bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of 3-Chloroaniline on the Biofilm Lifestyle of Comamonas testosteroni and Its Implications on Bioaugmentation
Authors: Wu Yichao , Mohanty Anee , Chia Wu Siang , Cao Bin 
Published: May 2016

ABSTRACT

Bioaugmentation has been frequently proposed in wastewater and soil treatment to remove toxic aromatic compounds. The performance of bioaugmentation is affected by a number of biological and environmental factors, including the interaction between the target pollutant and the augmented bacterial cells. In this study, using
Comamonas testosteroni
and 3-chloroaniline (3-CA) as the model organism and target pollutant, we explored the influence of toxic aromatic pollutants on the biofilm lifestyle of bacteria capable of degrading aromatic compounds toward a better understanding of cell-pollutant interaction in bioaugmentation. Our results showed that the exposure to 3-CA greatly reduced the retention of
C. testosteroni
cells in packed-bed bioreactors (from 22% to 15% after three pore volumes), which could be attributed to the altered bacterial motility and cell surface hydrophobicity. To further understand the molecular mechanisms, we employed an integrated genomic and transcriptomic analysis to examine the influence of 3-CA on the expression of genes important to the biofilm lifestyle of
C. testosteroni
. We found that exposure to 3-CA reduced the intracellular c-di-GMP level by downregulating the expression of genes encoding c-di-GMP synthases and induced massive cell dispersal from the biofilms. Our findings provide novel environmental implications on bioaugmentation, particularly in biofilm reactors, for the treatment of wastewater containing recalcitrant industrial pollutants.

IMPORTANCE
Bioaugmentation is a bioremediation approach that often has been described in the literature but has almost never been successfully applied in practice. Many biological and environmental factors influence the overall performance of bioaugmentation. Among these, the interaction between the target pollutant and the augmented bacterial cells is one of the most important factors. In this study, we revealed the influence of toxic aromatic pollutants on the biofilm lifestyle of bacteria capable of degrading aromatic compounds toward a better understanding of cell-pollutant interaction in bioaugmentation. Our findings provide novel environmental implications on bioaugmentation for the treatment of wastewater containing recalcitrant industrial pollutants; in particular, the exposure to toxic pollutants may reduce the retention of augmented organisms in biofilm reactors by reducing the c-di-GMP level, and approaches to elevating or maintaining a high c-di-GMP level may be promising to establish and maintain sustainable bioaugmentation activity.
Energetics and Application of Heterotrophy in Acetogenic Bacteria
Authors: Schuchmann Kai , Müller Volker 
Published: May 2016

ABSTRACTAcetogenic bacteria are a diverse group of strictly anaerobic bacteria that utilize the Wood-Ljungdahl pathway for CO2fixation and energy conservation. These microorganisms play an important part in the global carbon cycle and are a key component of the anaerobic food web. Their most prominent metabolic feature is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates. However, most members also show an outstanding metabolic flexibility for utilizing a vast variety of different substrates. In contrast to autotrophic growth, which is hardly competitive, metabolic flexibility is seen as a key ability of acetogens to compete in ecosystems and might explain the almost-ubiquitous distribution of acetogenic bacteria in anoxic environments. This review covers the latest findings with respect to the heterotrophic metabolism of acetogenic bacteria, including utilization of carbohydrates, lactate, and different alcohols, especially in the model acetogenAcetobacterium woodii. Modularity of metabolism, a key concept of pathway design in synthetic biology, together with electron bifurcation, to overcome energetic barriers, appears to be the basis for the amazing substrate spectrum. At the same time, acetogens depend on only a relatively small number of enzymes to expand the substrate spectrum. We will discuss the energetic advantages of coupling CO2reduction to fermentations that exploit otherwise-inaccessible substrates and the ecological advantages, as well as the biotechnological applications of the heterotrophic metabolism of acetogens.
Mechanism of Antiactivation at the Pseudomonas sp. Strain ADP σN-Dependent PatzTPromoter
Authors: Platero Ana Isabel , López-Sánchez Aroa , Tomás-Gallardo Laura , Santero Eduardo , Govantes Fernando 
Published: May 2016

ABSTRACTPatzTis an internal promoter of theatzRSTUVWoperon that directs the synthesis of AtzT, AtzU, AtzV, and AtzW, components of an ABC-type cyanuric acid transport system. PatzTis σNdependent, activated by the general nitrogen control regulator NtrC with the assistance of protein integration host factor (IHF), and repressed by the LysR-type transcriptional regulator (LTTR) AtzR. We have used a variety ofin vivoandin vitrogene expression and protein-DNA interaction assays to assess the mechanisms underlying AtzR-dependent repression of PatzT. Here, we show that repression only occurs when AtzR and NtrC interact simultaneously with the PatzTpromoter region, indicating that AtzR acts as an antiactivator to antagonize activation by NtrC. Furthermore, repression requires precise rotational orientation of the AtzR and NtrC binding sites, strongly suggesting protein-protein interaction between the two proteins on the promoter region. Further exploration of the antiactivation mechanism showed that although AtzR-dependent repression occurs prior to open complex formation, AtzR does not alter the oligomerization state of NtrC or inhibit NtrC ATPase activity when bound to the PatzTpromoter region. Taken together, these results strongly suggest that PatzT-bound AtzR interacts with NtrC to prevent the coupling of NtrC-mediated ATP hydrolysis with the remodeling of the interactions between E-σNand PatzTthat lead to open complex formation.IMPORTANCEHere, we describe a unique mechanism by which the regulatory protein AtzR prevents the activation of the σN-dependent promoter PatzT. Promoters of this family are always positively regulated, but there are a few examples of overlapping negative regulation. The mechanism described here is highly unconventional and involves an interaction between the repressor and activator proteins to prevent the action of the repressor protein on the RNA polymerase-promoter complex.
Exogenous Fatty Acids Protect Enterococcus faecalis from Daptomycin-Induced Membrane Stress Independently of the Response Regulator LiaR
Authors: Harp John R. , Saito Holly E. , Bourdon Allen K. , Reyes Jinnethe , Arias Cesar A. , Campagna Shawn R. , Fozo Elizabeth M. 
Published: May 2016

ABSTRACT

Enterococcus faecalis
is a commensal bacterium of the gastrointestinal tract that can cause nosocomial infections in immunocompromised humans. The hallmarks of this organism are its ability to survive in a variety of stressful habitats and, in particular, its ability to withstand membrane damage. One strategy used by
E. faecalis
to protect itself from membrane-damaging agents, including the antibiotic daptomycin, involves incorporation of exogenous fatty acids from bile or serum into the cell membrane. Additionally, the response regulator LiaR (a member of the LiaFSR [lipid II-interacting antibiotic response regulator and sensor] system associated with cell envelope stress responses) is required for the basal level of resistance
E. faecalis
has to daptomycin-induced membrane damage. This study aimed to determine if membrane fatty acid changes could provide protection against membrane stressors in a LiaR-deficient strain of
E. faecalis
. We noted that despite the loss of LiaR, the organism readily incorporated exogenous fatty acids into its membrane, and indeed growth in the presence of exogenous fatty acids increased the survival of LiaR-deficient cells when challenged with a variety of membrane stressors, including daptomycin. Combined, our results suggest that
E. faecalis
can utilize both LiaR-dependent and -independent mechanisms to protect itself from membrane damage.

IMPORTANCE
Enterococcus faecalis
is responsible for a significant number of nosocomial infections. Worse, many of the antibiotics used to treat
E. faecalis
infection are no longer effective, as this organism has developed resistance to them. The drug daptomycin has been successfully used to treat some of these resistant strains; however, daptomycin-resistant isolates have been identified in hospitals. Many daptomycin-resistant isolates are found to harbor mutations in the genetic locus
liaFSR
, which is involved in membrane stress responses. Another mechanism shown to increase tolerance to daptomycin involves the incorporation of exogenous fatty acids from host fluids like serum or bile. This improved tolerance was found to be independent of
liaFSR
and suggests that there are additional ways to impact sensitivity to daptomycin. Thus, further studies are needed to understand how host fatty acid sources can influence antibiotic susceptibility.
Molecular Epidemiology of Campylobacter coli Strains Isolated from Different Sources in New Zealand between 2005 and 2014
Authors: Nohra Antoine , Grinberg Alex , Midwinter Anne C. , Marshall Jonathan C. , Collins-Emerson Julie M. , French Nigel P. 
Published: May 2016

ABSTRACT

Campylobacteriosis is one of the most important foodborne diseases worldwide and a significant health burden in New Zealand.
Campylobacter jejuni
is the predominant species worldwide, accounting for approximately 90% of human cases, followed by
Campylobacter coli
. Most studies in New Zealand have focused on
C. jejuni
; hence, the impact of
C. coli
strains on human health is not well understood. The aim of this study was to genotype
C. coli
isolates collected in the Manawatu region of New Zealand from clinical cases, fresh poultry meat, ruminant feces, and environmental water sources, between 2005 and 2014, to study their population structure and estimate the contribution of each source to the burden of human disease.
Campylobacter
isolates were identified by PCR and typed by multilocus sequence typing.
C. coli
accounted for 2.9% (
n =
47/1,601) of
Campylobacter
isolates from human clinical cases, 9.6% (
n =
108/1,123) from poultry, 13.4% (
n =
49/364) from ruminants, and 6.4% (
n =
11/171) from water. Molecular subtyping revealed 27 different sequence types (STs), of which 18 belonged to clonal complex ST-828. ST-1581 was the most prevalent
C. coli
sequence type isolated from both human cases (
n =
12/47) and poultry (
n =
44/110). When classified using cladistics, all sequence types belonged to clade 1 except ST-7774, which belonged to clade 2. ST-854, ST-1590, and ST-4009 were isolated only from human cases and fresh poultry, while ST-3232 was isolated only from human cases and ruminant sources. Modeling indicated ruminants and poultry as the main sources of
C. coli
human infection.

IMPORTANCE
We performed a molecular epidemiological study of
Campylobacter coli
infection in New Zealand, one of few such studies globally. This study analyzed the population genetic structure of the bacterium and included a probabilistic source attribution model covering different animal and water sources. The results are discussed in a global context.
Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges
Authors: Blaser Martin J. , Cardon Zoe G. , Cho Mildred K. , Dangl Jeffrey L. , Donohue Timothy J. , Green Jessica L. , Knight Rob , Maxon Mary E. , Northen Trent R. , Pollard Katherine S. , Brodie Eoin L. 
Published: May 2016

ABSTRACT
Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.
Electroacupuncture for Reproductive Hormone Levels in Patients with Diminished Ovarian Reserve: A Prospective Observational Study
Authors: Wang Yang , Li Yanhong , Chen Ruixue , Cui Xiaoming , Yu Jinna , Liu Zhishun 
Published: May 2016

Background Effective methods for the treatment of reproductive dysfunction are limited. Previous studies have reported that acupuncture can modulate female hormone levels, improve menstrual disorders, alleviate depression and improve pregnancy rates. However, studies of acupuncture for diminished ovarian reserve (DOR) are lacking. Objective To carry out a prospective observational study aimed at assessing the effect of EA on the reproductive hormone levels of patients with DOR seeking fertility support and consider its safety. Methods Eligible patients with DOR received EA for 12 weeks: five times a week for 4 weeks followed by three times a week for 8 weeks. The primary outcome was the change in mean follicle-stimulating hormone (FSH) level at week 12. Mean luteinising hormone (LH) and serum oestradiol (E2) levels, FSH/LH ratios and symptom scale scores were simultaneously observed. Results Twenty-one patients with DOR were included in the final analysis. Mean FSH levels fell from 19.33±9.47 mIU/mL at baseline to 10.58±6.34 mIU/mL at week 12 and 11.25±6.68 mIU/mL at week 24. Change in mean FSH from baseline was −8.75±11.13 mIU/mL at week 12 (p=0.002) and −8.08±9.56 mIU/mL at week 24 (p=0.001). Mean E2 and LH levels, FSH/LH ratios and irritability scores were improved at weeks 12 and/or 24. Approximately 30% patients reported subjective increases in menstrual volume after treatment. Conclusions EA may modulate reproductive hormone levels and the effects seem to persist for at least 12 weeks after treatment with no significant side effects. EA may improve the ovarian reserve of patients with DOR, though further research is needed. Trial Registration Number NCT02229604; Results.
Role of sTREM-1 in predicting mortality of infection: a systematic review and meta-analysis
Authors: Su Longxiang , Liu Dan , Chai Wenzhao , Liu Dawei , Long Yun 
Published: May 2016

ObjectivesSeveral studies have investigated the prognostic value of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) in patients with infection. However, the result was controversial. Thus, the purpose of the present meta-analysis was to determine the prognostic value of the sTREM-1 level in predicting mortality at the initial stage of infection.MethodsThe literature was searched in the PubMed, EMBASE, Web of Knowledge and Cochrane databases. A 2×2 contingency table was constructed on the basis of mortality and sTREM-1 levels in patients with infection. 2 authors independently judged study eligibility and extracted data. The prognostic value of sTREM-1 in predicting mortality was determined using a bivariate meta-analysis model. Q-test and I2index were used to test heterogeneity.Results9 studies were selected from 803 studies. An elevated sTREM-1 level was associated with a higher risk of death in infection, with pooled risk ratio (RR) was 2.54 (95% CI 1.77 to 3.65) using a random-effects model (I2=53.8%). With the bivariate random-effects regression model, the pooled sensitivity and specificity of sTREM-1 to predict mortality in infection were 0.75 (95% CI 0.61 to 0.86) and 0.66 (95% CI 0.54 to 0.75), respectively. The diagnostic OR was 6 (95% CI 3 to 10). The overall area under the summary receiver operator characteristic (SROC) curve was 0.76 (95% CI 0.72 to 0.79). When we calculated the sepsis subgroup, the pooled RR was 2.98 (95% CI 2.19 to 4.40). The pooled sensitivity and specificity were 0.74 (95% CI 0.58 to 0.85) and 0.72 (95% CI 0.62 to 0.80), respectively. The overall area under the SROC curve was 0.78 (95% CI 0.74 to 0.81).ConclusionsElevated sTREM-1 concentrations had a moderate prognostic significance in assessing the mortality of infection in adult patients. However, sTREM-1 alone is insufficient to predict mortality as a biomarker.
Stroke survivors', caregivers' and GPs' attitudes towards a polypill for the secondary prevention of stroke: a qualitative interview study
Authors: Jamison James , Graffy Jonathan , Mullis Ricky , Mant Jonathan , Sutton Stephen 
Published: May 2016

ObjectivesTo understand the perspectives of stroke survivors, caregivers and general practitioners (GPs) on a polypill approach, consisting of blood pressure and cholesterol-lowering therapies, with or without aspirin, for the secondary prevention of stroke.MethodsA qualitative interview study was undertaken in 5 GP surgeries in the East of England. 28 survivors of stroke/transient ischaemic attack (TIA) were interviewed, 14 of them with a caregiver present, along with a convenience sample of 5 GPs, to assess attitudes towards a polypill and future use. Topic guides explored participants attitudes, potential uptake and long-term use, management of polypill medication and factors influencing the decision to prescribe. Data were analysed using a grounded theory approach. Key themes are presented and illustrated with verbatim quotes.ResultsThe analysis identified 3 key themes: polypill benefits, polypill concerns and polypill lessons for implementation. Stroke/TIA survivors were positive about the polypill concept and considered it acceptable in the secondary prevention of stroke. Perceived benefits of a polypill included convenience resulting in improved adherence and reduced burden of treatment. Caregivers felt that a polypill would improve medication-taking practices, and GPs were open to prescribing it to those at increased cardiovascular risk. However, concerns raised included whether a polypill provided equivalent therapeutic benefit, side effects through combining medications, consequences of non-adherence, lack of flexibility in regulating dosage, disruption to current treatment and suitability to the wider stroke population.ConclusionsParticipants acknowledged potential advantages in a polypill approach for secondary prevention of stroke; however, significant concerns remain. Further research on the efficacy of a polypill is needed to reassure practitioners whose concerns around inflexibility and treatment suitability are likely to influence the decision to prescribe a polypill for secondary prevention of stroke. Acceptability among survivors, caregivers and GPs is likely to determine the uptake and subsequent use of a polypill in the future.
Economic evaluation of manual therapy for musculoskeletal diseases: a protocol for a systematic review and narrative synthesis of evidence
Authors: Kim Chang-Gon , Mun Su-Jeong , Kim Ka-Na , Shin Byung-Cheul , Kim Nam-Kwen , Lee Dong-Hyo , Lee Jung-Han 
Published: May 2016

IntroductionManual therapy is the non-surgical conservative management of musculoskeletal disorders using the practitioner's hands on the patient's body for diagnosing and treating disease. The aim of this study is to systematically review trial-based economic evaluations of manual therapy relative to other interventions used for the management of musculoskeletal diseases.Methods and analysisRandomised clinical trials (RCTs) on the economic evaluation of manual therapy for musculoskeletal diseases will be included in the review. The following databases will be searched from their inception: Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Econlit, Mantis, Index to Chiropractic Literature, Science Citation Index, Social Science Citation Index, Allied and Complementary Medicine Database (AMED), Cochrane Database of Systematic Reviews (CDSR), National Health Service Database of Abstracts of Reviews of Effects (NHS DARE), National Health Service Health Technology Assessment Database (NHS HTA), National Health Service Economic Evaluation Database (NHS EED), CENTRAL, five Korean medical databases (Oriental Medicine Advanced Searching Integrated System (OASIS), Research Information Service System (RISS), DBPIA, Korean Traditional Knowledge Portal (KTKP) and KoreaMed) and three Chinese databases (China National Knowledge Infrastructure (CNKI), VIP and Wanfang). The evidence for the cost-effectiveness, cost-utility and cost-benefit of manual therapy for musculoskeletal diseases will be assessed as the primary outcome. Health-related quality of life and adverse effects will be assessed as secondary outcomes. We will critically appraise the included studies using the Cochrane risk of bias tool and the Drummond checklist. Results will be summarised using Slavin's qualitative best-evidence synthesis approach.Ethics and disseminationThe results of the study will be disseminated via a peer-reviewed journal and/or conference presentations.Trial registration numberPROSPERO CRD42015026757.
General practitioners’ justifications for therapeutic inertia in cardiovascular prevention: an empirically grounded typology
Authors: Lebeau Jean-Pierre , Cadwallader Jean-Sébastien , Vaillant-Roussel Hélène , Pouchain Denis , Yaouanc Virginie , Aubin-Auger Isabelle , Mercier Alain , Rusch Emmanuel , Remmen Roy , Vermeire Etienne , Hendrickx Kristin 
Published: May 2016

ObjectiveTo construct a typology of general practitioners’ (GPs) responses regarding their justification of therapeutic inertia in cardiovascular primary prevention for high-risk patients with hypertension.DesignEmpirically grounded construction of typology. Types were defined by attributes derived from the qualitative analysis of GPs’ reported reasons for inaction.Participants256 GPs randomised in the intervention group of a cluster randomised controlled trial.SettingGPs members of 23 French Regional Colleges of Teachers in General Practice, included in the EffectS of a multifaceted intervention on CArdiovascular risk factors in high-risk hyPErtensive patients (ESCAPE) trial.Data collection and analysisThe database consisted of 2638 written responses given by the GPs to an open-ended question asking for the reasons why drug treatment was not changed as suggested by the national guidelines. All answers were coded using constant comparison analysis. A matrix analysis of codes per GP allowed the construction of a response typology, where types were defined by codes as attributes. Initial coding and definition of types were performed independently by two teams.ResultsInitial coding resulted in a list of 69 codes in the final codebook, representing 4764 coded references in the question responses. A typology including seven types was constructed. 100 GPs were allocated to one and only one of these types, while 25 GPs did not provide enough data to allow classification. Types (numbers of GPs allocated) were: ‘optimists’ (28), ‘negotiators’ (20), ‘checkers’ (15), ‘contextualisers’ (13), ‘cautious’ (11), ‘rounders’ (8) and ‘scientists’ (5). For the 36 GPs that provided 50 or more coded references, analysis of the code evolution over time and across patients showed a consistent belonging to the initial type for any given GP.ConclusionThis typology could provide GPs with some insight into their general ways of considering changes in the treatment/management of cardiovascular risk factors and guide design of specific physician-centred interventions to reduce inappropriate inaction.Trial registration numberNCT00348855.