bluuebunny/crossref_metadata_2025_split huggingface dataset:
The
Legionella
Kinase LegK2 Targets the ARP2/3 Complex To Inhibit Actin Nucleation on Phagosomes and Allow Bacterial Evasion of the Late Endocytic Pathway
Authors: Michard Céline , Sperandio Daniel , Baïlo Nathalie , Pizarro-Cerdá Javier , LeClaire Lawrence , Chadeau-Argaud Elise , Pombo-Grégoire Isabel , Hervet Eva , Vianney Anne , Gilbert Christophe , Faure Mathias , Cossart Pascale , Doublet Patricia 
Published: May 2015

ABSTRACT

Legionella pneumophila
, the etiological agent of legionellosis, replicates within phagocytic cells. Crucial to biogenesis of the replicative vacuole is the Dot/Icm type 4 secretion system, which translocates a large number of effectors into the host cell cytosol. Among them is LegK2, a protein kinase that plays a key role in
Legionella
infection. Here, we identified the actin nucleator ARP2/3 complex as a target of LegK2. LegK2 phosphorylates the ARPC1B and ARP3 subunits of the ARP2/3 complex. LegK2-dependent ARP2/3 phosphorylation triggers global actin cytoskeleton remodeling in cells, and it impairs actin tail formation by
Listeria monocytogenes
, a well-known ARP2/3-dependent process. During infection, LegK2 is addressed to the
Legionella
-containing vacuole surface and inhibits actin polymerization on the phagosome, as revealed by legK2 gene inactivation. Consequently, LegK2 prevents late endosome/lysosome association with the phagosome and finally contributes to remodeling of the bacterium-containing phagosome into a replicative niche. The inhibition of actin polymerization by LegK2 and its effect on endosome trafficking are ARP2/3 dependent since it can be phenocopied by a specific chemical inhibitor of the ARP2/3 complex. Thus, LegK2-ARP2/3 interplay highlights an original mechanism of bacterial virulence with an unexpected role in local actin remodeling that allows bacteria to control vesicle trafficking in order to escape host defenses.

IMPORTANCE
Deciphering the individual contribution of each Dot/Icm type 4 secretion system substrate to the intracellular life-style of
L. pneumophila
remains the principal challenge in understanding the molecular basis of
Legionella
virulence. Our finding that LegK2 is a Dot/Icm effector that inhibits actin polymerization on the
Legionella
-containing vacuole importantly contributes to the deciphering of the molecular mechanisms evolved by
Legionella
to counteract the endocytic pathway. Indeed, our results highlight the essential role of LegK2 in preventing late endosomes from fusing with the phagosome. More generally, this work is the first demonstration of local actin remodeling as a mechanism used by bacteria to control organelle trafficking. Further, by characterizing the role of the bacterial protein kinase LegK2, we reinforce the concept that posttranslational modifications are key strategies used by pathogens to evade host cell defenses.
Adenylate Charge Regulates Sensor Kinase CheS
3
To Control Cyst Formation in Rhodospirillum centenum
Authors: He Kuang , Dragnea Vladimira , Bauer Carl E. 
Published: May 2015

ABSTRACT

Rhodospirillum centenum
forms metabolically dormant cysts under unfavorable growth conditions such as desiccation or nutrient starvation. The development of cysts is tightly regulated and involves a cyst-repressing chemotaxis-like signal transduction pathway called the Che
3
signaling cascade. The Che
3
cascade is comprised of a methyl chemoreceptor (MCP
3
), receptor-methylating/demethylating proteins CheB
3
and CheR
3
, two CheW
3
linker proteins, a CheA
3
-CheY hybrid histidine kinase, and a single-domain response regulator, CheY
3
. In addition to Che-like components, the Che
3
cascade also contains a second hybrid histidine kinase, CheS
3
. Recent biochemical and genetic studies show that CheA
3
does not serve as a phosphor donor for CheY
3
; instead, CheA
3
inhibits a CheS
3
→CheY
3
two-component system by phosphorylating an inhibitory receiver domain of CheS
3
. In this study, we show that in addition to phosphorylation by CheA
3
, the phosphorylation state of CheS
3
is also regulated by the cellular energy level as quantified by the molar ratio of ATP/(ATP + ADP). A 35% decrease in cellular energy is shown to occur
in vivo
upon a nutrient downshift that gives rise to cyst formation. When this energy decline is replicated
in vitro
, the phosphorylation level of CheS
3
is reduced by ~75%. Finally, we also show that ADP-mediated reduction of CheS
3
phosphorylation is a consequence of ADP enhancing autodephosphorylation of CheS
3
.

IMPORTANCE
Upon starvation,
Rhodospirillum centenum
undergoes a developmental process that forms metabolically dormant cysts, which withstand desiccation and nutritional limitation. This study explores the role of the cellular energy state as measured by the ratio of ATP to ADP as an important regulator of cyst formation in
Rhodospirillum centenum
. We show that
R. centenum
cells experience a significant reduction in ATP during cyst formation using ATP/(ATP + ADP) as a measurement. When this
in vivo
level of energy starvation is simulated
in vitro
, CheS
3
phosphorylation is reduced by 75%. This profound reduction in CheS
3
autophosphorylation is contrasted with a much lower 25% decrease in CheA
3
phosphorylation in response to a similar downward shift in ATP/(ATP + ADP). We argue that even though adenylate energy affects all ATP-dependent enzymes to an extent, the enhanced inhibition of CheS
3
activity in response to a reduction in the ATP/(ATP + ADP) ratio likely functions as an important input signal to regulate cyst development.
Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations
Authors: Xue Hong , Cordero Otto X. , Camas Francisco M. , Trimble William , Meyer Folker , Guglielmini Julien , Rocha Eduardo P. C. , Polz Martin F. 
Published: May 2015

ABSTRACT

Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine
Vibrionaceae
bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells. Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.

IMPORTANCE
Plasmids and other episomes are an integral part of bacterial biology in all environments, yet their study is heavily biased toward their role as vectors for antibiotic resistance genes. This study presents a comprehensive analysis of all episomes within several coexisting bacterial populations of
Vibrionaceae
from the coastal ocean and represents the largest-yet genomic survey of episomes from a single bacterial family. The host population framework allows analysis of the eco-evolutionary dynamics at unprecedented resolution, yielding several unexpected results. These include (i) discovery of novel, nonintegrative temperate phages, (ii) revision of a class of episomes, previously termed “nontransmissible,” as highly transmissible, and (iii) surprisingly high evolutionary turnover of episomes, manifest as frequent birth, spread, and loss.
The cost-effectiveness of initiating ranibizumab therapy in eyes with neovascular AMD with good vision: an economic model using real-world outcomes
Authors: Butt Thomas , Lee Aaron , Lee Cecilia , Tufail Adnan 
Published: May 2015

ObjectivesTo evaluate the cost-effectiveness of immediate treatment with ranibizumab in patients with neovascular age-related macular degeneration (nAMD) with good (better than 6/12) starting visual acuity compared with current UK clinical guidance of waiting until vision falls below 6/12 to begin treatment, using real-world outcomes data.DesignA patient-level health economic state transition model based on levels of visual acuity in the better seeing eye was constructed to simulate the costs and consequences of treating patients with nAMD with ranibizumab.SettingThe model took the perspective of the UK National Health Service (NHS).ParticipantsThe model was populated with real-world outcomes and resource use from a prospective multicentre national nAMD database study containing 92 976 ranibizumab treatment episodes.InterventionsTwo treatment approaches were compared: immediate intervention with 0.5 mg ranibizumab pro re nata, PRN (on detection of nAMD) or delayed intervention (waiting until vision fell to 6/12 before beginning treatment).Main outcome measuresQuality-adjusted life years (QALYs) for health states and healthcare costs were accrued for each strategy, and an incremental cost-effectiveness ratio (ICER) was calculated. One-way and probabilistic sensitivity analyses were employed to test the uncertainty of the model.ResultsOver a 2-year time horizon, based on 10 000 Monte Carlo simulations, the early treatment arm accumulated 1.59 QALYs and £8469.79 cost. The delayed treatment arm accumulated 1.35 QALYs and £7460.21 cost. The central ICER estimate was £4251.60.ConclusionsA model based on real-world data is likely to be a realistic reflection of the health gains and resource use of ranibizumab for nAMD in the UK NHS. Initiating treatment immediately with ranibizumab PRN regimen is a cost-effective strategy compared with current guidance of initiating treatment at a level of 6/12 or worse vision.
Evidence-informed recommendations to reduce dissemination bias in clinical research: conclusions from the OPEN (Overcome failure to Publish nEgative fiNdings) project based on an international consensus meeting
Authors: Meerpohl Joerg J , Schell Lisa K , Bassler Dirk , Gallus Silvano , Kleijnen Jos , Kulig Michael , La Vecchia Carlo , Marušić Ana , Ravaud Philippe , Reis Andreas , Schmucker Christine , Strech Daniel , Urrútia Gerard , Wager Elizabeth , Antes Gerd 
Published: May 2015

BackgroundDissemination bias in clinical research severely impedes informed decision-making not only for healthcare professionals and patients, but also for funders, research ethics committees, regulatory bodies and other stakeholder groups that make health-related decisions. Decisions based on incomplete and biased evidence cannot only harm people, but may also have huge financial implications by wasting resources on ineffective or harmful diagnostic and therapeutic measures, and unnecessary research. Owing to involvement of multiple stakeholders, it remains easy for any single group to assign responsibility for resolving the problem to others.ObjectiveTo develop evidence-informed general and targeted recommendations addressing the various stakeholders involved in knowledge generation and dissemination to help overcome the problem of dissemination bias on the basis of previously collated evidence.MethodsBased on findings from systematic reviews, document analyses and surveys, we developed general and targeted draft recommendations. During a 2-day workshop in summer 2013, these draft recommendations were discussed with external experts and key stakeholders, and refined following a rigorous and transparent methodological approach.ResultsFour general, overarching recommendations applicable to all or most stakeholder groups were formulated, addressing (1) awareness raising, (2) implementation of targeted recommendations, (3) trial registration and results posting, and (4) systematic approaches to evidence synthesis. These general recommendations are complemented and specified by 47 targeted recommendations tailored towards funding agencies, pharmaceutical and device companies, research institutions, researchers (systematic reviewers and trialists), research ethics committees, trial registries, journal editors and publishers, regulatory agencies, benefit (health technology) assessment institutions and legislators.ConclusionsDespite various recent examples of dissemination bias and several initiatives to reduce it, the problem of dissemination bias has not been resolved. Tailored recommendations based on a comprehensive approach will hopefully help increase transparency in biomedical research by overcoming the failure to disseminate negative findings.
Highly Expressed Genes in Rapidly Proliferating Tumor Cells as New Targets for Colorectal Cancer Treatment
Authors: Bazzocco Sarah , Dopeso Higinio , Carton-Garcia Fernando , Macaya Irati , Andretta Elena , Chionh Fiona , Rodrigues Paulo , Garrido Miriam , Alazzouzi Hafid , Nieto Rocio , Sanchez Alex , Schwartz Simo , Bilic Josipa , Mariadason John M. , Arango Diego 
Published: May 2015

AbstractPurpose: The clinical management of colorectal cancer patients has significantly improved because of the identification of novel therapeutic targets such as EGFR and VEGF. Because rapid tumor proliferation is associated with poor patient prognosis, here we characterized the transcriptional signature of rapidly proliferating colorectal cancer cells in an attempt to identify novel candidate therapeutic targets.Experimental Design: The doubling time of 52 colorectal cancer cell lines was determined and genome-wide expression profiling of a subset of these lines was assessed by microarray analysis. We then investigated the potential of genes highly expressed in cancer cells with faster growth as new therapeutic targets.Results: Faster proliferation rates were associated with microsatellite instability and poorly differentiated histology. The expression of 1,290 genes was significantly correlated with the growth rates of colorectal cancer cells. These included genes involved in cell cycle, RNA processing/splicing, and protein transport. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and protoporphyrinogen oxidase (PPOX) were shown to have higher expression in faster growing cell lines and primary tumors. Pharmacologic or siRNA-based inhibition of GAPDH or PPOX reduced the growth of colon cancer cells in vitro. Moreover, using a mouse xenograft model, we show that treatment with the specific PPOX inhibitor acifluorfen significantly reduced the growth of three of the seven (42.8%) colon cancer lines investigated.Conclusions: We have characterized at the transcriptomic level the differences between colorectal cancer cells that vary in their growth rates, and identified novel candidate chemotherapeutic targets for the treatment of colorectal cancer. Clin Cancer Res; 21(16); 3695–704. ©2015 AACR.
EphB1 Suppression in Acute Myelogenous Leukemia: Regulating the DNA Damage Control System
Authors: Kampen K.R. , Scherpen F.J.G. , Garcia-Manero G. , Yang H. , Kaspers G.J.L. , Cloos J. , Zwaan C.M. , van den Heuvel-Eibrink M.M. , Kornblau S.M. , De Bont E.S.J.M. 
Published: May 2015

AbstractLoss of ephrin receptor (EphB1) expression may associate with aggressive cancer phenotypes; however, the mechanism of action remains unclear. To gain detailed insight into EphB1 function in acute myelogenous leukemia (AML), comprehensive analysis of EphB1 transcriptional regulation was conducted. In AML cells, EphB1 transcript was inversely correlated with EphB1 promoter methylation. The presence of EphB1 allowed EfnB1 ligand–mediated p53 DNA binding, leading to restoration of the DNA damage response (DDR) cascade by the activation of ATR, Chk1, p53, p21, p38, CDK1tyr15, and Bax, and downregulation of HSP27 and Bcl2. Comparatively, reintroduction of EphB1 expression in EphB1-methylated AML cells enhanced the same cascade of ATR, Chk1, p21, and CDK1tyr15, which consequently enforced programmed cell death. Interestingly, in pediatric AML samples, EphB1 peptide phosphorylation and mRNA expression were actively suppressed as compared with normal bone marrow, and a significant percentage of the primary AML specimens had EphB1 promoter hypermethylation. Finally, EphB1 repression associated with a poor overall survival in pediatric AML. Combined, the contribution of EphB1 to the DDR system reveals a tumor-suppressor function for EphB1 in pediatric AML.Implications: The tumor-suppressor function of EphB1 is clinically relevant across many malignancies, suggesting that EphB1 is an important regulator of common cancer cell transforming pathways. Mol Cancer Res; 13(6); 982–92. ©2015 AACR.
Effect of Intensive Versus Standard Blood Glucose Control in Patients With Type 2 Diabetes Mellitus in Different Regions of the World: Systematic Review and Meta‐analysis of Randomized Controlled Trials
Authors: Sardar Partha , Udell Jacob A. , Chatterjee Saurav , Bansilal Sameer , Mukherjee Debabrata , Farkouh Michael E. 
Published: May 2015

Background
Regional variation in type 2 diabetes mellitus care may affect outcomes in patients treated with intensive versus standard blood glucose control. We sought to evaluate these differences between North America and the rest of the world.

Methods and Results

Databases were searched from their inception through December 2013. Randomized controlled trials comparing the effects of intensive therapy with standard therapy for macro‐ and microvascular complications in adults with type 2 diabetes mellitus were selected. We calculated summary odds ratios (
OR
s) and 95%
CI
s with the random‐effects model. The analysis included 34 967 patients from 17 randomized controlled trials (7 in North America and 10 in the rest of the world). There were no significant differences between intensive and standard therapy groups for all‐cause mortality (
OR
1.03, 95%
CI
0.93 to 1.13) and cardiovascular mortality (
OR
1.09, 95%
CI
0.90 to 1.32). For trials conducted in North America, intensive therapy compared with standard glycemic control resulted in significantly higher all‐cause mortality (
OR
1.21, 95%
CI
1.05 to 1.40) and cardiovascular mortality (
OR
1.41, 95%
CI
1.05 to 1.90) than trials conducted in the rest of the world (all‐cause mortality
OR
0.93, 95%
CI
0.85 to 1.03; interaction P=0.006; cardiovascular mortality
OR
0.89, 95%
CI
, 0.79 to 1.00; interaction P=0.007). Analysis of individual macro‐ and microvascular outcomes revealed no significant regional differences; however, the risk of severe hypoglycemia was significantly higher in trials of intensive therapy in North America (
OR
3.52, 95%
CI
3.07 to 4.03) compared with the rest of the world (
OR
1.45, 95%
CI
0.85 to 2.47; interaction P=0.001).

Conclusion
Randomization to intensive glycemic control in type 2 diabetes mellitus patients was associated with increases in all‐cause mortality, cardiovascular mortality, and severe hypoglycemia in North America compared with the rest of the world. Further investigation into the pathobiology or patient variability underlying these findings is warranted.
Volume Overload and Adverse Outcomes in Chronic Kidney Disease: Clinical Observational and Animal Studies
Authors: Hung Szu‐Chun , Lai Yi‐Shin , Kuo Ko‐Lin , Tarng Der‐Cherng 
Published: May 2015

Background

Volume overload is frequently encountered and is associated with cardiovascular risk factors in patients with chronic kidney disease (
CKD)
. However, the relationship between volume overload and adverse outcomes in
CKD
is not fully understood.

Methods and Results

A prospective cohort of 338 patients with stage 3 to 5
CKD
was followed for a median of 2.1 years. The study participants were stratified by the presence or absence of volume overload, defined as an overhydration index assessed by bioimpedance spectroscopy exceeding 7%, the 90th percentile for the healthy population. The primary outcome was the composite of estimated glomerular filtration rate decline ≥50% or end‐stage renal disease. The secondary outcome included a composite of morbidity and mortality from cardiovascular causes. Animal models were used to simulate fluid retention observed in human
CKD
. We found that patients with volume overload were at a higher risk of the primary and secondary end points in the adjusted Cox models. Furthermore, overhydration appears to be more important than hypertension in predicting an elevated risk. In rats subjected to unilateral nephrectomy and a high‐salt diet, the extracellular water significantly increased. This fluid retention was associated with an increase in blood pressure, proteinuria, renal inflammation with macrophage infiltration and tumor necrosis factor‐α overexpression, glomerular sclerosis, and cardiac fibrosis. Diuretic treatment with indapamide attenuated these changes, suggesting that fluid retention might play a role in the development of adverse outcomes.

Conclusions

Volume overload contributes to
CKD
progression and cardiovascular diseases. Further research is warranted to clarify whether the correction of volume overload would improve outcomes for
CKD
patients.
Is Visual Evaluation of Aneurysm Coiling a Reliable Study End Point?
Authors: Ernst Marielle , Yoo Albert J. , Kriston Levente , Schönfeld Michael H. , Vettorazzi Eik , Fiehler Jens 
Published: May 2015

Background and Purpose—
Angiographic occlusion as a surrogate marker of satisfactory aneurysm treatment is commonly used in clinical trials although some pitfalls have to be considered. To investigate the inter-rater reliability of visual rating of aneurysm occlusion as study end point, we performed a systematic review and meta-analysis.

Methods—
Electronic databases (MEDLINE, EMBASE, PubMed, and the Cochrane Library) were searched up to June 2014. Assessment of risk for bias was based on the Quality Appraisal Tool for Studies of Diagnostic Reliability and the Guidelines for Reporting Reliability and Agreement studies. Inter-rater reliability estimates were pooled across studies using meta-analysis, and the influence of several factors (eg, imaging methods, grading scales, and occlusion rate) was tested with meta-regression.

Results—
From 1193 titles, 644 abstracts and 87 full-text versions were reviewed. Twenty-six articles met the inclusion criteria and provided 77 reliability estimates. Twenty-one different rating scales were used, and statistical analysis varied. Mean inter-rater agreement of the pooled studies was substantial (κ=0.65; 95% confidence interval, 0.60–0.69). Reliability varied significantly as a function of imaging methods, grading scales, occlusion rates, and their interaction. Observer agreement substantially increased with increasing occlusion rate in digital subtraction angiography but not in MR angiography. Reliability was higher in studies using 2- or 3-value grading scales than in studies with 4-value grading scales.

Conclusions—
There is significant heterogeneity between studies evaluating the reliability of visual evaluation of aneurysm coiling. On the basis of our analysis, we found that the combination of magnetic resonance angiography, 3-value grading scale, and 2 trained raters seems most promising for usage as surrogate study end points.