bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the rates of Clostridium difficile and bacteremia after delaying fluoroquinolone prophylaxis from day 0 to day +3 post autologous stem cell transplantation
Authors: Koseck Karin , Steinberg Amir , Caliendo Gina , Meyer Joanne , Kim Sara S. 
Published: April 2017

AbstractProphylactic fluoroquinolones are routinely administered after stem cell transplantation (SCT) to prevent bacterial infection; however, fluoroquinolones may increase the risk of Clostridium difficile infection, particularly in immunocompromised patients. This study is designed to evaluate the effect of a delay by 3 days in fluoroquinolone prophylaxis after autologous SCT (ASCT) on the rates of C. difficile infection and bacteremia. A single‐center retrospective cohort study was performed in 118 patients who received levofloxacin prophylaxis following ASCT at our institution between November 2014 and October 2015. In efforts to reduce the rate of C. difficile, initiation of levofloxacin prophylaxis was delayed from day 0 to day +3 of SCT beginning April 30, 2015. The incidence of C. difficile infection and of bacteremia in patients who initiated levofloxacin on day 0 was compared with those who started prophylaxis on day +3. We found no difference in the rates of C. difficile (7.9% vs 5.5%, P=.593) and bacteremia (7.9% vs 3.6%, P=.323) in patients who initiated levofloxacin on day 0 compared with those who initiated prophylaxis on day +3. Delaying the initiation of levofloxacin prophylaxis by 3 days post ASCT showed no difference in the incidence of C. difficile or bacteremia. Future studies are warranted to show feasibility of delaying the initiation of antibiotic prophylaxis until neutropenia post ASCT, to further minimize the duration of antibiotic exposure.
Does the intercept of the heat–stress relation provide an accurate estimate of cardiac activation heat?
Authors: Pham Toan , Tran Kenneth , Mellor Kimberley M , Hickey Anthony , Power Amelia , Ward Marie‐Louise , Taberner Andrew , Han June‐Chiew , Loiselle Denis 
Published: April 2017

Key points
The heat of activation of cardiac muscle reflects the metabolic cost of restoring ionic homeostasis following a contraction. The accuracy of its measurement depends critically on the abolition of crossbridge cycling.
We abolished crossbridge activity in isolated rat ventricular trabeculae by use of blebbistatin, an agent that selectively inhibits myosin II ATPase.
We found cardiac activation heat to be muscle length independent and to account for 15–20% of total heat production at body temperature.
We conclude that it can be accurately estimated at minimal muscle length.
AbstractActivation heat arises from two sources during the contraction of striated muscle. It reflects the metabolic expenditure associated with Ca2+ pumping by the sarcoplasmic reticular Ca2+‐ATPase and Ca2+ translocation by the Na+/Ca2+ exchanger coupled to the Na+,K+‐ATPase. In cardiac preparations, investigators are constrained in estimating its magnitude by reducing muscle length to the point where macroscopic twitch force vanishes. But this experimental protocol has been criticised since, at zero force, the observed heat may be contaminated by residual crossbridge cycling activity. To eliminate this concern, the putative thermal contribution from crossbridge cycling activity must be abolished, at least at minimal muscle length. We achieved this using blebbistatin, a selective inhibitor of myosin II ATPase. Using a microcalorimeter, we measured the force production and heat output, as functions of muscle length, of isolated rat trabeculae from both ventricles contracting isometrically at 5 Hz and at 37°C. In the presence of blebbistatin (15 μmol l−1), active force was zero but heat output remained constant, at all muscle lengths. Activation heat measured in the presence of blebbistatin was not different from that estimated from the intercept of the heat–stress relation in its absence. We thus reached two conclusions. First, activation heat is independent of muscle length. Second, residual crossbridge heat is negligible at zero active force; hence, the intercept of the cardiac heat–force relation provides an estimate of activation heat uncontaminated by crossbridge cycling. Both results resolve long‐standing disputes in the literature.
A Novel Quorum-Quenching
N
-Acylhomoserine Lactone Acylase from Acidovorax sp. Strain MR-S7 Mediates Antibiotic Resistance
Authors: Kusada Hiroyuki , Tamaki Hideyuki , Kamagata Yoichi , Hanada Satoshi , Kimura Nobutada 
Published: April 2017

ABSTRACT

N
-Acylhomoserine lactone acylase (AHL acylase) is a well-known enzyme responsible for disrupting cell-cell communication (quorum sensing) in bacteria. Here, we isolated and characterized a novel and unique AHL acylase (designated MacQ) from a multidrug-resistant bacterium,
Acidovorax
sp. strain MR-S7. The purified MacQ protein heterologously expressed in
Escherichia coli
degraded a wide variety of AHLs, ranging from C
6
to C
14
side chains with or without 3-oxo substitutions. We also observed that AHL-mediated virulence factor production in a plant pathogen,
Pectobacterium carotovorum
, was dramatically attenuated by coculture with MacQ-overexpressing
Escherichia coli
, whereas
E. coli
with an empty vector was unable to quench the pathogenicity, which strongly indicates that MacQ can act
in vivo
as a quorum-quenching enzyme and interfere with the quorum-sensing system in the pathogen. In addition, this enzyme was found to be capable of degrading a wide spectrum of β-lactams (penicillin G, ampicillin, amoxicillin, carbenicillin, cephalexin, and cefadroxil) by deacylation, clearly indicating that MacQ is a bifunctional enzyme that confers both quorum quenching and antibiotic resistance on strain MR-S7. MacQ has relatively low amino acid sequence identity to any of the known acylases (<39%) and has among the broadest substrate range. Our findings provide the possibility that AHL acylase genes can be an alternative source of antibiotic resistance genes posing a threat to human health if they migrate and transfer to pathogenic bacteria.

IMPORTANCE
N
-Acylhomoserine lactones (AHLs) are well-known signal molecules for bacterial cell-cell communication (quorum sensing), and AHL acylase, which is able to degrade AHLs, has been recognized as a major target for quorum-sensing interference (quorum quenching) in pathogens. In this work, we succeeded in isolating a novel AHL acylase (MacQ) from a multidrug-resistant bacterium and demonstrated that the MacQ enzyme could confer multidrug resistance as well as quorum quenching on the host organism. Indeed, the purified MacQ protein was found to be bifunctional and capable of degrading not only various AHL derivatives but also multiple β-lactam antibiotics by deacylation activities. Although quorum quenching and antibiotic resistance have been recognized to be distinct biological functions, our findings clearly link the two functions by discovering the novel bifunctional enzyme and further providing the possibility that a hitherto-overlooked antibiotic resistance mechanism mediated by the quorum-quenching enzyme may exist in natural environments and perhaps in clinical settings.
Novel Method for Reliable Identification of Siccibacter and Franconibacter Strains: from “Pseudo-Cronobacter” to New Enterobacteriaceae Genera
Authors: Svobodová Barbora , Vlach Jiří , Junková Petra , Karamonová Ludmila , Blažková Martina , Fukal Ladislav 
Published: April 2017

ABSTRACT

In the last decade, strains of the genera
Franconibacter
and
Siccibacter
have been misclassified as first
Enterobacter
and later
Cronobacter
. Because
Cronobacter
is a serious foodborne pathogen that affects premature neonates and elderly individuals, such misidentification may not only falsify epidemiological statistics but also lead to tests of powdered infant formula or other foods giving false results. Currently, the main ways of identifying
Franconibacter
and
Siccibacter
strains are by biochemical testing or by sequencing of the
fusA
gene as part of
Cronobacter
multilocus sequence typing (MLST), but in relation to these strains the former is generally highly difficult and unreliable while the latter remains expensive. To address this, we developed a fast, simple, and most importantly, reliable method for
Franconibacter
and
Siccibacter
identification based on intact-cell matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). Our method integrates the following steps: data preprocessing using mMass software; principal-component analysis (PCA) for the selection of mass spectrum fingerprints of
Franconibacter
and
Siccibacter
strains; optimization of the Biotyper database settings for the creation of main spectrum projections (MSPs). This methodology enabled us to create an in-house MALDI MS database that extends the current MALDI Biotyper database by including
Franconibacter
and
Siccibacter
strains. Finally, we verified our approach using seven previously unclassified strains, all of which were correctly identified, thereby validating our method.

IMPORTANCE
We show that the majority of methods currently used for the identification of
Franconibacter
and
Siccibacter
bacteria are not able to properly distinguish these strains from those of
Cronobacter
. While sequencing of the
fusA
gene as part of
Cronobacter
MLST remains the most reliable such method, it is highly expensive and time-consuming. Here, we demonstrate a cost-effective and reliable alternative that correctly distinguishes between
Franconibacter
,
Siccibacter
, and
Cronobacter
bacteria and identifies
Franconibacter
and
Siccibacter
at the species level. Using intact-cell MALDI-TOF MS, we extend the current MALDI Biotyper database with 11
Franconibacter
and
Siccibacter
MSPs. In addition, the use of our approach is likely to lead to a more reliable identification scheme for
Franconibacter
and
Siccibacter
strains and, consequently, a more trustworthy epidemiological picture of their involvement in disease.
Rational Engineering of a Cold-Adapted α-Amylase from the Antarctic Ciliate Euplotes focardii for Simultaneous Improvement of Thermostability and Catalytic Activity
Authors: Yang Guang , Yao Hua , Mozzicafreddo Matteo , Ballarini Patrizia , Pucciarelli Sandra , Miceli Cristina 
Published: April 2017

ABSTRACT

The α-amylases are endo-acting enzymes that hydrolyze starch by randomly cleaving the 1,4-α-
d
-glucosidic linkages between the adjacent glucose units in a linear amylose chain. They have significant advantages in a wide range of applications, particularly in the food industry. The eukaryotic α-amylase isolated from the Antarctic ciliated protozoon
Euplotes focardii
(
Ef
Amy) is an alkaline enzyme, different from most of the α-amylases characterized so far. Furthermore,
Ef
Amy has the characteristics of a psychrophilic α-amylase, such as the highest hydrolytic activity at a low temperature and high thermolability, which is the major drawback of cold-active enzymes in industrial applications. In this work, we applied site-directed mutagenesis combined with rational design to generate a cold-active
Ef
Amy with improved thermostability and catalytic efficiency at low temperatures. We engineered two
Ef
Amy mutants. In one mutant, we introduced Pro residues on the A and B domains in surface loops. In the second mutant, we changed Val residues to Thr close to the catalytic site. The aim of these substitutions was to rigidify the molecular structure of the enzyme. Furthermore, we also analyzed mutants containing these combined substitutions. Biochemical enzymatic assays of engineered versions of
Ef
Amy revealed that the combination of mutations at the surface loops increased the thermostability and catalytic efficiency of the enzyme. The possible mechanisms responsible for the changes in the biochemical properties are discussed by analyzing the three-dimensional structural model.

IMPORTANCE
Cold-adapted enzymes have high specific activity at low and moderate temperatures, a property that can be extremely useful in various applications as it implies a reduction in energy consumption during the catalyzed reaction. However, the concurrent high thermolability of cold-adapted enzymes often limits their applications in industrial processes. The α-amylase from the psychrophilic Antarctic ciliate
Euplotes focardii
(named
Ef
Amy) is a cold-adapted enzyme with optimal catalytic activity in an alkaline environment. These unique features distinguish it from most α-amylases characterized so far. In this work, we engineered a novel
Ef
Amy with improved thermostability, substrate binding affinity, and catalytic efficiency to various extents, without impacting its pH preference. These characteristics can be considered important properties for use in the food, detergent, and textile industries and in other industrial applications. The enzyme engineering strategy developed in this study may also provide useful knowledge for future optimization of molecules to be used in particular industrial applications.
Improved α-Amylase Production by Dephosphorylation Mutation of CreD, an Arrestin-Like Protein Required for Glucose-Induced Endocytosis of Maltose Permease and Carbon Catabolite Derepression in Aspergillusoryzae
Authors: Tanaka Mizuki , Hiramoto Tetsuya , Tada Hinako , Shintani Takahiro , Gomi Katsuya 
Published: April 2017

ABSTRACT

Aspergillus
oryzae
produces copious amount of amylolytic enzymes, and MalP, a major maltose permease, is required for the expression of amylase-encoding genes. The expression of these genes is strongly repressed by carbon catabolite repression (CCR) in the presence of glucose. MalP is transported from the plasma membrane to the vacuole by endocytosis, which requires the homolog of E6-AP carboxyl terminus ubiquitin ligase HulA, an ortholog of yeast Rsp5. In yeast, arrestin-like proteins mediate endocytosis as adaptors of Rsp5 and transporters. In the present study, we examined the involvement of CreD, an arrestin-like protein, in glucose-induced MalP endocytosis and CCR of amylase-encoding genes. Deletion of
creD
inhibited the glucose-induced endocytosis of MalP, and CreD showed physical interaction with HulA. Phosphorylation of CreD was detected by Western blotting, and two serine residues were determined as the putative phosphorylation sites. However, the phosphorylation state of the serine residues did not regulate MalP endocytosis and its interaction with HulA. Although α-amylase production was significantly repressed by
creD
deletion, both phosphorylation and dephosphorylation mimics of CreD had a negligible effect on α-amylase activity. Interestingly, dephosphorylation of CreD was required for CCR relief of amylase genes that was triggered by disruption of the deubiquitinating enzyme-encoding gene
creB
. The α-amylase activity of the
creB
mutant was 1.6-fold higher than that of the wild type, and the dephosphorylation mimic of CreD further improved the α-amylase activity by 2.6-fold. These results indicate that a combination of the dephosphorylation mutation of CreD and
creB
disruption increased the production of amylolytic enzymes in
A. oryzae
.

IMPORTANCE
In eukaryotes, glucose induces carbon catabolite repression (CCR) and proteolytic degradation of plasma membrane transporters via endocytosis. Glucose-induced endocytosis of transporters is mediated by their ubiquitination, and arrestin-like proteins act as adaptors of transporters and ubiquitin ligases. In this study, we showed that CreD, an arrestin-like protein, is involved in glucose-induced endocytosis of maltose permease and carbon catabolite derepression of amylase gene expression in
Aspergillus
oryzae
. Dephosphorylation of CreD was required for CCR relief triggered by the disruption of
creB
, which encodes a deubiquitinating enzyme; a combination of the phosphorylation-defective mutation of CreD and
creB
disruption dramatically improved α-amylase production. This study shows the dual function of an arrestin-like protein and provides a novel approach for improving the production of amylolytic enzymes in
A. oryzae
.
Yersinia pestis Resists Predation by Acanthamoeba castellanii and Exhibits Prolonged Intracellular Survival
Authors: Benavides-Montaño Javier A. , Vadyvaloo Viveka 
Published: April 2017

ABSTRACT

Plague is a flea-borne rodent-associated zoonotic disease caused by
Yersinia pestis
. The disease is characterized by epizootics with high rodent mortalities, punctuated by interepizootic periods when the bacterium persists in an unknown reservoir. This study investigates the interaction between
Y. pestis
and the ubiquitous soil free-living amoeba (FLA)
Acanthamoeba castellanii
to assess if the bacterium can survive within soil amoebae and whether intracellular mechanisms are conserved between infection of mammalian macrophages and soil amoebae. The results demonstrate that during coculture with amoebae, representative
Y. pestis
strains of epidemic biovars Medievalis, Orientalis, and Antiqua are phagocytized and able to survive within amoebae for at least 5 days. Key
Y. pestis
determinants of the intracellular interaction of
Y. pestis
and phagocytic macrophages, PhoP and the type three secretion system (T3SS), were then tested for their roles in the
Y. pestis
-amoeba interaction. Consistent with a requirement for the PhoP transcriptional activator in the intracellular survival of
Y. pestis
in macrophages, a PhoP mutant is unable to survive when cocultured with amoebae. Additionally, induction of the T3SS blocks phagocytic uptake of
Y. pestis
by amoebae, similar to that which occurs during macrophage infection. Electron microscopy revealed that in
A. castellanii
,
Y. pestis
resides intact within spacious vacuoles which were characterized using lysosomal trackers as being separated from the lysosomal compartment. This evidence for prolonged survival and subversion of intracellular digestion of
Y. pestis
within FLA suggests that protozoa may serve as a protective soil reservoir for
Y. pestis
.

IMPORTANCE
Yersinia pestis
is a reemerging flea-borne zoonotic disease. Sylvatic plague cycles are characterized by an epizootic period during which the disease spreads rapidly, causing high rodent mortality, and an interepizootic period when the bacterium quiescently persists in an unknown reservoir. An understanding of the ecology of
Y. pestis
in the context of its persistence in the environment and its reactivation to initiate a new epizootic cycle is key to implementing novel surveillance strategies to more effectively predict and prevent new disease outbreaks. Here, we demonstrate prolonged survival and subversion of intracellular digestion of
Y. pestis
within a soil free-living amoeba. This suggests the potential role for protozoa as a protective soil reservoir for
Y. pestis
, which may help explain the recrudescence of plague epizootics.
Lack of Methylated Hopanoids Renders the Cyanobacterium Nostoc punctiforme Sensitive to Osmotic and pH Stress
Authors: Garby Tamsyn J. , Matys Emily D. , Ongley Sarah E. , Salih Anya , Larkum Anthony W. D. , Walter Malcolm R. , Summons Roger E. , Neilan Brett A. 
Published: April 2017

ABSTRACT

To investigate the function of 2-methylhopanoids in modern cyanobacteria, the
hpnP
gene coding for the radical
S
-adenosyl methionine (SAM) methylase protein that acts on the C-2 position of hopanoids was deleted from the filamentous cyanobacterium
Nostoc punctiforme
ATCC 29133S. The resulting Δ
hpnP
mutant lacked all 2-methylhopanoids but was found to produce much higher levels of two bacteriohopanepentol isomers than the wild type. Growth rates of the Δ
hpnP
mutant cultures were not significantly different from those of the wild type under standard growth conditions. Akinete formation was also not impeded by the absence of 2-methylhopanoids. The relative abundances of the different hopanoid structures in akinete-dominated cultures of the wild-type and Δ
hpnP
mutant strains were similar to those of vegetative cell-dominated cultures. However, the Δ
hpnP
mutant was found to have decreased growth rates under both pH and osmotic stress, confirming a role for 2-methylhopanoids in stress tolerance. Evidence of elevated photosystem II yield and NAD(P)H-dependent oxidoreductase activity in the Δ
hpnP
mutant under stress conditions, compared to the wild type, suggested that the absence of 2-methylhopanoids increases cellular metabolic rates under stress conditions.

IMPORTANCE
As the first group of organisms to develop oxygenic photosynthesis,
Cyanobacteria
are central to the evolutionary history of life on Earth and the subsequent oxygenation of the atmosphere. To investigate the origin of cyanobacteria and the emergence of oxygenic photosynthesis, geobiologists use biomarkers, the remnants of lipids produced by different organisms that are found in geologic sediments. 2-Methylhopanes have been considered indicative of cyanobacteria in some environmental settings, with the parent lipids 2-methylhopanoids being present in many contemporary cyanobacteria. We have created a
Nostoc punctiforme
Δ
hpnP
mutant strain that does not produce 2-methylhopanoids to assess the influence of 2-methylhopanoids on stress tolerance. Increased metabolic activity in the mutant under stress indicates compensatory alterations in metabolism in the absence of 2-methylhopanoids.
Effect of cardiorespiratory and strength exercises on disease activity in patients with inflammatory rheumatic diseases: a systematic review and meta-analysis
Authors: Sveaas Silje Halvorsen , Smedslund Geir , Hagen Kåre Birger , Dagfinrud Hanne 
Published: April 2017

ObjectiveTo investigate the effects of cardiorespiratory and strength exercises on disease activity for patients with inflammatory rheumatic diseases (IRDs).DesignA systematic review with meta-analysis registered at PROSPERO (CRD42015020004).ParticipantsPatients with IRDs.Data sourcesThe databases MEDLINE, AMED, Embase and CINAHL were searched from inception up to April 2016.Eligibility criteria for selecting studiesTrials were included if they were randomised controlled trials of adults with IRDs, comparing the effect of cardiorespiratory and strength exercises with usual care on disease activity and followed the American College of Sports Medicine's exercise recommendations. The primary outcome was disease activity in terms of inflammation, joint damage and symptoms.Data synthesisData were pooled in a random-effect model for all outcomes, and standardised mean differences (SMDs) were calculated. The quality of evidence was evaluated according to the Grading of Recommendations Assessment, Development and Evaluation approach.ResultsTwenty-six trials with a total of 1286 participants were included. There was high to moderate quality evidence, for a small beneficial effect on disease activity scores (0.19 (95% CI 0.05 to 0.33), p<0.01) and joint damage (SMD 0.27 (95% CI 0.07 to 0.46), p<0.01). Furthermore, moderate quality evidence for a small beneficial effect on erythrocyte sedimentation rate (SMD 0.20 (95% CI 0.0 to 0.39), p=0.04) and for no effect on C reactive protein (SMD −0.14 (95% CI −0.37 to 0.08), p=0.21). Beneficial effects were also seen for symptoms.ConclusionsThe results of this review suggest beneficial effects of exercises on inflammation, joint damage and symptoms in patients with IRDs.