bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome, catabolic sub‐proteomes and key‐metabolites of Desulfobacula toluolica Tol2, a marine, aromatic compound‐degrading, sulfate‐reducing bacterium
Authors: Wöhlbrand Lars , Jacob Jacob H. , Kube Michael , Mussmann Marc , Jarling René , Beck Alfred , Amann Rudolf , Wilkes Heinz , Reinhardt Richard , Rabus Ralf 
Published: September 2012

SummaryAmong the dominant deltaproteobacterial sulfate‐reducing bacteria (SRB), members of the genus Desulfobacula are not only present in (hydrocarbon‐rich) marine sediments, but occur also frequently in the anoxic water bodies encountered in marine upwelling areas. Here, we present the 5.2 Mbp genome of Desulfobacula toluolica Tol2, which is the first of an aromatic compound‐degrading, marine SRB. The genome has apparently been shaped by viral attacks (e.g. CRISPRs) and its high plasticity is reflected by 163 detected genes related to transposases and integrases, a total of 494 paralogous genes and 24 group II introns. Prediction of the catabolic network of strain Tol2 was refined by differential proteome and metabolite analysis of substrate‐adapted cells. Toluene and p‐cresol are degraded by separate suites of specific enzymes for initial arylsuccinate formation via addition to fumarate (p‐cresol‐specific enzyme HbsA represents a new phylogenetic branch) as well as for subsequent modified β‐oxidation of arylsuccinates to the central intermediate benzoyl‐CoA. Proteogenomic evidence suggests specific electron transfer (EtfAB) and membrane proteins to channel electrons from dehydrogenation of both arylsuccinates directly to the membrane redox pool. In contrast to the known anaerobic degradation pathways in other bacteria, strain Tol2 deaminates phenylalanine non‐oxidatively to cinnamate by phenylalanine ammonia‐lyase and subsequently forms phenylacetate (both metabolites identified in 13C‐labelling experiments). Benzoate degradation involves CoA activation, reductive dearomatization by a class II benzoyl‐CoA reductase and hydrolytic ring cleavage as found in the obligate anaerobe Geobacter metallireducens GS‐15. The catabolic sub‐proteomes displayed high substrate specificity, reflecting the genomically predicted complex and fine‐tuned regulatory network of strain Tol2. Despite the genetic equipment for a TCA cycle, proteomic evidence supports complete oxidation of acetyl‐CoA to CO2 via the Wood‐Ljungdahl pathway. Strain Tol2 possesses transmembrane redox complexes similar to that of other Desulfobacteraceae members. The multiple heterodisulfide reductase‐like proteins (more than described for Desulfobacterium autotrophicum HRM2) may constitute a multifaceted cytoplasmic electron transfer network.
Patronage and secularization: social obligation and church support
Authors: Bruce Steve 
Published: September 2012

AbstractAs a contribution to our understanding of secularization in Britain, this paper examines the role of religious patronage. It illustrates nineteenth and early twentieth century support for the churches from rural landowners and major industrial employers, considers its benefits, and explains its rapid disappearance. The paper argues that the end of the expectation that high status individuals and major employers would actively promote organized religion is both significant evidence of secularization and a cause of further decline.
Polymorphic infection and organogenesis patterns induced by a Rhizobium leguminosarum isolate from Lotus root nodules are determined by the host genotype
Authors: Gossmann Jasmin A. , Markmann Katharina , Brachmann Andreas , Rose Laura E. , Parniske Martin 
Published: September 2012

Summary

To sample the natural variation in genes controlling compatibility in the legume–rhizobium symbiosis, we isolated rhizobia from nodules of endemic Lotus species from 21 sites across Europe.

The majority of isolates were identified as Mesorhizobium‐ or Bradyrhizobium‐related and formed nitrogen‐fixing root nodules on Lotus corniculatus and L. pendunculatus, respectively, thus confirming previously defined cross‐inoculation groups.

Rhizobium leguminosarum (Rl) strain Norway, isolated from L. corniculatus nodules, displayed an exceptional phenotypic variation on different Lotus genotypes. On L. burttii, Rl Norway formed infected nodules, whereas tumors and elongated infected swellings were induced on L. glaber and L. japonicus ecotype Nepal, respectively. A symbiosis‐ and Nod‐factor‐responsive promoter:uidA fusion was strongly and rapidly induced in L. japonicus Gifu, but infection threads or signs of nodule organogenesis were absent. This complex phenotypic pattern was not mimicked by either of three engineered R. leguminosarum bv viciae strains producing different Nod‐factor variants. Intriguingly, Rl Norway formed infection threads on Pisum sativum cv Sparkle, but failed to induce organogenesis.

Rl Norway thus uncovered variation in symbiotic capabilities among diploid Lotus species and ecotypes that are obscured by optimally adapted M. loti strains. These contrasting infection and organogenesis phenotypes reveal recent diversification of recognition determinants in Lotus.
Autophagy, mitochondria and 3‐nitropropionic acid joined in the same model
Authors: González‐Polo Rosa A , Bravo‐San Pedro José M , Gómez‐Sánchez Rubén , Pizarro‐Estrella Elisa , Niso‐Santano Mireia , Fuentes José M 
Published: September 2012

Huntington's disease (HD) is a neurodegenerative disorder caused by a mutation in the gene encoding the huntingtin protein. Although the precise mechanism by which neuronal degeneration occurs is still unclear, several elements are important to its development: (1) altered gene expression and protein synthesis, (2) mitochondrial damage and (3) improper regulation of the autophagy programme. In this issue of British Journal of Pharmacology, Galindo and co‐workers provide the first evidence for a role of the mitochondrial permeability transition pore (mPTP) in mitochondrial fragmentation and autophagy activation. In a model of cell death induced by 3‐nitropropionic acid (3‐NP) in human neural cells, the authors describe clear functions for mPTP and Bax, but not the mitochondrial fusion/fission machinery, mitochondrial fragmentation and autophagy (mitophagy). This commentary summarises the significance of this relationship and suggests several points for future development.Linked ArticleThis article is a commentary on Solesio et al., pp. 63–75 of this issue. To view this paper visit http://dx.doi.org/10.1111/j.1476‐5381.2012.01994.x
Exclusion netting may alter reproduction of the codling moth (Cydia pomonella) and prevent associated fruit damage to apple orchards
Authors: Sauphanor Benoit , Severac Guilhem , Maugin Sandrine , Toubon Jean François , Capowiez Yvan 
Published: September 2012

AbstractInsecticide‐based management programmes targeting codling moth, Cydia pomonella L. (Lepidoptera: Tortricidae: Olethreutinae), in apple orchards in southern France have incurred increasing levels of fruit injury in recent years. An alternative programme incorporating the use of exclusion netting named Alt'carpo has been developed. This study aimed at studying its efficiency and gaining more insight into its mode of action. This was achieved through laboratory and field behavioural tests and observations in a network of commercial orchards in southern France. The moths were able to lay eggs through the nets and escape from net cages in the laboratory. Male moths released in the netted rows were poorly recaptured using sexual pheromone trapping, whereas over 20% of the released males were recaptured in unprotected rows. The netting reduced fruit injury by up to 91% compared to the unprotected rows in the experimental orchard. The efficacy of this netting was even higher in commercial orchards in which fruit injury did not exceed 0.1% without any application of specific insecticide. These results lead us to assume that netting alters the reproduction of the pest, mainly by preventing it from flying over the canopy to find mates.
Application of Selected Ion Flow Tube Mass Spectrometry Coupled with Chemometrics to Study the Effect of Location and Botanical Origin on Volatile Profile of Unifloral American Honeys
Authors: Agila Amal , Barringer Sheryl 
Published: September 2012

Abstract:  Ten Ohio and Indiana honey samples from star thistle (Centaurea Americana), blueberry (Vaccinium spp.), clover (Trifolium spp.), cranberry (Vaccinium spp.), wildflower, and an unknown source were collected. The headspace of these honeys was analyzed by selected ion flow tube mass spectrometry and soft independent modeling of class analogy (SIMCA). SIMCA was utilized to statistically differentiate between honeys based on their composition. Ohio honeys from star thistle, blueberry, and clover were similar to each other in volatile composition, while Ohio wildflower honey was different. Indiana honeys from star thistle, blueberry, and wildflower were different from each other in volatile composition, while clover and cranberry honeys were similar. Honeys from Ohio and Indiana with the same floral origins were different in volatile composition. Furfural, 1‐octen‐3‐ol, butanoic, and pentanoic acids were the volatiles with the highest discriminating power between types of floral honey. Methanol and ethanol followed by acetic acid were at the highest levels in most honeys, though furfural was at the highest concentration in Indiana blueberry honey, while 1‐octen‐3‐ol was at the highest concentration in Indiana wildflower honey. The highest concentration of volatile compounds was in Indiana wildflower honey followed by Ohio wildflower honey, while the lowest concentration of volatile compounds was observed in Ohio clover honey followed by Indiana clover honey.Practical Application:  Using chemometrics, concentrations of volatile compounds in different honeys can be used to determine the influence of botanical and geographical origins on aroma, which is important for the quality of honey. Characterization of volatile compounds can also be a useful tool for assessing honey quality.
Killing Bacterial Spores with Blue Light: When Innate Resistance Meets the Power of Light
Authors: St. Denis Tyler G. , Dai Tianhong , Hamblin Michael R. 
Published: September 2012

AbstractThis article is a highlight of the study by Maclean et al. in this issue of Photochemistry and Photobiology describing the sporicidal effects 405 nm visible light alone on endospores of the Clostridium and Bacillus genera. 1.73 kJ cm−2 was capable of reducing endospore colony‐forming units by up to 4‐log10. These findings have never been previously demonstrated and may be incorporated into decontamination methods that span medical, military and food preparatory applications.
Differences in peri‐implant conditions between fully and partially edentulous subjects: a systematic review
Authors: de Waal Yvonne C. M. , van Winkelhoff Arie Jan , Meijer Henny J. A. , Raghoebar Gerry M. , Winkel Edwin G. 
Published: September 2012

AbstractAimThe aim of this study was to compare peri‐implant conditions between fully edentulous (FES) and partially edentulous subjects (PES).Material and methodsA systematic review was conducted. The MEDLINE, EMBASE and COCHRANE databases were searched for publications up to January 1st 2012. Studies reporting on the bleeding tendency of the peri‐implant mucosa and/or studies reporting on the prevalence of peri‐implant mucositis and/or peri‐implantitis were considered.ResultsFifty‐five publications describing 46 studies were selected. One study described both FES and PES, and all other studies described either FES or PES. Subgroup analyses were performed according to dental status (fully/partially edentulous), follow‐up time (≥5 years and ≥ 10 years) and study design (prospective/cross‐sectional). FES harboured more plaque at their implants than PES. Modified bleeding index scores were significantly higher in FES, but no differences in bleeding on probing, implant loss and probing pocket depth were observed between FES and PES. No meta‐analysis could be performed on prevalence of peri‐implant mucositis and peri‐implantitis. Overall prevalence of peri‐implantitis was 0–3.4% after 5 years and 5.8–16.9% after 10 years of implant evaluation.ConclusionFES and PES show comparable implant survival rates. However, no conclusion can be drawn regarding differences in prevalence of peri‐implant mucositis and peri‐implantitis between FES and PES.
Effects of periodontal therapy on disease activity and systemic inflammation in rheumatoid arthritis patients
Authors: Erciyas K , Sezer U , Üstün K , Pehlivan Y , Kısacık B , Şenyurt SZ , Tarakçıoğlu M , Onat AM 
Published: September 2012

ObjectiveThis observational prospective cohort study aimed to evaluate the effects of non‐surgical periodontal treatment on clinical periodontal measurements and systemic inflammatory mediator levels in low or moderate to highly active rheumatoid arthritis (RA) patients with chronic periodontitis.Subjects and methodsRheumatoid arthritis activity was assessed with disease activity score test (DAS28). Thirty patients with RA with moderate to high disease activity (DAS28 ≥ 3.2) and chronic periodontitis (MHDA group) and thirty patients with RA with low disease activity (DAS28 < 3.2) and chronic periodontitis (LDA group) were enrolled in the study. The patients were monitored at the beginning and 3 months after undergoing periodontal therapy. Erythrocyte sedimentation rate (ESR), C‐reactive protein (CRP), tumour necrosis factor‐alpha (TNF‐α) levels in serum, DAS28 and periodontal parameters were evaluated.ResultsErythrocyte sedimentation rate, CRP, TNF‐α levels in serum, DAS28 and periodontal parameters exhibited similar and significant reduction 3 months after the non‐surgical periodontal treatment.ConclusionNon‐surgical periodontal treatment may prove beneficial in reducing RA severity as measured by ESR, CRP, TNF‐α levels in serum and DAS28 in low or moderate to highly active RA patients with chronic periodontitis.
Inhibitors of Reactive Oxygen Species Accumulation Delay and/or Reduce the Lethality of Several Antistaphylococcal Agents
Authors: Liu Yuanli , Liu Xinghan , Qu Yilin , Wang Xiuhong , Li Liping , Zhao Xilin 
Published: September 2012

ABSTRACT

Perturbation of hydroxyl radical accumulation by subinhibitory concentrations of 2,2′-bipyridyl plus thiourea protects
Escherichia coli
from being killed by 3 lethal antimicrobial classes. Here, we show that 2,2′-bipyridyl plus thiourea delays and/or reduces antimicrobial killing of
Staphylococcus aureus
by daptomycin, moxifloxacin, and oxacillin. While the protective effect of 2,2′-bipyridyl plus thiourea varied among strains and compounds, the data support the hypothesis that hydroxyl radical enhances antimicrobial lethality.
Effect of Maraviroc on HIV Disease Progression-Related Biomarkers
Authors: Romero-Sánchez M. Concepción , Machmach Kawthar , Gonzalez-Serna Alejandro , Genebat Miguel , Pulido Ildefonso , García-García María , Álvarez-Ríos Ana Isabel , Ferrando-Martinez Sara , Ruiz-Mateos Ezequiel , Leal Manuel 
Published: September 2012

ABSTRACT

The potential effect of blocking the CCR5 receptor on HIV disease progression biomarkers is not well understood. We showed that an 8-day maraviroc (MVC) monotherapy clinical test (MCT) can be used in selecting patients to receive MVC-containing combined antiretroviral therapy (cART). Using this MCT model, we assessed the effect of MVC on several HIV disease progression biomarkers during the MCT (MVC-specific effect) and following short-term (12-week) cART. We compared 45 patients on MVC monotherapy with a control group of 25 patients on MVC-sparing cART. We found that MVC did not modify any biomarkers in patients that had no virological response after the MCT. MVC-specific effects in patients with virological responses included increased CD8
+
T-cell activation and senescence levels, preservation of an increase in soluble CD14 (sCD14), and a decrease in D dimer levels. After 12 weeks, MVC-containing cART increased CD8
+
T-cell counts and preserved CD4
+
T-cell senescence levels compared with MVC-sparing cART. Moreover, there was a decrease in sCD14 levels in patients that received MVC-containing cART. In conclusion, effects compatible with CD8
+
T-cell redistribution in peripheral blood were observed after MVC therapy. However, MVC was associated with a favorable profile in HIV disease progression biomarkers only in patients with a virological response. These results support a potential clinical benefit of a therapy which includes MVC in HIV-infected patients.
Mode of Action,
In Vitro
Activity, and
In Vivo
Efficacy of AFN-1252, a Selective Antistaphylococcal FabI Inhibitor
Authors: Kaplan Nachum , Albert Monique , Awrey Donald , Bardouniotis Elias , Berman Judd , Clarke Teresa , Dorsey Mandy , Hafkin Barry , Ramnauth Jaillal , Romanov Vladimir , Schmid Molly B. , Thalakada Rosanne , Yethon Jeremy , Pauls Henry W. 
Published: September 2012

ABSTRACT

The mechanism of action of AFN-1252, a selective inhibitor of
Staphylococcus aureus
enoyl-acyl carrier protein reductase (FabI), which is involved in fatty acid biosynthesis, was confirmed by using biochemistry, macromolecular synthesis, genetics, and cocrystallization of an AFN-1252–FabI complex. AFN-1252 demonstrated a low propensity for spontaneous resistance development and a time-dependent reduction of the viability of both methicillin-susceptible and methicillin-resistant
S. aureus
, achieving a ≥2-log
10
reduction in
S. aureus
counts over 24 h, and was extremely potent against clinical isolates of
S. aureus
(MIC
90
, 0.015 μg/ml) and coagulase-negative staphylococci (MIC
90
, 0.12 μg/ml), regardless of their drug resistance, hospital- or community-associated origin, or other clinical subgroup. AFN-1252 was orally available in mouse pharmacokinetic studies, and a single oral dose of 1 mg/kg AFN-1252 was efficacious in a mouse model of septicemia, providing 100% protection from an otherwise lethal peritoneal infection of
S. aureus
Smith. A median effective dose of 0.15 mg/kg indicated that AFN-1252 was 12 to 24 times more potent than linezolid in the model. These studies, demonstrating a selective mode of action, potent
in vitro
activity, and
in vivo
efficacy, support the continued investigation of AFN-1252 as a targeted therapeutic for staphylococcal infections.
Monte Carlo simulation of the radiolysis of the ceric sulfate dosimeter by low linear energy transfer radiation
Authors: Plante Ianik , Tippayamontri Thititip , Autsavapromporn Narongchai , Meesungnoen Jintana , Jay-Gerin Jean-Paul 
Published: September 2012

The ceric sulfate dosimeter is based on the radio-induced reduction of Ce4+ in acidic medium. For low linear energy transfer (LET) radiation, the yield of Ce3+ is 2.4 molecules / 100 eV, regardless of the presence of oxygen. To investigate the reaction mechanisms of the ceric sulfate dosimeter, we simulated the chemical reaction kinetics curves and the evolution of G(Ce3+), G(O2), and G(H2) in the ceric sulfate solution with and without oxygen. Studies of G(Ce3+) as function of the initial concentration of Ce3+ and of the LET were also done. One important finding of this study is that •OH radicals are scavenged by the reaction •OH + HSO4– → SO4•– + H2O, rather than by the reaction •OH + Ce3+ → Ce4+ + OH–.
Sorafenib Has Potent Antitumor Activity against Multiple Myeloma In Vitro, Ex Vivo, and In Vivo in the 5T33MM Mouse Model
Authors: Kharaziha Pedram , De Raeve Hendrik , Fristedt Charlotte , Li Qiao , Gruber Astrid , Johnsson Per , Kokaraki Georgia , Panzar Maria , Laane Edward , Österborg Anders , Zhivotovsky Boris , Jernberg-Wiklund Helena , Grandér Dan , Celsing Fredrik , Björkholm Magnus , Vanderkerken Karin , Panaretakis Theocharis 
Published: September 2012

Abstract
Multiple myeloma (MM) is a B-cell malignancy characterized by the expansion of clonal plasma blasts/plasma cells within the bone marrow that relies on multiple signaling cascades, including tyrosine kinase activated pathways, to proliferate and evade cell death. Despite emerging new treatment strategies, multiple myeloma remains at present incurable. Thus, novel approaches targeting several signaling cascades by using the multi-tyrosine kinase inhibitor (TKI), sorafenib, seem a promising treatment approach for multiple myeloma. Here, we show that sorafenib induces cell death in multiple myeloma cell lines and in CD138+-enriched primary multiple myeloma patient samples in a caspase-dependent and -independent manner. Furthermore, sorafenib has a strong antitumoral and -angiogenic activity in the 5T33MM mouse model leading to increased overall survival. Multiple myeloma cells undergo autophagy in response to sorafenib, and inhibition of this cytoprotective pathway potentiated the efficacy of this TKI. Mcl-1, a survival factor in multiple myeloma, is downregulated at the protein level by sorafenib allowing for the execution of cell death, as ectopic overexpression of this protein protects multiple myeloma cells. Concomitant targeting of Mcl-1 by sorafenib and of Bcl-2/Bcl-xL by the antagonist ABT737 improves the efficacy of sorafenib in multiple myeloma cell lines and CD138+-enriched primary cells in the presence of bone marrow stromal cells. Altogether, our data support the use of sorafenib as a novel therapeutic modality against human multiple myeloma, and its efficacy may be potentiated in combination with ABT737. Cancer Res; 72(20); 5348–62. ©2012 AACR.
Development of 2 Registry-Based Risk Models Suitable for Characterizing Hospital Performance on 30-Day All-Cause Mortality Rates Among Patients Undergoing Percutaneous Coronary Intervention
Authors: Curtis Jeptha P. , Geary Lori L. , Wang Yongfei , Chen Jersey , Drye Elizabeth E. , Grosso Laura M. , Spertus John A. , Rumsfeld John S. , Weintraub William S. , Masoudi Frederick A. , Brindis Ralph G. , Krumholz Harlan M. 
Published: September 2012

Background—
Variation in outcomes after percutaneous coronary interventions (PCI) may reflect differences in quality of care. To date, however, we lack a methodology to monitor and improve national hospital 30-day mortality rates among patients undergoing PCI.

Methods and Results—
We developed hierarchical logistic regression models to calculate hospital risk-standardized 30-day all-cause PCI mortality rates. Due to differences in risk, patients were divided into 2 cohorts: those with ST-segment elevation myocardial infarction or cardiogenic shock, and those with no ST-segment elevation myocardial infarction and no cardiogenic shock. The models were derived using 2006 data from the CathPCI Registry linked with administrative claims data, and validated using comparable 2005 data. In the derivation cohort of the ST-segment elevation myocardial infarction or shock model (n=15 123), the unadjusted 30-day mortality rate was 9.2%. The final model included 13 variables with the observed mortality rates ranging from 1.4% to 40.3% across deciles of the predicted patient mortality rates. The 25th and 75th percentiles of the risk-standardized mortality rate were 8.5% and 9.7%, with 5th and 95th percentiles of 7.6% and 11.0%. In the derivation cohort of the no ST-segment elevation myocardial infarction and no shock model (n=110 529), the unadjusted 30-day mortality rate was 1.4%. The final model included 16 variables with the observed predicted mortality rates ranging from 0.1% to 7.0% across deciles of the predicted patient mortality rates. The 25th and 75th percentiles of the risk-standardized mortality rate across 612 hospitals were 1.3% and 1.6%, with 5th and 95th percentiles of 1.0% and 2.0%.

Conclusions—
These National Quality Forum endorsed registry-based models produce estimates of hospital risk-standardized mortality rates for patients undergoing PCI.