bluuebunny/crossref_metadata_2025_split huggingface dataset:
C/N Ratio Drives Soil Actinobacterial Cellobiohydrolase Gene Diversity
Authors: de Menezes Alexandre B. , Prendergast-Miller Miranda T. , Poonpatana Pabhon , Farrell Mark , Bissett Andrew , Macdonald Lynne M. , Toscas Peter , Richardson Alan E. , Thrall Peter H. 
Published: February 2015

ABSTRACTCellulose accounts for approximately half of photosynthesis-fixed carbon; however, the ecology of its degradation in soil is still relatively poorly understood. The role of actinobacteria in cellulose degradation has not been extensively investigated despite their abundance in soil and known cellulose degradation capability. Here, the diversity and abundance of the actinobacterial glycoside hydrolase family 48 (cellobiohydrolase) gene in soils from three paired pasture-woodland sites were determined by using terminal restriction fragment length polymorphism (T-RFLP) analysis and clone libraries with gene-specific primers. For comparison, the diversity and abundance of general bacteria and fungi were also assessed. Phylogenetic analysis of the nucleotide sequences of 80 clones revealed significant new diversity of actinobacterial GH48 genes, and analysis of translated protein sequences showed that these enzymes are likely to represent functional cellobiohydrolases. The soil C/N ratio was the primary environmental driver of GH48 community compositions across sites and land uses, demonstrating the importance of substrate quality in their ecology. Furthermore, mid-infrared (MIR) spectrometry-predicted humic organic carbon was distinctly more important to GH48 diversity than to total bacterial and fungal diversity. This suggests a link between the actinobacterial GH48 community and soil organic carbon dynamics and highlights the potential importance of actinobacteria in the terrestrial carbon cycle.
An Inexpensive, Accurate, and Precise Wet-Mount Method for Enumerating Aquatic Viruses
Authors: Cunningham Brady R. , Brum Jennifer R. , Schwenck Sarah M. , Sullivan Matthew B. , John Seth G. 
Published: February 2015

ABSTRACT

Viruses affect biogeochemical cycling, microbial mortality, gene flow, and metabolic functions in diverse environments through infection and lysis of microorganisms. Fundamental to quantitatively investigating these roles is the determination of viral abundance in both field and laboratory samples. One current, widely used method to accomplish this with aquatic samples is the “filter mount” method, in which samples are filtered onto costly 0.02-μm-pore-size ceramic filters for enumeration of viruses by epifluorescence microscopy. Here we describe a cost-effective (ca. 500-fold-lower materials cost) alternative virus enumeration method in which fluorescently stained samples are wet mounted directly onto slides, after optional chemical flocculation of viruses in samples with viral concentrations of <5 × 10
7
viruses ml
−1
. The concentration of viruses in the sample is then determined from the ratio of viruses to a known concentration of added microsphere beads via epifluorescence microscopy. Virus concentrations obtained by using this wet-mount method, with and without chemical flocculation, were significantly correlated with, and had precision equivalent to, those obtained by the filter mount method across concentrations ranging from 2.17 × 10
6
to 1.37 × 10
8
viruses ml
−1
when tested by using cultivated viral isolates and natural samples from marine and freshwater environments. In summary, the wet-mount method is significantly less expensive than the filter mount method and is appropriate for rapid, precise, and accurate enumeration of aquatic viruses over a wide range of viral concentrations (≥1 × 10
6
viruses ml
−1
) encountered in field and laboratory samples.
Preferential Association of Endophytic Bradyrhizobia with Different Rice Cultivars and Its Implications for Rice Endophyte Evolution
Authors: Piromyou Pongdet , Greetatorn Teerana , Teamtisong Kamonluck , Okubo Takashi , Shinoda Ryo , Nuntakij Achara , Tittabutr Panlada , Boonkerd Nantakorn , Minamisawa Kiwamu , Teaumroong Neung 
Published: February 2015

ABSTRACT

Plant colonization by bradyrhizobia is found not only in leguminous plants but also in nonleguminous species such as rice. To understand the evolution of the endophytic symbiosis of bradyrhizobia, the effect of the ecosystems of rice plantations on their associations was investigated. Samples were collected from various rice (
Oryza sativa
) tissues and crop rotational systems. The rice endophytic bradyrhizobia were isolated on the basis of oligotrophic properties, selective medium, and nodulation on siratro (
Macroptilium atropurpureum
). Six bradyrhizobial strains were obtained exclusively from rice grown in a crop rotational system. The isolates were separated into photosynthetic bradyrhizobia (PB) and nonphotosynthetic bradyrhizobia (non-PB). Thai bradyrhizobial strains promoted rice growth of Thai rice cultivars better than the Japanese bradyrhizobial strains. This implies that the rice cultivars possess characteristics that govern rice-bacterium associations. To examine whether leguminous plants in a rice plantation system support the persistence of rice endophytic bradyrhizobia, isolates were tested for legume nodulation. All PB strains formed symbioses with
Aeschynomene indica
and
Aeschynomene evenia
. On the other hand, non-PB strains were able to nodulate
Aeschynomene americana
,
Vigna radiata
, and
M. atropurpureum
but unable to nodulate either
A. indica
or
A. evenia
. Interestingly, the
nodABC
genes of all of these bradyrhizobial strains seem to exhibit low levels of similarity to those of
Bradyrhizobium diazoefficiens
USDA110 and
Bradyrhizobium
sp. strain ORS285. From these results, we discuss the evolution of the plant-bradyrhizobium association, including nonlegumes, in terms of photosynthetic lifestyle and
nod
-independent interactions.
Monitoring F165
1
P-Like Fimbria Expression at the Single-Cell Level Reveals a Highly Heterogeneous Phenotype
Authors: Graveline Richard , Lavoie Rémi , Garneau Philippe , Daigle France , Sénéchal Serge , Martin Christine , Harel Josée 
Published: February 2015

ABSTRACT

F165
1
and the pyelonephritis-associated pili (Pap) are two members of the type P family of adhesive factors. They play a key role in establishing disease caused by extraintestinal pathogenic
Escherichia coli
(ExPEC) strains in animals and humans. Both F165
1
and Pap are under the control of an epigenetic and reversible switch that defines the number of fimbriated (ON) and afimbriated (OFF) cells within a clonal population. Using the Gfp reporter system, we monitored
in vitro
the level of fluorescence intensity corresponding to the F165
1
and Pap fimbrial synthesis. Monitoring individual
Escherichia coli
cells by flow cytometry and by real-time fluorescence microscopy, we identified cells associated with a low or high level of fluorescence intensity and a large amount of cells with partial levels of fluorescence, mostly present in the F165
1
system. This mixed population identified through fluorescence intensity could be attributed to the high switching rate previously observed in F165
1
-positive bacteria. The fimbrial heterogeneous phenotype for these ExPEC could represent increased fitness in unpredictable environments. Our study illustrates that within the large repertoire of fimbrial variants such as the well-characterized Pap, F165
1
is an exquisite example of regulatory expression that arms the bacterium with strategies for surviving in more than one particular environment.
In Vitro
Passage Selects for Chlamydia muridarum with Enhanced Infectivity in Cultured Cells but Attenuated Pathogenicity in Mouse Upper Genital Tract
Authors: Chen Chaoqun , Zhou Zhou , Conrad Turner , Yang Zhangsheng , Dai Jin , Li Zhongyu , Wu Yimou , Zhong Guangming 
Published: February 2015

ABSTRACT

Although modern
Chlamydia muridarum
has been passaged for decades, there are no reports on the consequences of serial passage with strong selection pressure on its fitness. In order to explore the potential for Pasteurian selection to induce genomic and phenotypic perturbations to
C. muridarum
, a starter population was passaged in cultured cells for 28 generations without standard infection assistance. The resultant population, designated CMG28, displays markedly reduced
in vitro
dependence on centrifugation for infection and low incidence and severity of upper genital tract pathology following intravaginal inoculation into mice compared to the parental
C. muridarum
population, CMG0. Deep sequencing of CMG0 and CMG28 revealed novel protein variants in the hypothetical genes TC0237 (Q117E) and TC0668 (G322R).
In vitro
attachment assays of isogenic plaque clone pairs with mutations in either TC0237 and TC0668 or only TC0237 reveal that TC0237(Q117E) is solely responsible for enhanced adherence to host cells. Paradoxically, double mutants, but not TC0237(Q117E) single mutants, display severely attenuated
in vivo
pathogenicity. These findings implicate TC0237 and TC0668 as novel genetic factors involved in chlamydial attachment and pathogenicity, respectively, and show that serial passage under selection pressure remains an effective tool for studying
Chlamydia
pathogenicity.
High-Throughput Analysis of Gene Essentiality and Sporulation in Clostridium difficile
Authors: Dembek Marcin , Barquist Lars , Boinett Christine J. , Cain Amy K. , Mayho Matthew , Lawley Trevor D. , Fairweather Neil F. , Fagan Robert P. 
Published: February 2015

ABSTRACT

Clostridium difficile
is the most common cause of antibiotic-associated intestinal infections and a significant cause of morbidity and mortality. Infection with C. difficile requires disruption of the intestinal microbiota, most commonly by antibiotic usage. Therapeutic intervention largely relies on a small number of broad-spectrum antibiotics, which further exacerbate intestinal dysbiosis and leave the patient acutely sensitive to reinfection. Development of novel targeted therapeutic interventions will require a detailed knowledge of essential cellular processes, which represent attractive targets, and species-specific processes, such as bacterial sporulation. Our knowledge of the genetic basis of C. difficile infection has been hampered by a lack of genetic tools, although recent developments have made some headway in addressing this limitation. Here we describe the development of a method for rapidly generating large numbers of transposon mutants in clinically important strains of C. difficile. We validated our transposon mutagenesis approach in a model strain of C. difficile and then generated a comprehensive transposon library in the highly virulent epidemic strain R20291 (027/BI/NAP1) containing more than 70,000 unique mutants. Using transposon-directed insertion site sequencing (TraDIS), we have identified a core set of 404 essential genes, required for growth
in vitro
. We then applied this technique to the process of sporulation, an absolute requirement for C. difficile transmission and pathogenesis, identifying 798 genes that are likely to impact spore production. The data generated in this study will form a valuable resource for the community and inform future research on this important human pathogen.

IMPORTANCE
Clostridium difficile
is a common cause of potentially fatal intestinal infections in hospital patients, particularly those who have been treated with antibiotics. Our knowledge of this bacterium has been hampered by a lack of tools for dissecting the organism. We have developed a method to study the function of every gene in the bacterium simultaneously. Using this tool, we have identified a set of 404 genes that are required for growth of the bacteria in the laboratory. C. difficile also produces a highly resistant spore that can survive in the environment for a long time and is a requirement for transmission of the bacteria between patients. We have applied our genetic tool to identify all of the genes required for production of a spore. All of these genes represent attractive targets for new drugs to treat infection.
Toxin Synthesis by Clostridium difficile Is Regulated through Quorum Signaling
Authors: Darkoh Charles , DuPont Herbert L. , Norris Steven J. , Kaplan Heidi B. 
Published: February 2015

ABSTRACT

Clostridium difficile
infection (CDI) is dramatically increasing as a cause of antibiotic- and hospital-associated diarrhea worldwide. C. difficile, a multidrug-resistant pathogen, flourishes in the colon after the gut microbiota has been altered by antibiotic therapy. Consequently, it produces toxins A and B that directly cause disease. Despite the enormous public health problem posed by this pathogen, the molecular mechanisms that regulate production of the toxins, which are directly responsible for disease, remained largely unknown until now. Here, we show that C. difficile toxin synthesis is regulated by an accessory gene regulator quorum-signaling system, which is mediated through a small (<1,000-Da) thiolactone that can be detected directly in stools of CDI patients. These findings provide direct evidence of the mechanism of regulation of C. difficile toxin synthesis and offer exciting new avenues both for rapid detection of C. difficile infection and development of quorum-signaling-based non-antibiotic therapies to combat this life-threatening emerging pathogen.

IMPORTANCE
Clostridium difficile
infection (CDI) is the most common definable cause of hospital-acquired and antibiotic-associated diarrhea in the United States, with the total cost of treatment estimated between 1 and 4.8 billion U.S. dollars annually. C. difficile, a Gram-positive, spore-forming anaerobe, flourishes in the colon after the gut microbiota has been altered by antibiotic therapy. As a result, there is an urgent need for non-antibiotic CDI treatments that preserve the colonic microbiota. C. difficile produces toxins A and B, which are directly responsible for disease. Here, we report that C. difficile regulates its toxin synthesis by quorum signaling, in which a novel signaling peptide activates transcription of the disease-causing toxin genes. This finding provides new therapeutic targets to be harnessed for novel nonantibiotic therapy for C. difficile infections.
The ‘Best Practice Guide to Conservative Management of Patellofemoral Pain’: incorporating level 1 evidence with expert clinical reasoning
Authors: Barton Christian John , Lack Simon , Hemmings Steph , Tufail Saad , Morrissey Dylan 
Published: February 2015

ImportancePatellofemoral pain (PFP) is both chronic and prevalent; it has complex aetiology and many conservative treatment options.ObjectiveDevelop a comprehensive contemporary guide to conservative management of PFP outlining key considerations for clinicians to follow.DesignMixed methods.MethodsWe synthesised the findings from sixhigh-qualitysystematic reviews to September 2013 with the opinions of 17 experts obtained via semistructured interviews. Experts had at least 5 years clinical experience with PFP as a specialist focus, were actively involved in PFP research and contributed to specialist international meetings. The interviews covered clinical reasoning, perception of current evidence and research priorities.ResultsMultimodal intervention including exercise to strengthen the gluteal and quadriceps musculature, manual therapy and taping possessed the strongest evidence. Evidence also supports use of foot orthoses and acupuncture. Interview transcript analysis identified 23 themes and 58 subthemes. Four key over-arching principles to ensure effective management included—(1) PFP is a multifactorial condition requiring an individually tailored multimodal approach. (2) Immediate pain relief should be a priority to gain patient trust. (3) Patient empowerment by emphasising active over passive interventions is important. (4) Good patient education and activity modification is essential. Future research priorities include identifying risk factors, testing effective prevention, developing education strategies, evaluating the influence of psychosocial factors on treatment outcomes and how to address them, evaluating the efficacy of movement pattern retraining and improving clinicians’ assessment skills to facilitate optimal individual prescription.Conclusions and relevanceEffective management of PFP requires consideration of a number of proven conservative interventions. An individually tailored multimodal intervention programme including gluteal and quadriceps strengthening, patellar taping and an emphasis on education and activity modification should be prescribed for patients with PFP. We provide a ‘Best Practice Guide to Conservative Management of Patellofemoral Pain’ outlining key considerations.
Abortion legislation, maternal healthcare, fertility, female literacy, sanitation, violence against women and maternal deaths: a natural experiment in 32 Mexican states
Authors: Koch Elard , Chireau Monique , Pliego Fernando , Stanford Joseph , Haddad Sebastian , Calhoun Byron , Aracena Paula , Bravo Miguel , Gatica Sebastián , Thorp John 
Published: February 2015

ObjectiveTo test whether there is an association between abortion legislation and maternal mortality outcomes after controlling for other factors thought to influence maternal health.DesignPopulation-based natural experiment.Setting and data sourcesOfficial maternal mortality data from 32 federal states of Mexico between 2002 and 2011.Main outcomesMaternal mortality ratio (MMR), MMR with any abortive outcome (MMRAO) and induced abortion mortality ratio (iAMR).Independent variablesAbortion legislation grouped as less (n=18) or more permissive (n=14); constitutional amendment protecting the unborn (n=17); skilled attendance at birth; all-abortion hospitalisation ratio; low birth weight rate; contraceptive use; total fertility rates (TFR); clean water; sanitation; female literacy rate and intimate-partner violence.Main resultsOver the 10-year period, states with less permissive abortion legislation exhibited lower MMR (38.3 vs 49.6; p<0.001), MMRAO(2.7 vs 3.7; p<0.001) and iAMR (0.9 vs 1.7; p<0.001) than more permissive states. Multivariate regression models estimating effect sizes (β-coefficients) for mortality outcomes showed independent associations (p values between 0.001 and 0.055) with female literacy (β=−0.061 to −1.100), skilled attendance at birth (β=−0.032 to −0.427), low birth weight (β=0.149 to 2.166), all-abortion hospitalisation ratio (β=−0.566 to −0.962), clean water (β=−0.048 to −0.730), sanitation (β=−0.052 to −0.758) and intimate-partner violence (β=0.085 to 0.755). TFR showed an inverse association with MMR (β=−14.329) and MMRAO(β=−1.750) and a direct association with iAMR (β=1.383). Altogether, these factors accounted for (R2) 51–88% of the variance among states in overall mortality rates. No statistically independent effect was observed for abortion legislation, constitutional amendment or other covariates.ConclusionsAlthough less permissive states exhibited consistently lower maternal mortality rates, this finding was not explained by abortion legislation itself. Rather, these differences were explained by other independent factors, which appeared to have a more favourable distribution in these states.
Evaluating variation in use of definitive therapy and risk-adjusted prostate cancer mortality in England and the USA
Authors: Sachdeva Ashwin , van der Meulen Jan H , Emberton Mark , Cathcart Paul J 
Published: February 2015

ObjectivesProstate cancer mortality (PCM) in the USA is among the lowest in the world, whereas PCM in England is among the highest in Europe. This paper aims to assess the association of variation in use of definitive therapy on risk-adjusted PCM in England as compared with the USA.DesignObservational study.SettingCancer registry data from England and the USA.ParticipantsMen diagnosed with non-metastatic prostate cancer (PCa) in England and the USA between 2004 and 2008.Outcome measuresCompeting-risks survival analyses to estimate subhazard ratios (SHR) of PCM adjusted for age, ethnicity, year of diagnosis, Gleason score (GS) and clinical tumour (cT) stage.Results222 163 men were eligible for inclusion. Compared with American patients, English patients were more likely to present at an older age (70–79 years: England 44.2%, USA 29.3%, p<0.001), with higher tumour stage (cT3-T4: England 25.1%, USA 8.6%, p<0.001) and higher GS (GS 8–10: England 20.7%, USA 11.2%, p<0.001). They were also less likely to receive definitive therapy (England 38%, USA 77%, p<0.001).English patients were more likely to die of PCa (SHR=1.9, 95% CI 1.7 to 2.0, p<0.001). However, this difference was no longer statistically significant when also adjusted for use of definitive therapy (SHR=1.0, 95% CI 1.0 to 1.1, p=0.3).ConclusionsRisk-adjusted PCM is significantly higher in England compared with the USA. This difference may be explained by less frequent use of definitive therapy in England.
Statin use and risk of haemorrhagic stroke in a community-based cohort of postmenopausal women: an observational study from the Women's Health Initiative
Authors: Salmoirago-Blotcher Elena , Hovey Kathleen M , Andrews Christopher A , Robinson Jennifer G , Johnson Karen C , Wassertheil-Smoller Sylvia , Crawford Sybil , Qi Lihong , Martin Lisa W , Ockene Judith , Manson JoAnn E 
Published: February 2015

ObjectivesTo determine whether statin treatment is associated with increased risk of haemorrhagic stroke (HS) in older women. A secondary objective was to evaluate HS risk in users of combined statin and antiplatelet treatment.DesignObservational study: secondary data analysis from the Women's Health Initiative (WHI) clinical trials.SettingWomen were recruited from 40 participating sites.ParticipantsCohort of 68 132 women followed through 2005 (parent study) and for an additional 5 years in the extension study.Main outcome measuresStatin use was assessed at baseline and at follow-up visits (1, 3, 6 and 9 years). Women brought medications in original containers for inventory. Strokes were ascertained semiannually and centrally adjudicated. Risk of HS by statin use (time-varying covariate, with the ‘no use’ category as the referent) was estimated from Cox proportional hazard regression models adjusted for age (model 1); risk factors for HS (model 2); and possible confounders by indication (model 3). Prespecified subgroup analyses were conducted by use of antiplatelet medications.ResultsFinal models included 67 882 women (mean age, 63±7 years). Over a mean follow-up of 12 years, incidence rates of HS were 6.4/10 000 person-years among statin users and 5.0/10 000 person-years among non-users (p=0.11). The unadjusted risk of HS in statin users was 1.21 (CI 0.96 to 1.53); after adjusting for age and HS risk factors the HR was 0.98 (CI 0.76 to 1.26). Risk of HS was higher among women on statins and antiplatelet agents versus women on antiplatelet medications alone (HR=1.59; CI 1.03 to 2.47); p for interaction=0.011.ConclusionsThis retrospective analysis did not show an association between statin use and HS risk among older women. HS risk was higher among women taking statins with antiplatelet agents. These findings warrant further investigation, given potential implications for clinical decision-making.