the RNA Chaperone Hfq in the Opportunistic Human Pathogen Stenotrophomonas maltophilia
Authors: Roscetto Emanuela , Angrisano Tiziana , Costa Valerio , Casalino Mariassunta , Förstner Konrad U. , Sharma Cynthia M. , Di Nocera Pier Paolo , De Gregorio Eliana 
Published: August 2012

ABSTRACT

Hfq is an RNA-binding protein known to regulate a variety of cellular processes by interacting with small RNAs (sRNAs) and mRNAs in prokaryotes.
Stenotrophomonas maltophilia
is an important opportunistic pathogen affecting primarily hospitalized and immunocompromised hosts. We constructed an
hfq
deletion mutant (Δ
hfq
) of
S. maltophilia
and compared the behaviors of wild-type and Δ
hfq S. maltophilia
cells in a variety of assays. This revealed that
S. maltophilia
Hfq plays a role in biofilm formation and cell motility, as well as susceptibility to antimicrobial agents. Moreover, Hfq is crucial for adhesion to bronchial epithelial cells and is required for the replication of
S. maltophilia
in macrophages. Differential RNA sequencing analysis (dRNA-seq) of RNA isolated from
S. maltophilia
wild-type and Δ
hfq
strains showed that Hfq regulates the expression of genes encoding flagellar and fimbrial components, transmembrane proteins, and enzymes involved in different metabolic pathways. Moreover, we analyzed the expression of several sRNAs identified by dRNA-seq in wild-type and Δ
hfq
S. maltophilia
cells grown in different conditions on Northern blots. The accumulation of two sRNAs was strongly reduced in the absence of Hfq. Furthermore, based on our dRNA-seq analysis we provide a genome-wide map of transcriptional start sites in
S. maltophilia
.
Localization of Poly(3-Hydroxybutyrate) (PHB) Granule-Associated Proteins during PHB Granule Formation and Identification of Two New Phasins, PhaP6 and PhaP7, in Ralstonia eutropha H16
Authors: Pfeiffer Daniel , Jendrossek Dieter 
Published: August 2012

ABSTRACT

Poly(3-hydroxybutyrate) (PHB) granules are covered by a surface layer consisting of mainly phasins and other PHB granule-associated proteins (PGAPs). Phasins are small amphiphilic proteins that determine the number and size of accumulated PHB granules. Five phasin proteins (PhaP1 to PhaP5) are known for
Ralstonia eutropha
. In this study, we identified three additional potential phasin genes (H16_B1988, H16_B2296, and H16_B2326) by inspection of the
R. eutropha
genome for sequences with “phasin 2 motifs.” To determine whether the corresponding proteins represent true PGAPs, fusions with eYFP (enhanced yellow fluorescent protein) were constructed. Similar fusions of eYFP with PhaP1 to PhaP5 as well as fusions with PHB synthase (PhaC1), an inactive PhaC1 variant (PhaC1-C319A), and PhaC2 were also made. All fusions were investigated in wild-type and PHB-negative backgrounds. Colocalization with PHB granules was found for all PhaC variants and for PhaP1 to PhaP5. Additionally, eYFP fusions with H16_B1988 and H16_B2326 colocalized with PHB. Fusions of H16_B2296 with eYFP, however, did not colocalize with PHB granules but did colocalize with the nucleoid region. Notably, all fusions (except H16_B2296) were soluble in a Δ
phaC1
strain. These data confirm that H16_B1988 and H16_B2326 but not H16_B2296 encode true PGAPs, for which we propose the designation PhaP6 (H16_B1988) and PhaP7 (H16_B2326). When localization of phasins was investigated at different stages of PHB accumulation, fusions of PhaP6 and PhaP7 were soluble in the first 3 h under PHB-permissive conditions, although PHB granules appeared after 10 min. At later time points, the fusions colocalized with PHB. Remarkably, PHB granules of strains expressing eYFP fusions with PhaP5, PhaP6, or PhaP7 localized predominantly near the cell poles or in the area of future septum formation. This phenomenon was not observed for the other PGAPs (PhaP1 to PhaP4, PhaC1, PhaC1-C319A, and PhaC2) and indicated that some phasins can have additional functions. A chromosomal deletion of
phaP6
or
phaP7
had no visible effect on formation of PHB granules.
Whole Surface Image of Mycoplasma mobile, Suggested by Protein Identification and Immunofluorescence Microscopy
Authors: Wu Heng Ning , Miyata Makoto 
Published: August 2012

ABSTRACT

Mycoplasma mobile
, a freshwater fish pathogen featured with robust gliding motility, binds to the surface of the gill, where it then colonizes. Here, to obtain a whole image of its cell surface, we identified the proteins exposed on the surface using the following methods. (i) The cell surface was labeled with sulfosuccinimidyl-6-(biotinamido) hexanoate and recovered by an avidin column. (ii) The cells were subjected to phase partitioning using Triton X-114, and the hydrophobic proteins were recovered. (iii) The membrane fraction was analyzed by two-dimensional gel electrophoresis. These recovered proteins were subjected to peptide mass fingerprinting, and a final list of 36 expressed surface proteins was established. The ratio of identified proteins to whole surface proteins was estimated through two-dimensional gel electrophoresis of the membrane fraction. The localization of three newly found proteins, Mvsps C, E, and F, has been clarified by immunofluorescence microscopy. Integrating all information, a whole image of the cell surface showed that the proteins for gliding that were localized at the base of the protrusion of flask-shaped
M. mobile
account for more than 12% of all surface proteins and that Mvsps, surface variants that were localized at both parts other than the neck, account for 49% of all surface proteins.
Characterization of Novel Phages Isolated in Coagulase-Negative Staphylococci Reveals Evolutionary Relationships with Staphylococcus aureus Phages
Authors: Deghorain Marie , Bobay Louis-Marie , Smeesters Pierre R. , Bousbata Sabrina , Vermeersch Marjorie , Perez-Morga David , Drèze Pierre-Alexandre , Rocha Eduardo P. C. , Touchon Marie , Van Melderen Laurence 
Published: August 2012

ABSTRACT

Despite increasing interest in coagulase-negative staphylococci (CoNS), little information is available about their bacteriophages. We isolated and sequenced three novel temperate
Siphoviridae
phages (StB12, StB27, and StB20) from the CoNS
Staphylococcus hominis
and
S. capitis
species. The genome sizes are around 40 kb, and open reading frames (ORFs) are arranged in functional modules encoding lysogeny, DNA metabolism, morphology, and cell lysis. Bioinformatics analysis allowed us to assign a potential function to half of the predicted proteins. Structural elements were further identified by proteomic analysis of phage particles, and DNA-packaging mechanisms were determined. Interestingly, the three phages show identical integration sites within their host genomes. In addition to this experimental characterization, we propose a novel classification based on the analysis of 85 phage and prophage genomes, including 15 originating from CoNS. Our analysis established 9 distinct clusters and revealed close relationships between
S. aureus
and CoNS phages. Genes involved in DNA metabolism and lysis and potentially in phage-host interaction appear to be widespread, while structural genes tend to be cluster specific. Our findings support the notion of a possible reciprocal exchange of genes between phages originating from
S. aureus
and CoNS, which may be of crucial importance for pathogenesis in staphylococci.
Three Mutations in Escherichia coli That Generate Transformable Functional Flagella
Authors: Wang Wenjing , Jiang Zhengzeng , Westermann Martin , Ping Liyan 
Published: August 2012

ABSTRACT

Hydrodynamics predicts that swimming bacteria generate a propulsion force when a helical flagellum rotates because rotating helices necessarily translate at a low Reynolds number. It is generally believed that the flagella of motile bacteria are semirigid helices with a fixed pitch determined by hydrodynamic principles. Here, we report the characterization of three mutations in laboratory strains of
Escherichia coli
that produce different steady-state flagella without losing cell motility.
E. coli
flagella rotate counterclockwise during forward swimming, and the normal form of the flagella is a left-handed helix. A single amino acid exchange A45G and a double mutation of A48S and S110A change the resting flagella to right-handed helices. The stationary flagella of the triple mutant were often straight or slightly curved at neutral pH. Deprotonation facilitates the helix formation of it. The helical and curved flagella can be transformed to the normal form by torsion upon rotation and thus propel the cell. These mutations arose in the long-term laboratory cultivation. However, flagella are under strong selection pressure as extracellular appendages, and similar transformable flagella would be common in natural environments.
Two Systems for Conditional Gene Expression in Myxococcus xanthus Inducible by Isopropyl-β-
d
-Thiogalactopyranoside or Vanillate
Authors: Iniesta Antonio A. , García-Heras Francisco , Abellón-Ruiz Javier , Gallego-García Aránzazu , Elías-Arnanz Montserrat 
Published: August 2012

ABSTRACT

Conditional expression of a gene is a powerful tool to study its function and is typically achieved by placing the gene under the control of an inducible promoter. There is, however, a dearth of such inducible systems in
Myxococcus xanthus
, a well-studied prokaryotic model for multicellular development, cell differentiation, motility, and light response and a promising source of secondary metabolites. The few available systems have limitations, and exogenously based ones are unavailable. Here, we describe two new, versatile inducible systems for conditional expression of genes in
M. xanthus
. One employs isopropyl-β-
d
-thiogalactopyranoside (IPTG) as an inducer and is inspired by those successfully applied in some other bacteria. The other requires vanillate as an inducer and is based on the system developed originally for
Caulobacter crescentus
and recently adapted for mammalian cells. Both systems are robust, with essentially no expression in the absence of an inducer. Depending on the inducer and the amounts added, expression levels can be modulated such that either system can conditionally express genes, including ones that are essential and are required at high levels such as
ftsZ
. The two systems operate during vegetative growth as well as during
M. xanthus
development. Moreover, they can be used to simultaneously induce expression of distinct genes within the same cell. The conditional expression systems we describe substantially expand the genetic tool kit available for studying
M. xanthus
gene function and cellular biology.
Glucose Transport in Escherichia coli Mutant Strains with Defects in Sugar Transport Systems
Authors: Steinsiek Sonja , Bettenbrock Katja 
Published: August 2012

ABSTRACT

In
Escherichia coli
, several systems are known to transport glucose into the cytoplasm. The main glucose uptake system under batch conditions is the glucose phosphoenolpyruvate:carbohydrate phosphotransferase system (glucose PTS), but the mannose PTS and the galactose and maltose transporters also can translocate glucose. Mutant strains which lack the enzyme IIBC (EIIBC) protein of the glucose PTS have been investigated previously because their lower rate of acetate formation offers advantages in industrial applications. Nevertheless, a systematic study to analyze the impact of the different glucose uptake systems has not been undertaken. Specifically, how the bacteria cope with the deletion of the major glucose uptake system and which alternative transporters react to compensate for this deficit have not been studied in detail. Therefore, a series of mutant strains were analyzed in aerobic and anaerobic batch cultures, as well as glucose-limited continuous cultivations. Deletion of EIIBC disturbs glucose transport severely in batch cultures; cyclic AMP (cAMP)-cAMP receptor protein (CRP) levels rise, and induction of the
mgl
operon occurs. Nevertheless, Mgl activity is not essential for growth of these mutants, since deletion of this transporter did not affect the growth rate; the activities of the remaining transporters seem to be sufficient. Under conditions of glucose limitation,
mgl
is upregulated 23-fold compared to levels for growth under glucose excess. Despite the strong induction of
mgl
upon glucose limitation, deletion of this transport system did not lead to further changes. Although the galactose transporters are often regarded as important for glucose uptake at micromolar concentrations, the glucose as well as mannose PTS might be sufficient for growth at this relatively low dilution rate.
Relevance of anxiety in clinical practice of Guillain-Barré syndrome: a cohort study
Authors: Sharshar Tarek , Polito Andrea , Porcher Raphaël , Merhbene Takoua , Blanc Morgane , Antona Marion , Durand Marie-Christine , Friedman Diane , Orlikowski David , Annane Djillali , Marcadet Marie-Hélène 
Published: August 2012

ObjectivesIllness is often associated with anxiety, but few data exist about the prognostic significance of this phenomenon. To address this issue, we assessed whether patient anxiety is associated with subsequent need for intubation in Guillain-Barré syndrome (GBS).DesignIncident case-cohort study.SettingAcute secondary care in a teaching hospital (France) from 2006 to 2010.Participants110 adult GBS patients. Either language barrier or cognitive decline that precluded understanding was considered as exclusion criteria.Primary outcomeAcute respiratory failure.InterventionsAt admission, anxiety and clinical factors (including known predictors of respiratory failure: delay between GBS onset and admission, inability to lift head, vital capacity (VC)) were assessed and related to subsequent need for mechanical ventilation (MV). Anxiety was assessed using a Visual Analogical Scale (VAS), the State Anxiety Inventory form Y1 (STAI-Y1) score and a novel-specific questionnaire, evaluating fears potentially triggered by GBS. Patients were asked to choose which they found most stressful from weakness, pain, breathlessness and uncertainty.Results23 (22%) were subsequently ventilated. Mean STAI-Y1 was 47.2 (range 22–77) and anxiety VAS 5.2 (range 0–10). STAI was above 60/80 in 22 (21%) patients and anxiety VAS above 7/10 in 28 (27%) patients. Fear of remaining paralysed, uncertainty as to how the disease would progress and fear of intubation were the most stressful. Factors significantly associated with anxiety were weakness and bulbar dysfunction. STAI-Y1 was higher and uncertainty more frequent in subsequently ventilated patients, who had shorter onset-admission delay and greater weakness but not a lower VC. Uncertainty was independently associated with subsequent MV.ConclusionsEarly management of patients with GBS should evaluate anxiety and assess its causes both to adjust psychological support and to anticipate subsequent deterioration.
Adverse drug reaction-related admissions in paediatrics, a prospective single-centre study
Authors: Posthumus Anke A G , Alingh Carien C W , Zwaan Christian C M , van Grootheest Kees K , Hanff Lidwien L M , Witjes Bregje B C M , ‘t Jong Geert W , de Hoog Matthijs 
Published: August 2012

ObjectiveTo investigate the incidence and characteristics of hospital admissions related to adverse drug events in the paediatric setting.DesignProspective single-centre study.SettingA secondary and tertiary paediatric care centre.ParticipantsA total of 683 acutely admitted patients, aged 0–18 year. All acutely admitted patients, using medication before admission, were prospectively screened for possible Adverse Drug Reactions (ADR)-related admission with a trigger list. Included cases were analysed with the Naranjo score for the assessment of causality.Main outcome measuresThis research explored the incidence of ADR-related admissions and investigated the relation between ADR and the licensing status of the medicines, as well as the severity and potential to prevent the ADRs.ResultsA total of 683 patients were admitted acutely during the study period, 47 of them were exposed to cancer chemotherapy. Fifteen patients not exposed to chemotherapy (2.4%) were admitted due to an ADR. Five of these 15 ADRs (33%) were caused by unlicensed or off-label used drugs. Thirty-two patients exposed to chemotherapy (68.1%) were admitted due to an ADR; 27 of these (84%) were caused by unlicensed or off-label used drugs.ConclusionsIn conclusion, this study shows that ADR-related hospital admissions occur more frequently in the paediatric population compared with adults, and more frequently in patients exposed to cancer chemotherapy. No relation was found between the unlicensed and off-label used drugs and the incidence of ADRs.
Reporting of lifetime fractures: methodological considerations and results from the Thai Cohort Study
Authors: Berecki-Gisolf Janneke , McClure Rod , Seubsman Sam-ang , Sleigh Adrian 
Published: August 2012

ObjectivesTo provide estimates of fracture incidence among young adults in Thailand.DesignCross-sectional analysis of a large national cohort.SettingThailand.ParticipantsA total of 60 569 study participants residing nationwide responded to the 2009 follow-up survey; 55% were women and median age was 34 years (range 19–92).Outcome measuresSelf-reported lifetime fractures, along with age at fracture. Fracture incidence rates per person-year were then compared using lifetime fracture reports, and again selecting only fractures reported for the last year. Incidence rates were compared by age and sex.Results18 010 lifetime fractures were reported; 11 645(65%) by men. Lifetime fracture prevalence was 30% for men and 15% for women. Lifetime incidence per 10 000 person-years was 83; analysing only fractures from the last year yielded a corresponding incidence rate of 187. For ages 21–30, fractures per 10 000 person-years were more common among men than women (283 (95% CI 244 to 326) and 150 (130 to 173), respectively); with increasing age, rates decreased among men and increased among women (for ages 51–60, 97 (58 to 151) and 286 (189 to 417), respectively).ConclusionsLarge-scale surveys provide a feasible method for establishing relative fracture incidence among informative subgroups in a population. Limiting analyses to fractures reported to have occurred recently minimises bias due to poor recall. The pattern of self-reported fracture incidence among Thais aged 20–60 was similar to that reported for Western countries: high falling rates in young men and high rising rates in older women.