bluuebunny/crossref_metadata_2025 huggingface dataset:
Postglacial recolonization in a cold climate specialist in western Europe: patterns of genetic diversity in the adder (Vipera berus) support the central–marginal hypothesis
Authors: Ursenbacher Sylvain , Guillon Michaël , Cubizolle Hervé , Dupoué Andréaz , Blouin‐Demers Gabriel , Lourdais Olivier
Published: June 2015

Understanding the impact of postglacial recolonization on genetic diversity is essential in explaining current patterns of genetic variation. The central–marginal hypothesis (CMH) predicts a reduction in genetic diversity from the core of the distribution to peripheral populations, as well as reduced connectivity between peripheral populations. While the CMH has received considerable empirical support, its broad applicability is still debated and alternative hypotheses predict different spatial patterns of genetic diversity. Using microsatellite markers, we analysed the genetic diversity of the adder (Vipera berus) in western Europe to reconstruct postglacial recolonization. Approximate Bayesian Computation (ABC) analyses suggested a postglacial recolonization from two routes: a western route from the Atlantic Coast up to Belgium and a central route from the Massif Central to the Alps. This cold‐adapted species likely used two isolated glacial refugia in southern France, in permafrost‐free areas during the last glacial maximum. Adder populations further from putative glacial refugia had lower genetic diversity and reduced connectivity; therefore, our results support the predictions of the CMH. Our study also illustrates the utility of highly variable nuclear markers, such as microsatellites, and ABC to test competing recolonization hypotheses.
Pathophysiology of gastroesophageal reflux disease: new understanding in a new era
Authors: Herregods T. V. K. , Bredenoord A. J. , Smout A. J. P. M.
Published: June 2015

Background

The prevalence of gastroesophageal reflux disease (GERD) has increased in the last decades and it is now one of the most common chronic diseases. Throughout time our insight in the pathophysiology of GERD has been characterized by remarkable back and forth swings, often prompted by new investigational techniques. Even today, the pathophysiology of GERD is not fully understood but it is now recognized to be a multifactorial disease. Among the factors that have been shown to be involved in the provocation or increase of reflux, are sliding hiatus hernia, low lower esophageal sphincter pressure, transient lower esophageal sphincter relaxation, the acid pocket, obesity, increased distensibility of the esophagogastric junction, prolonged esophageal clearance, and delayed gastric emptying. Moreover, multiple mechanisms influence the perception of GERD symptoms, such as the acidity of the refluxate, its proximal extent, the presence of gas in the refluxate, duodenogastroesophageal reflux, longitudinal muscle contraction, mucosal integrity, and peripheral and central sensitization. Understanding the pathophysiology of GERD is important for future targets for therapy as proton pump inhibitor‐refractory GERD symptoms remain a common problem.

Purpose

In this review we provide an overview of the mechanisms leading to reflux and the factors influencing perception, in the light of historical developments. It is clear that further research remains necessary despite the recent advances in the understanding of the pathophysiology of GERD.
Toll‐like receptors 2 and 4 modulate the contractile response induced by serotonin in mouse ileum: analysis of the serotonin receptors involved
Authors: Forcén R. , Latorre E. , Pardo J. , Alcalde A. I. , Murillo M. D. , Grasa L.
Published: June 2015

Background

Microbiota through toll‐like receptors (TLR) may regulate gastrointestinal motility by activating neuroendocrine mechanisms. We evaluated the influence of TLR2 and TLR4 in the spontaneous contractions and serotonin (5‐HT)‐induced motor response in mouse ileum, and the 5‐HT receptors involved.

Methods

Muscle contractility studies to evaluate the spontaneous intestinal motility and the response to 5‐HT were performed in the ileum from wild type (WT), TLR2−/−, TLR4−/−, and TLR2/4 double knockout (DKO) mice. 5‐HT receptor expression was determined by real‐time PCR.

Key Results

The amplitude of spontaneous contractions in ileum was higher in TLR2−/−, TLR4−/−, and TLR2/4 DKO mice with respect to WT. 5‐HT evoked concentration‐dependent contractile responses in the ileum from TLR2−/− and TLR4−/− mice similar to WT. However, in ileum from TLR2/4 DKO, 5‐HT did not induce any contractile response. Expression of 5‐HT2A, 5‐HT2B, 5‐HT2C, and 5‐HT3 receptors resulted increased in ileum from TLR4−/− and TLR2/4 DKO. Expression of the 5‐HT4 receptor was diminished in TLR2−/− and TLR2/4 DKO. High levels of 5‐HT7 receptor expression were found in TLR2/4 DKO but not in TLR2−/− or TLR4−/−. In WT and TLR4−/−, 5‐HT2, 5‐HT3, 5‐HT4, and 5‐HT7 receptor antagonists reduced the contractile response evoked by 5‐HT. In TLR2−/− mice, 5‐HT4 antagonist did not reduce the 5‐HT response. In TLR2/4 DKO mice, only 5‐HT4 and 5‐HT7 receptor antagonists reduced the relaxing response induced by 5‐HT.

Conclusions & Inferences

TLR2 and TLR4 signaling may modulate the spontaneous contractions and the serotonin contractile response by acting on 5‐HT2, 5‐HT3, 5‐HT4, and 5‐HT7 receptors.
Treatment of solar urticaria using antihistamine and leukotriene receptor antagonist combinations tailored to disease severity
Authors: Levi Assi , Enk Claes D.
Published: June 2015

Background

Solar urticarial (SU) is characterized by erythema, whealing, and/or pruritus occurring minutes after sun exposure. Treatment is difficult and often unsatisfactory.

Objectives

To determine the action spectra and minimal urticaria dose (MUD) and to tailor a treatment regimen graded according to disease severity in a series of patients with SU.

Patients and Methods

Eleven patients (seven females, four males, age range: 5–60 years) with a clinical history suggestive of SU, verified by photo‐provocation tests to ultraviolet A (UVA), visible light, and/or UVB, were treated with various combinations of antihistamines and leukotriene receptor antagonist.

Results

All patients were sensitive to visible light (median MUD 50 J/cm2). Three patients were sensitive to UVA (median MUD 3.75 J/cm2), and one patient was sensitive to UVB (MUD of 0.03 J/cm2). Two patients experienced a spontaneous remission without treatment. One patient declined treatment. The remaining eight patients were managed by a combination of antihistamines (desloratidine, fexofenadine, cetirizine HCl) and a leukotriene receptor antagonist (montelukast). Seven of the 8 patients experienced a sustained remission of symptoms and signs following treatment.

Conclusions

Photoprovocation for SU with determination of action spectra and MUD enables specifically tailored treatment regimens consisting of combinations of antihistamines and leukotriene receptor antagonist.
Two‐year post‐transplantation cytomegalovirus DNAemia in asymptomatic kidney transplant recipients: incidence, risk factors, and outcome
Authors: Viot B. , Garrigue I. , Taton B. , Bachelet T. , Moreau J.‐F. , Dechanet‐Merville J. , Merville P. , Couzi L.
Published: June 2015

Background

The incidence and the impact of asymptomatic cytomegalovirus (CMV) DNAemia occurring after the first year post transplantation is unknown.

Methods

In this retrospective cross‐sectional study, we analyzed the incidence, risk factors, and impact of 2‐year post‐transplantation asymptomatic CMV DNAemia (2YCD) on graft function. We included 892 consecutive asymptomatic kidney transplant recipients transplanted for at least 2 years and all were monitored using whole blood CMV quantitative nucleic acid amplification testing (CMV‐QNAT).

Results

Twenty‐eight patients displayed 2YCD (3.1%). Using multivariate analysis in 578 patients, we found that female gender (odds ratio [OR] = 2.57, P = 0.02), a past history of CMV drug‐resistance mutation (OR = 8.73, P = 0.005), and corticosteroid use (OR = 2.37, P = 0.03) were independently associated with an increased risk of 2YCD. 2YCD was associated with an increased incidence of subsequent CMV disease over the year following its diagnosis (7% vs. 0.6%, P = 0.02). Patients with 2YCD also exhibited a declining estimated glomerular filtration rate more frequently (77%) than patients with a negative CMV‐QNAT (56%, P = 0.02).

Conclusion

2YCD appears to be a rare entity, which appears to be associated with chronic graft dysfunction.
Peroxide‐based oxygen generating topical wound dressing for enhancing healing of dermal wounds
Authors: Chandra Prafulla K. , Ross Christina L. , Smith Leona C. , Jeong Seon S. , Kim Jaehyun , Yoo James J. , Harrison Benjamin S.
Published: June 2015

Oxygen generating biomaterials represent a new trend in regenerative medicine that aims to generate and supply oxygen at the site of requirement, to support tissue healing and regeneration. To enhance the healing of dermal wounds, we have developed a highly portable, in situ oxygen generating wound dressings that uses sodium percarbonate (SPO) and calcium peroxide (CPO) as chemical oxygen sources. The dressing continuously generated oxygen for more than 3 days, after which it was replaced. In the in vivo testing on porcine full‐thickness porcine wound model, the SPO/CPO dressing showed enhanced wound healing during the 8 week study period. Quantitative measurements of wound healing related parameters, such as wound closure, reepithelialization, epidermal thickness and collagen content of dermis showed that supplying oxygen topically using the SPO/CPO dressing significantly accelerated the wound healing. An increase in neovascularization, as determined using Von Willebrand factor (vWF) and CD31 staining, was also observed in the presence of SPO/CPO dressing. This novel design for a wound dressing that contains oxygen generating biomaterials (SPO/CPO) for supplying topical oxygen, may find utility in treating various types of acute to chronic wounds.
High levels of positive end‐expiratory pressure preserve diaphragmatic contractility during acute respiratory distress syndrome in rats
Authors: Jiao Guang‐Yu , Hao Li‐Ying , Chen Lie , Gao Chun‐E , Feng Rui , Hu Hui‐Yuan , Tan Shu‐Tao , Wang Meng‐Meng , Zhong Bin , Wang Ping‐Ping
Published: June 2015

New Findings

What is the central question of this study?

Higher levels of positive end‐expiratory pressure (PEEP) have recently been used in patients with acute respiratory distress syndrome (ARDS). In normal physiological conditions, the ability of the diaphragm to generate pressure is reduced when the lung volume is elevated beyond its functional residual capacity. It is unknown whether higher levels of PEEP will have a negative impact on diaphragmatic contraction in the presence of the pathophysiology of ARDS.

What is the main finding and its importance?

Mechanical ventilation with higher levels of PEEP reduced lung injury, improved diaphragmatic contractility and increased the expression of both dihydropyridine receptor and ryanodine receptor in the diaphragms of rats with ARDS.

Higher levels of positive end‐expiratory pressure (PEEP) have recently been used in patients with acute respiratory distress syndrome (ARDS). In normal physiological conditions, the ability of the diaphragm to generate pressure is reduced when the lung volume is elevated beyond its functional residual capacity. Thus, it is critical to understand whether higher levels of PEEP will have a negative impact on diaphragmatic contraction in the presence of the pathophysiology of ARDS. This study was designed to determine whether higher levels of PEEP reduce diaphragmatic contractility in a rat model of ARDS generated using i.p. lipopolysaccharide. Forty rats were randomly assigned to the following five groups: a control group with no special treatment; an ARDS group with no mechanical ventilation; and three ARDS groups with mechanical ventilation with PEEP at 0, 5 or 10 cmH2O, respectively. We found that mechanical ventilation with PEEP reduced lung injury, improved diaphragmatic contractility and increased the expression of both dihydropyridine receptor and ryanodine receptor in the diaphragms of rats with ARDS. These changes were most significant at a PEEP of 10 cmH2O among all applied levels of PEEP. In conclusion, using a rat ARDS model, this study confirmed that diaphragmatic contractility was preserved by mechanical ventilation with high levels of PEEP.
Tracks through the genome to physiological events
Authors: Lipscombe Diane , Pan Jen Q. , Schorge Stephanie
Published: June 2015

New Findings

What is the topic of this review?

We discuss tools available to access genome‐wide data sets that harbour cell‐specific, brain region‐specific and tissue‐specific information on exon usage for several species, including humans. In this Review, we demonstrate how to access this information in genome databases and its enormous value to physiology.

What advances does it highlight?

The sheer scale of protein diversity that is possible from complex genes, including those that encode voltage‐gated ion channels, is vast. But this choice is critical for a complete understanding of protein function in the most physiologically relevant context.

Many proteins of great interest to physiologists and neuroscientists are structurally complex and located in specialized subcellular domains, such as neuronal synapses and transverse tubules of muscle. Genes that encode these critical signalling molecules (receptors, ion channels, transporters, enzymes, cell adhesion molecules, cell–cell interaction proteins and cytoskeletal proteins) are similarly complex. Typically, these genes are large; human Dystrophin (DMD) encodes a cytoskeletal protein of muscle and it is the largest naturally occurring gene at a staggering 2.3 Mb. Large genes contain many non‐coding introns and coding exons; human Titin (TTN), which encodes a protein essential for the assembly and functioning of vertebrate striated muscles, has over 350 exons and consequently has an enormous capacity to generate different forms of Titin mRNAs that have unique exon combinations. Functional and pharmacological differences among protein isoforms originating from the same gene may be subtle but nonetheless of critical physiological significance. Standard functional, immunological and pharmacological approaches, so useful for characterizing proteins encoded by different genes, typically fail to discriminate among splice isoforms of individual genes. Tools are now available to access genome‐wide data sets that harbour cell‐specific, brain region‐specific and tissue‐specific information on exon usage for several species, including humans. In this Review, we demonstrate how to access this information in genome databases and its enormous value to physiology.
Metabolic aspects of high‐altitude adaptation in Tibetans
Authors: Ge Ri‐Li , Simonson Tatum S. , Gordeuk Victor , Prchal Josef T. , McClain Donald A.
Published: June 2015

New Findings

What is the topic of this review?

The topic of this review is how Tibetans have adapted genetically to high altitude, particularly with reference to altitude‐induced changes in metabolism.

What advances does it highlight?

It highlights recent work on metabolic phenotyping in Tibetans and demonstrates that selected genetic haplotypes influence their metabolism of fats and glucose.

Recent studies have identified genes involved in high‐altitude adaptation in Tibetans. Three of these genes (EPAS1, EGLN1 and PPARA) are associated with decreased haemoglobin levels compared with non‐Tibetans living at altitude. Consistent with the phenotype, EGLN1 in Tibetans has a gain‐of‐function mutation that confers a higher affinity for oxygen, hence less sensitivity to hypoxia. Considering the demands imposed upon metabolism in meeting energy demands despite limitations on fuel oxidation, we hypothesized that other selected genes might alter metabolism to allow adaptation to altitude despite the desensitization of the upstream hypoxia sensing caused by the EGLN1 mutation that results in the failure to sense hypoxia. A shift in fuel preference to glucose oxidation and glycolysis at the expense of fatty acid oxidation would provide adaptation to decreased oxygen availability. Measurements of serum metabolites from Tibetans living at high altitude are consistent with this hypothesis; the EPAS1 haplotype is significantly associated with increased lactate levels (suggesting increased anaerobic metabolism), and the PPARA haplotype and serum free fatty acids are positively related (suggesting decreased fat oxidation). These data suggest that the high‐altitude adaptations may offer protection from diabetes at high altitude but increase the risk of diabetes at lower elevations and/or with adoption of a non‐traditional diet. It should also be considered in future work in the field that because iron is a cofactor for EGLN1, there may be significant associations of phenotypes with the significant degrees of variation seen in tissue iron among human populations.
Physiology, Genomics, and Pathway Engineering of an Ethanol-Tolerant Strain of Clostridium phytofermentans
Authors: Tolonen Andrew C. , Zuroff Trevor R. , Ramya Mohandass , Boutard Magali , Cerisy Tristan , Curtis Wayne R.
Published: June 2015

Novel processing strategies for hydrolysis and fermentation of lignocellulosic biomass in a single reactor offer large potential cost savings for production of biocommodities and biofuels. One critical challenge is retaining high enzyme production in the presence of elevated product titers. Toward this goal, the cellulolytic, ethanol-producing bacterium
Clostridium phytofermentans
was adapted to increased ethanol concentrations. The resulting ethanol-tolerant (ET) strain has nearly doubled ethanol tolerance relative to the wild-type level but also reduced ethanol yield and growth at low ethanol concentrations. The genome of the ET strain has coding changes in proteins involved in membrane biosynthesis, the Rnf complex, cation homeostasis, gene regulation, and ethanol production. In particular, purification of the mutant bifunctional acetaldehyde coenzyme A (CoA)/alcohol dehydrogenase showed that a G609D variant abolished its activities, including ethanol formation. Heterologous expression of
Zymomonas mobilis
pyruvate decarboxylase and alcohol dehydrogenase in the ET strain increased cellulose consumption and restored ethanol production, demonstrating how metabolic engineering can be used to overcome disadvantageous mutations incurred during adaptation to ethanol. We discuss how genetic changes in the ET strain reveal novel potential strategies for improving microbial solvent tolerance.
Microbial Infections Are Associated with Embryo Mortality in Arctic-Nesting Geese
Authors: Hansen Cristina M. , Meixell Brandt W. , Van Hemert Caroline , Hare Rebekah F. , Hueffer Karsten
Published: June 2015

To address the role of bacterial infection in hatching failure of wild geese, we monitored embryo development in a breeding population of Greater white-fronted geese (
Anser albifrons
) on the Arctic Coastal Plain of Alaska. During 2013, we observed mortality of normally developing embryos and collected 36 addled eggs for analysis. We also collected 17 infertile eggs for comparison. Using standard culture methods and gene sequencing to identify bacteria within collected eggs, we identified a potentially novel species of
Neisseria
in 33 eggs,
Macrococcus caseolyticus
in 6 eggs, and
Streptococcus uberis
and
Rothia nasimurium
in 4 eggs each. We detected seven other bacterial species at lower frequencies. Sequences of the 16S rRNA genes from the
Neisseria
isolates most closely matched sequences from
N. animaloris
and
N. canis
(96 to 97% identity), but phylogenetic analysis suggested substantial genetic differentiation between egg isolates and known
Neisseria
species. Although definitive sources of the bacteria remain unknown, we detected
Neisseria
DNA from swabs of eggshells, nest contents, and cloacae of nesting females. To assess the pathogenicity of bacteria identified in contents of addled eggs, we inoculated isolates of
Neisseria
,
Macrococcus
,
Streptococcus
, and
Rothia
at various concentrations into developing chicken eggs. Seven-day mortality rates varied from 70 to 100%, depending on the bacterial species and inoculation dose. Our results suggest that bacterial infections are a source of embryo mortality in wild geese in the Arctic.
pSW2, a Novel Low-Temperature-Inducible Gene Expression Vector Based on a Filamentous Phage of the Deep-Sea Bacterium Shewanella piezotolerans WP3
Authors: Yang Xin-Wei , Jian Hua-Hua , Wang Feng-Ping
Published: June 2015

A low-temperature-inducible protein expression vector (pSW2) based on a filamentous phage (SW1) of the deep-sea bacterium
Shewanella piezotolerans
WP3 was constructed. This vector replicated stably in
Escherichia coli
and
Shewanella
species, and its copy number increased at low temperatures. The pSW2 vector can be utilized as a complementation plasmid in WP3, and it can also be used for the production of complex cytochromes with multiple heme groups, which has the potential for application for metal ion recovery or bioremediation. Promoters of low-temperature-inducible genes in WP3 were fused into the vector to construct a series of vectors for enhancing protein expression at low temperature. The maximum green fluorescent protein intensity was obtained when the promoter for the
hfq
gene was used. The WP3/pSW2 system can efficiently produce a patatin-like protein (PLP) from a metagenomic library that tends to form inclusion bodies in
E. coli
. The yields of PLP in the soluble fraction were 8.3 mg/liter and 4.7 mg/liter of culture at 4°C and 20°C, respectively. Moreover, the pSW2 vector can be broadly utilized in other
Shewanella
species, such as
S. oneidensis
and
S. psychrophila
.
Acromyrmex Leaf-Cutting Ants Have Simple Gut Microbiota with Nitrogen-Fixing Potential
Authors: Sapountzis Panagiotis , Zhukova Mariya , Hansen Lars H. , Sørensen Søren J. , Schiøtt Morten , Boomsma Jacobus J.
Published: June 2015

Ants and termites have independently evolved obligate fungus-farming mutualisms, but their gardening procedures are fundamentally different, as the termites predigest their plant substrate whereas the ants deposit it directly on the fungus garden. Fungus-growing termites retained diverse gut microbiota, but bacterial gut communities in fungus-growing leaf-cutting ants have not been investigated, so it is unknown whether and how they are specialized on an exclusively fungal diet. Here we characterized the gut bacterial community of Panamanian
Acromyrmex
species, which are dominated by only four bacterial taxa:
Wolbachia
,
Rhizobiales
, and two
Entomoplasmatales
taxa. We show that the
Entomoplasmatales
can be both intracellular and extracellular across different gut tissues,
Wolbachia
is mainly but not exclusively intracellular, and the
Rhizobiales
species is strictly extracellular and confined to the gut lumen, where it forms biofilms along the hindgut cuticle supported by an adhesive matrix of polysaccharides. Tetracycline diets eliminated the
Entomoplasmatales
symbionts but hardly affected
Wolbachia
and only moderately reduced the
Rhizobiales
, suggesting that the latter are protected by the biofilm matrix. We show that the
Rhizobiales
symbiont produces bacterial NifH proteins that have been associated with the fixation of nitrogen, suggesting that these compartmentalized hindgut symbionts alleviate nutritional constraints emanating from an exclusive fungus garden diet reared on a substrate of leaves.
Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy
Authors: Weigand Michael R. , Pena-Gonzalez Angela , Shirey Timothy B. , Broeker Robin G. , Ishaq Maliha K. , Konstantinidis Konstantinos T. , Raphael Brian H.
Published: June 2015

Taxonomic classification of
Clostridium botulinum
is based on the production of botulinum neurotoxin (BoNT), while closely related, nontoxic organisms are classified as
Clostridium sporogenes
. However, this taxonomic organization does not accurately mirror phylogenetic relationships between these species. A phylogenetic reconstruction using 2,016 orthologous genes shared among strains of
C. botulinum
group I and
C. sporogenes
clearly separated these two species into discrete clades which showed ∼93% average nucleotide identity (ANI) between them. Clustering of strains based on the presence of variable orthologs revealed 143
C. sporogenes
clade-specific genetic signatures, a subset of which were further evaluated for their ability to correctly classify a panel of presumptive
C. sporogenes
strains by PCR. Genome sequencing of several
C. sporogenes
strains lacking these signatures confirmed that they clustered with
C. botulinum
strains in a core genome phylogenetic tree. Our analysis also identified
C. botulinum
strains that contained
C. sporogenes
clade-specific signatures and phylogenetically clustered with
C. sporogenes
strains. The genome sequences of two
bont/B2
-containing strains belonging to the
C. sporogenes
clade contained regions with similarity to a
bont
-bearing plasmid (pCLD), while two different strains belonging to the
C. botulinum
clade carried
bont/B2
on the chromosome. These results indicate that
bont/B2
was likely acquired by
C. sporogenes
strains through horizontal gene transfer. The genome-based classification of these species used to identify candidate genes for the development of rapid assays for molecular identification may be applicable to additional bacterial species that are challenging with respect to their classification.
Ecology, Virulence, and Phylogeny of Blastulidium paedophthorum, a Widespread Brood Parasite of Daphnia spp
Authors: Duffy Meghan A. , James Timothy Y. , Longworth Alan
Published: June 2015

Parasitism is now recognized as a major factor impacting the ecology and evolution of plankton, including
Daphnia
. Parasites that attack the developing embryos of daphniids, known as brood parasites, were first described in the early 1900s but have received relatively little study. Here, we link previous morphological descriptions of the oomycete brood parasite
Blastulidium paedophthorum
with information on its phylogenetic placement, ecology, and virulence. Based on the morphology and phylogenetic relationship with other members of the
Leptomitales
, we show that a brood parasite observed in daphniids in the Midwestern United States is
B. paedophthorum
. We used morphology, DNA sequences, and laboratory infection experiments to show that
B. paedophthorum
is a multihost parasite that can be transmitted between species and genera. A field survey of six hosts in 15 lakes revealed that
B. paedophthorum
is common in all six host taxa (present on 38.3% of our host species-lake-sampling date combinations; the maximum infection prevalences were 8.7% of the population and 20% of the asexual adult female population). Although
B. paedophthorum
was observed in all 15 lakes, presence and infection prevalence varied among lakes. Infection with
B. paedophthorum
did not reduce host life span but significantly impacted host fecundity. Theory predicts that parasites that affect host fecundity without affecting host life span should have the strongest impact on host population dynamics. Based on its virulence and commonness in natural populations and on the central role of daphniids in freshwater food webs, we predict that
B. paedophthorum
will influence daphniid ecology and evolution, as well as the larger food web.
Genotyping and Source Tracking of Cronobacter sakazakii and C. malonaticus Isolates from Powdered Infant Formula and an Infant Formula Production Factory in China
Authors: Fei Peng , Man Chaoxin , Lou Binbin , Forsythe Stephen J. , Chai Yunlei , Li Ran , Niu Jieting , Jiang Yujun
Published: June 2015

Cronobacter
spp. (formerly defined as
Enterobacter sakazakii
) are opportunistic bacterial pathogens of both infants and adults. In this study, we analyzed 70
Cronobacter
isolates from powdered infant formula (PIF) and an infant formula production facility in China to determine possible contamination routes. The strains were profiled by multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), PCR-based O-antigen serotyping, and
ompA
and
rpoB
sequence analyses. The isolates were primarily
Cronobacter sakazakii
(66/70) or
Cronobacter
malonaticus
(4/70). The strains were divided into 38 pulsotypes (PTs) using PFGE and 19 sequence types (STs) by MLST. In contrast,
rpoB
and
ompA
sequence analyses divided the strains into 10 overlapping clusters each. PCR serotyping of the 66
C. sakazakii
and 4
C. malonaticus
strains resulted in the identification of four
C. sakazakii
serotypes (O1, O2, O4, and O7) and a single
C. malonaticus
serotype, O2. The dominant
C. sakazakii
sequence types from PIF and an infant formula production factory in China were
C. sakazakii
clonal complex 4 (CC4) (
n
= 19), ST1 (
n
= 14), and ST64 (
n
= 11).
C. sakazakii
CC4 is a clonal lineage strongly associated with neonatal meningitis. In the process of manufacturing PIF, the spray-drying, fluidized-bed-drying, and packing areas were the main areas with
Cronobacter
contamination.
C. sakazakii
strains with the same pulsotypes (PT3 and PT2) and sequence types (ST1 and ST64) were isolated both from processing equipment and from the PIF finished product.
Survival and Competitiveness of Bradyrhizobium japonicum Strains 20 Years after Introduction into Field Locations in Poland
Authors: Narożna Dorota , Pudełko Krzysztof , Króliczak Joanna , Golińska Barbara , Sugawara Masayuki , Mądrzak Cezary J. , Sadowsky Michael J.
Published: June 2015

It was previously demonstrated that there are no indigenous strains of
Bradyrhizobium japonicum
forming nitrogen-fixing root nodule symbioses with soybean plants in arable field soils in Poland. However, bacteria currently classified within this species are present (together with
Bradyrhizobium canariense
) as indigenous populations of strains specific for nodulation of legumes in the Genisteae tribe. These rhizobia, infecting legumes such as lupins, are well established in Polish soils. The studies described here were based on soybean nodulation field experiments, established at the Poznań University of Life Sciences Experiment Station in Gorzyń, Poland, and initiated in the spring of 1994. Long-term research was then conducted in order to study the relation between
B. japonicum
USDA 110 and USDA 123, introduced together into the same location, where no soybean rhizobia were earlier detected, and nodulation and competitive success were followed over time. Here we report the extra-long-term saprophytic survival of
B. japonicum
strains nodulating soybeans that were introduced as inoculants 20 years earlier and where soybeans were not grown for the next 17 years. The strains remained viable and symbiotically competent, and molecular and immunochemical methods showed that the strains were undistinguishable from the original inoculum strains USDA 110 and USDA 123. We also show that the strains had balanced numbers and their mobility in soil was low. To our knowledge, this is the first report showing the extra-long-term persistence of soybean-nodulating strains introduced into Polish soils and the first analyzing the long-term competitive relations of USDA 110 and USDA 123 after the two strains, neither of which was native, were introduced into the environment almost 2 decades ago.
Identification of a Chemoreceptor for C
2
and C
3
Carboxylic Acids
Authors: García Vanina , Reyes-Darias Jose-Antonio , Martín-Mora David , Morel Bertrand , Matilla Miguel A. , Krell Tino
Published: June 2015

Chemoreceptors are at the beginnings of chemosensory signaling cascades that mediate chemotaxis. Most bacterial chemoreceptors are functionally unannotated and are characterized by a diversity in the structure of their ligand binding domains (LBDs). The data available indicate that there are two major chemoreceptor families at the functional level, namely, those that respond to amino acids or to Krebs cycle intermediates. Since pseudomonads show chemotaxis to many different compounds and possess different types of chemoreceptors, they are model organisms to establish relationships between chemoreceptor structure and function. Here, we identify PP2861 (termed McpP) of
Pseudomonas putida
KT2440 as a chemoreceptor with a novel ligand profile. We show that the recombinant McpP LBD recognizes acetate, pyruvate, propionate, and
l
-lactate, with

K
D

(equilibrium dissociation constant) values ranging from 34 to 107 μM. Deletion of the
mcpP
gene resulted in a dramatic reduction in chemotaxis toward these ligands, and complementation restored a native-like phenotype, indicating that McpP is the major chemoreceptor for these compounds. McpP has a CACHE-type LBD, and we present data indicating that CACHE-containing chemoreceptors of other species also mediate taxis to C
2
and C
3
carboxylic acids. In addition, the LBD of NbaY of
Pseudomonas fluorescens
, an McpP homologue mediating chemotaxis to 2-nitrobenzoate, bound neither nitrobenzoates nor the McpP ligands. This work provides further insight into receptor structure-function relationships and will be helpful to annotate chemoreceptors of other bacteria.
Novel Route for Agmatine Catabolism in Aspergillus niger Involves 4-Guanidinobutyrase
Authors: Kumar Sunil , Saragadam Tejaswani , Punekar Narayan S.
Published: June 2015

Agmatine, a significant polyamine in bacteria and plants, mostly arises from the decarboxylation of arginine. The functional importance of agmatine in fungi is poorly understood. The metabolism of agmatine and related guanidinium group-containing compounds in
Aspergillus niger
was explored through growth, metabolite, and enzyme studies. The fungus was able to metabolize and grow on
l
-arginine, agmatine, or 4-guanidinobutyrate as the sole nitrogen source. Whereas arginase defined the only route for arginine catabolism, biochemical and bioinformatics approaches suggested the absence of arginine decarboxylase in
A. niger
. Efficient utilization by the parent strain and also by its arginase knockout implied an arginase-independent catabolic route for agmatine. Urea and 4-guanidinobutyrate were detected in the spent medium during growth on agmatine. The agmatine-grown
A. niger
mycelia contained significant levels of amine oxidase, 4-guanidinobutyraldehyde dehydrogenase, 4-guanidinobutyrase (GBase), and succinic semialdehyde dehydrogenase, but no agmatinase activity was detected. Taken together, the results support a novel route for agmatine utilization in
A. niger
. The catabolism of agmatine by way of 4-guanidinobutyrate to 4-aminobutyrate into the Krebs cycle is the first report of such a pathway in any organism.
A. niger
GBase peptide fragments were identified by tandem mass spectrometry analysis. The corresponding open reading frame from the
A. niger
NCIM 565 genome was located and cloned. Subsequent expression of GBase in both
Escherichia coli
and
A. niger
along with its disruption in
A. niger
functionally defined the GBase locus (
gbu
) in the
A. niger
genome.
Evidence for Extracellular ATP as a Stress Signal in a Single-Celled Organism
Authors: Sivaramakrishnan Venketesh , Fountain Samuel J.
Published: June 2015

ATP is omnipresent in biology and acts as an extracellular signaling molecule in mammals. Information regarding the signaling function of extracellular ATP in single-celled eukaryotes is lacking. Here, we explore the role of extracellular ATP in cell volume recovery during osmotic swelling in the amoeba
Dictyostelium
. Release of micromolar ATP could be detected during cell swelling and regulatory cell volume decrease (RVD) phases during hypotonic challenge. Scavenging ATP with apyrase caused profound cell swelling and loss of RVD. Apyrase-induced swelling could be rescued by 100 μM βγ-imidoATP.
N
-Ethylmalemide (NEM), an inhibitor of vesicular exocytosis, caused heightened cell swelling, loss of RVD, and inhibition of ATP release. Amoebas with impaired contractile vacuole (CV) fusion (drainin knockout [KO] cells) displayed increased swelling but intact ATP release. One hundred micromolar Gd
3+
caused cell swelling while blocking any recovery by βγ-imidoATP. ATP release was 4-fold higher in the presence of Gd
3+
. Cell swelling was associated with an increase in intracellular nitric oxide (NO), with NO-scavenging agents causing cell swelling. Swelling-induced NO production was inhibited by both apyrase and Gd
3+
, while NO donors rescued apyrase- and Gd
3+
-induced swelling. These data suggest extracellular ATP released during cell swelling is an important signal that elicits RVD. Though the cell surface receptor for ATP in
Dictyostelium
remains elusive, we suggest ATP operates through a Gd
3+
-sensitive receptor that is coupled with intracellular NO production.
Deletion of the DNA Ligase IV Gene in Candida glabrata Significantly Increases Gene-Targeting Efficiency
Authors: Cen Yuke , Fiori Alessandro , Van Dijck Patrick
Published: June 2015

Candida glabrata
is reported as the second most prevalent human opportunistic fungal pathogen in the United States. Over the last decades, its incidence increased, whereas that of
Candida albicans
decreased slightly. One of the main reasons for this shift is attributed to the inherent tolerance of
C. glabrata
toward the commonly used azole antifungal drugs. Despite a close phylogenetic distance to
Saccharomyces cerevisiae
, homologous recombination works with poor efficiency in
C. glabrata
compared to baker's yeast, in fact limiting targeted genetic alterations of the pathogen's genome. It has been shown that nonhomologous DNA end joining is dominant over specific gene targeting in
C. glabrata
. To improve the homologous recombination efficiency, we have generated a strain in which the
LIG4
gene has been deleted, which resulted in a significant increase in correct gene targeting. The very specific function of Lig4 in mediating nonhomologous end joining is the reason for the absence of clear side effects, some of which affect the
ku80
mutant, another mutant with reduced nonhomologous end joining. We also generated a
LIG4
reintegration cassette. Our results show that the
lig4
mutant strain may be a valuable tool for the
C. glabrata
research community.
Association of pneumococcal conjugate vaccination with rates of ventilation tube insertion in Denmark: population-based register study
Authors: Groth Christina , Thomsen Reimar W , Ovesen Therese
Published: June 2015

Objective

To examine if the introduction of pneumococcal conjugate vaccine (PCV) in Denmark was associated with a decrease in the rate of ventilation tube (VT) insertions performed by office-based practising ear, nose and throat (ENT) specialists.

Design

Population-based register study based on prospectively collected data.

Setting

Central Denmark Region. Data on VT insertions performed by any office-based practising ENT specialist in the region were collected from the National Health Service Registry.

Participants

All children below the age of 2 years with a first-time VT insertion from 2001 through 2011.

Main outcome measures

Age-stratified and gender-stratified standardised incidence rates of first-time VT insertion, and incidence rate ratio for PCV period 2008–2011 compared with pre-PCV period 2001–2007.

Results

The annual incidence rate of first-time VT insertion in small children increased steadily from 64/1000 person-years in 2001 to 100/1000 person-years in 2011. The incidence rate ratio was 1.27 (95% CI 1.24 to 1.30) in the PCV period compared with the pre-PCV period.

Conclusions

The introduction of PCV into the Danish childhood immunisation programme in 2007 was not associated with a subsequent decrease in the rate of VT insertions among children below the age of 2 years. Instead, the rate continued to rise, as before the introduction of PCV.

Trial registration number

Danish Data Protection Agency: 2007-58-0010.
Comparative efficacy and safety of approved treatments for macular oedema secondary to branch retinal vein occlusion: a network meta-analysis
Authors: Regnier Stephane A , Larsen Michael , Bezlyak Vladimir , Allen Felicity
Published: June 2015

Objective

To compare the efficacy and safety of approved treatments for macular oedema secondary to branch retinal vein occlusion (BRVO).

Design

Randomised controlled trials (RCTs) evaluating the efficacy and safety of approved treatments for macular oedema secondary to BRVO were identified from an updated systematic review.

Setting

A Bayesian network meta-analysis of RCTs of treatments for macular oedema secondary to BRVO.

Interventions

Ranibizumab 0.5 mg pro re nata, aflibercept 2 mg monthly (2q4), dexamethasone 0.7 mg implant, laser photocoagulation, ranibizumab+laser, or sham intervention. Bevacizumab and triamcinolone were excluded.

Outcome measures

Efficacy outcomes were mean change in best corrected visual acuity (Early Treatment Diabetic Retinopathy Study scale) and the percentage of patients gaining ≥15 letters. Safety outcome was the percentage of patients with increased intraocular pressure (IOP)/ocular hypertension (OH).

Results

8 RCTs were identified for inclusion with 1743 adult patients. The probability of being the most efficacious treatment at month 6 or 12 based on letters gained was 54% for ranibizumab monotherapy, 30% for aflibercept, 16% for ranibizumab plus laser (adjunctive or prompt), and 0% for dexamethasone implant, laser or sham. The probability of being the most efficacious treatment for patients gaining ≥15 letters was 39% for aflibercept, 35% for ranibizumab monotherapy, 24% for ranibizumab plus laser, 2% for dexamethasone implant, and less than 1% for laser or sham. There was no statistical difference between ranibizumab monotherapy and aflibercept for letters gained (+1.4 letters for ranibizumab vs aflibercept with 95% credible interval (CrI) of −5.2 to +8.5 letters) or the OR for gaining ≥15 letters: 1.06 (95% CrI 0.16 to 8.94)). Dexamethasone implant was associated with significantly higher IOP/OH than antivascular endothelial growth factor agents (OR 13.1 (95% CrI 1.7 to 116.9)).

Conclusions

There was no statistically significant difference between ranibizumab and aflibercept.
Hospitalisation for heart failure and mortality associated with dipeptidyl peptidase 4 (DPP-4) inhibitor use in an unselected population of subjects with type 2 diabetes: a nested case–control study
Authors: Giorda Carlo B , Picariello Roberta , Tartaglino Barbara , Marafetti Lisa , Di Noi Fabiana , Alessiato Annalisa , Costa Giuseppe , Gnavi Roberto
Published: June 2015

Objective

The SAVOR TIMI–53 study reported a significant increase in the risk of hospitalisation for heart failure (HF) in patients treated with a DPP-4 inhibitor (DPP-4i) in comparison with placebo. A recent case-control study in part confirmed this risk signal. Our aim was to compare the occurrence of HF in relation to DPP-4i use versus any antidiabetic treatment.

Design

Population-based matched case-control study conducted using administrative data.

Setting

The Italian Region of Piedmont (4.4 million inhabitants).

Participants

From a database of 282 000 patients treated with antidiabetic drugs, we identified 14 613 hospitalisations for HF, 7212 incident cases, and 1727 hospital re-admissions between 2008 and 2012; each case was matched for gender, age and antidiabetic therapy with 10 controls; cases and controls were compared for exposure to DPP-4i.

Outcome measures

ORs and 95% CIs were calculated by fitting a conditional logistic model. All analyses were adjusted for available risk factors for HF.

Results

We found no increased risk of hospitalisation for HF associated with the use of DPP-4i (OR for admission for HF 1.00 (0.94 to 1.07), incident HF1.01 (0.92 to 1.11), recurrent HF 1.02 (0.84 to 1.22)). All-cause mortality was 6% lower in DPP-4i users (p<0.001), whereas insulin users showed an excess of risk for any type of hospital admission (19%) and death (20%) (p<0.001).

Conclusions

Our findings suggest that, in an unselected population of diabetic patients, the use of DPP-4i is not associated with an increased risk of HF. The favourable impact on all-cause mortality should be viewed with caution and also other explanations investigated.
Discrepancy between early neurological course and mid-term outcome in older stroke patients after mechanical thrombectomy
Authors: Kleine Justus F , Boeckh-Behrens Tobias , Prothmann Sascha , Zimmer Claus , Liebig Thomas
Published: June 2015

Background

Stroke in aged patients has a relatively poor prognosis, even after recanalizing therapy. Potential reasons include mechanisms that relate directly to the extent of brain tissue damage, but also age-dependent factors which are not, or only indirectly, stroke-related, such as pre-existing functional deficits, comorbidities, and post-stroke complications (eg, infections).

Objective

To compare early neurological course with subsequent functional outcome in older (≥80 years) and younger stroke patients in order to estimate the relative impact of these factors. Specifically, to examine if the strong age-dependency of modified Rankin Scale (mRS) outcome scores in stroke patients after mechanical thrombectomy is paralleled by a similar age dependency of early postinterventional National Institute of Health Stroke Scale (NIHSS) scores—a more specific measure of stroke-induced brain damage.

Methods

We evaluated technical results, pre- and postinterventional NIHSS scores, mid-term mRS scores and early and overall mortality and their relation to age in 125 patients, 40 of them ≥80 years, with acute middle cerebral artery occlusion, treated by mechanical thrombectomy.

Results

Technical success, pre- and postinterventional NIHSS scores and early mortality were age-independent. Early neurological improvement depended on successful recanalization, but not on age. Nevertheless, good mRS outcome (mRS 0–2) was much rarer, and overall mortality almost threefold higher in aged patients.

Conclusions

Older patients exhibit a similar early neurological course and responsiveness to mechanical thrombectomy as younger patients, but this is not reflected in mid-term functional outcome scores. This indicates that post-stroke complications and other factors that are not, or only indirectly, related to the brain tissue damage induced by the incident stroke have a dominant role in their poor prognosis.
Republished: Targeted epidural patch with n-butyl cyanoacrylate (n-BCA) through a single catheter access site for treatment of a cerebral spinal fluid leak causing spontaneous intracranial hypotension
Authors: Woolen Sean , Gemmete Joseph J , Pandey Aditya S , Chaudhary Neeraj
Published: June 2015

Spontaneous intracranial hypotension (SIH) usually occurs in the setting of a spontaneous cerebral spinal fluid (CSF) leak. We report the first description of a case of SIH caused by a CSF leak which improved after a targeted epidural patch with n-butyl cyanoacrylate (n-BCA) at the right T1–T2 level. An 81-year-old woman presented with an orthostatic headache for 6 days. MRI of the brain with contrast demonstrated low lying cerebellar tonsils, an engorged transverse sinus flow void, bifrontal small subdural fluid collections, and diffuse dural enhancement. CT myelography showed extravasation of intrathecal contrast at the right T1–T2 level. A targeted epidural patch was performed by injection of n-BCA through a catheter at the right T1–T2 level. After treatment, the patient's symptoms immediately improved and she was without a headache at 1-year follow-up.