bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ObjectiveTo 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.DesignPopulation-based register study based on prospectively collected data.SettingCentral 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.ParticipantsAll children below the age of 2 years with a first-time VT insertion from 2001 through 2011.Main outcome measuresAge-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.ResultsThe 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.ConclusionsThe 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 numberDanish 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

ObjectiveTo compare the efficacy and safety of approved treatments for macular oedema secondary to branch retinal vein occlusion (BRVO).DesignRandomised controlled trials (RCTs) evaluating the efficacy and safety of approved treatments for macular oedema secondary to BRVO were identified from an updated systematic review.SettingA Bayesian network meta-analysis of RCTs of treatments for macular oedema secondary to BRVO.InterventionsRanibizumab 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 measuresEfficacy 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).Results8 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)).ConclusionsThere 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

ObjectiveThe 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.DesignPopulation-based matched case-control study conducted using administrative data.SettingThe Italian Region of Piedmont (4.4 million inhabitants).ParticipantsFrom 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 measuresORs and 95% CIs were calculated by fitting a conditional logistic model. All analyses were adjusted for available risk factors for HF.ResultsWe 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).ConclusionsOur 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

BackgroundStroke 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).ObjectiveTo 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.MethodsWe 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.ResultsTechnical 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.ConclusionsOlder 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.
The transthyretin amyloidoses: advances in therapy
Authors: Dubrey Simon , Ackermann Elizabeth , Gillmore Julian 
Published: June 2015

ABSTRACT
There are two forms of transthyretin (TTR) amyloidosis: non-hereditary and hereditary. The non-hereditary form (ATTRwt) is caused by native or wild-type TTR and was previously referred to as senile systemic amyloidosis. The hereditary form (ATTRm) is caused by variant TTR which results from a genetic mutation of TTR. The predominant effect of ATTRwt amyloidosis is on the heart, with patients having a greater left ventricular wall thickness at presentation than the devastating form which is light chain (AL) amyloidosis. ATTRm amyloidosis is broadly split into two categories: a type that predominantly affects the nervous system (often called familial amyloid polyneuropathy (FAP)) and one with a predilection for the heart (often called familial amyloid cardiomyopathy (FAC)). Approximately half of all TTR mutations known to express a clinical phenotype cause a cardiomyopathy. Since the introduction of orthotopic liver transplantation for ATTRm amyloidosis in 1991, several additional therapies have been developed. These therapies aim to provide a reduction or elimination of TTR from the plasma (through genetic approaches), stabilisation of the TTR molecule (to prevent deposition) and dissolution of the amyloid matrix. We describe the latest developments in these approaches to management, many of which are also applicable to wild-type amyloidosis.
Exome Sequencing to Predict Neoantigens in Melanoma
Authors: Pritchard Antonia L. , Burel Julie G. , Neller Michelle A. , Hayward Nicholas K. , Lopez J. Alejandro , Fatho Martina , Lennerz Volker , Wölfel Thomas , Schmidt Christopher W. 
Published: June 2015

Abstract
The ability to use circulating peripheral blood cells and matched tumor sequencing data as a basis for neoantigen prediction has exciting possibilities for application in the personalized treatment of cancer patients. We have used a high-throughput screening approach, combining whole-exome sequence data, mRNA microarrays, and publicly available epitope prediction algorithm output to identify mutated proteins processed and displayed by patient tumors and recognized by circulating immune cells. Matched autologous melanoma cell lines and peripheral blood mononuclear cells were used to create mixed lymphocyte tumor cell cultures, resulting in an expansion of tumor-reactive T cells to use for mutated peptide screening. Five patients were investigated, three of whom had a durable complete response (CR; 15+ years) in an autologous melanoma-pulsed dendritic cell clinical trial. We identified seven mutated antigens in total that stimulated T-effector memory cells in two of the five patients. While the procedure did not result in clinically applicable neoantigens for all patients, those identified were likely important in tumor clearance, leading to durable CR. The nature of the screening process allows results to be obtained rapidly and is easily applicable to a wide variety of different tumor types. Cancer Immunol Res; 3(9); 992–8. ©2015 AACR.