bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular evolution of dihydrouridine synthases
Authors: Kasprzak Joanna M , Czerwoniec Anna , Bujnicki Janusz M 
Published: June 2012

Abstract

Background
Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus enhance its conformational flexibility. D is generated post-transcriptionally by the reduction of the 5,6-double bond of a uridine residue in RNA transcripts. The reaction is carried out by dihydrouridine synthases (DUS). DUS constitute a conserved family of enzymes encoded by the orthologous gene family COG0042. In protein sequence databases, members of COG0042 are typically annotated as “predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family”.

Results
To elucidate sequence-structure-function relationships in the DUS family, a comprehensive bioinformatic analysis was carried out. We performed extensive database searches to identify all members of the currently known DUS family, followed by clustering analysis to subdivide it into subfamilies of closely related sequences. We analyzed phylogenetic distributions of all members of the DUS family and inferred the evolutionary tree, which suggested a scenario for the evolutionary origin of dihydrouridine-forming enzymes. For a human representative of the DUS family, the hDus2 protein suggested as a potential drug target in cancer, we generated a homology model. While this article was under review, a crystal structure of a DUS representative has been published, giving us an opportunity to validate the model.

Conclusions
We compared sequences and phylogenetic distributions of all members of the DUS family and inferred the phylogenetic tree, which provides a framework to study the functional differences among these proteins and suggests a scenario for the evolutionary origin of dihydrouridine formation. Our evolutionary and structural classification of the DUS family provides a background to study functional differences among these proteins that will guide experimental analyses.
Bayesian models for comparative analysis integrating phylogenetic uncertainty
Authors: Villemereuil Pierre de , Wells Jessie A , Edwards Robert D , Blomberg Simon P 
Published: June 2012

AbstractBackgroundUncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable.MethodsWe developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses.ResultsWe demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS.ConclusionsIncorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible general purpose tool for phylogenetic comparative analyses, particularly for modelling in the face of phylogenetic uncertainty and accounting for measurement error or individual variation in explanatory variables. Code for all models is provided in the BUGS model description language.
A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers
Authors: Palhares Alessandra C , Rodrigues-Morais Taislene B , Van Sluys Marie-Anne , Domingues Douglas S , Maccheroni Walter , Jordão Hamilton , Souza Anete P , Marconi Thiago G , Mollinari Marcelo , Gazaffi Rodrigo , Garcia Antonio Augusto F , Vieira Maria Lucia Carneiro 
Published: June 2012

Abstract

Background
The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily.

Results
The mapping population parents (‘IAC66-6’ and ‘TUC71-7’) contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization.

Conclusions
Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.
Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery
Authors: Neusser Thomas , Polen Tino , Geissen René , Wagner Rolf 
Published: June 2012

Abstract

Background
6S RNA from E. coli is known to bind to RNA polymerase interfering with transcription initiation. Because 6S RNA concentrations are maximal at stationary phase and binding occurs preferentially to the holoenzyme associated with σ70 (Eσ70) it is believed that 6S RNA supports adjustment to stationary phase transcription. Previous studies have also suggested that inhibition is specific for σ70-dependent promoters characterized by a weak -35 recognition motif or extended -10 promoters. There are many exceptions to this precept, showing that other types of promoters, including stationary phase-specific (σ38-dependent) promoters are inhibited.

Results
To solve this apparent ambiguity and to better understand the role of 6S RNA in stationary phase transition we have performed a genome-wide transcriptional analysis of wild-type and 6S RNA deficient cells growing to mid-log or early stationary phase. We found 245 genes at the exponential growth phase and 273 genes at the early stationary phase to be ≥ 1.5-fold differentially expressed. Up- and down-regulated genes include many transcriptional regulators, stress-related proteins, transporters and several enzymes involved in purine metabolism. As the most striking result during stationary phase, however, we obtained in the 6S RNA deficient strain a concerted expression reduction of genes constituting the translational apparatus. In accordance, primer extension analysis showed that transcription of ribosomal RNAs, representing the key molecules for ribosome biogenesis, is also significantly reduced under the same conditions. Consistent with this finding biochemical analysis of the 6S RNA deficient strain indicates that the lack of 6S RNA is apparently compensated by an increase of the basal ppGpp concentration, known to affect growth adaptation and ribosome biogenesis.

Conclusions
The analysis demonstrated that the effect of 6S RNA on transcription is not strictly confined to σ70-dependent promoters. Moreover, the results indicate that 6S RNA is embedded in stationary phase adaptation, which is governed by the capacity of the translational machinery.
The first wave of pandemic influenza (H1N1) 2009 in Germany: From initiation to acceleration
Authors: Poggensee Gabriele , Gilsdorf Andreas , Buda Silke , Eckmanns Tim , Claus Hermann , Altmann Doris ,   RKI Working Group Pandemic Influenza, Krause Gérard , Haas Walter 
Published: June 2012

Abstract

Background
The first imported case of pandemic influenza (H1N1) 2009 in Germany was confirmed in April 2009. However, the first wave with measurable burden of disease started only in October 2009. The basic epidemiological and clinical characteristics of the pandemic were analysed in order to understand the course of the pandemic in Germany.

Methods
The analysis was based on data from the case-based, mandatory German surveillance system for infectious diseases. Cases notified between 27 April and 11 November 2009 and fulfilling the case definition were included in the study.

Results
Two time periods with distinct epidemiologic characteristics could be determined: 23,789 cases (44.1%) occurred during the initiation period (IP, week 18 to 41), and 30,179 (55.9%) during the acceleration period (AP, week 42 to 45). During IP, coinciding with school summer holidays, 61.1% of cases were travel-related and one death occurred. Strict containment efforts were performed until week 32. During AP the majority of cases (94.3%) was autochthonous, 12 deaths were reported. The main affected age group shifted from 15 to 19 years in IP to 10 to 14 years in AP (median age 19 versus 15 years; p < 0.001). The proportion of cases with underlying medical conditions increased from 4.7% to 6.9% (p < 0.001). Irrespective of the period, these cases were more likely to be hospitalised (OR = 3.6 [95% CI: 3.1; 4.3]) and to develop pneumonia (OR = 8.1 [95% CI: 6.1; 10.7]). Furthermore, young children (0 to 2 years) (OR = 2.8 [95% CI: 1.5; 5.2]) and persons with influenza-like illness (ILI, OR = 1.4 [95% CI: 1.0; 2.1]) had a higher risk to develop pneumonia compared to other age groups and individuals without ILI.

Conclusion
The epidemiological differences we could show between summer and autumn 2009 might have been influenced by the school summer holidays and containment efforts. The spread of disease did not result in change of risk groups or severity. Our results show that analyses of case-based information can advise future public health measures.
Seroprevalence of Human Papillomavirus Types 6, 11, 16 and 18 in Chinese Women
Authors: Ji Jia , Sun Hai-Kui , Smith Jennifer S , Wang He , Esser Mark T , Hu Shangying , Pretorius Robert G , Chen Wen , Belinson Jerome L , Qiao You-Lin 
Published: June 2012

Abstract

Background
Human papillomavirus (HPV) seroprevalence data have not previously been reported for different geographical regions of China. This study investigated the cross-sectional seroprevalence of antibodies to HPV 6, 11, 16, and 18 virus-like particles in Chinese women.

Methods
Population-based samples of women were enrolled from 2006 to 2007 in 3 rural and 2 urban areas of China. Each consenting woman completed a questionnaire and provided a blood sample. Serum antibodies were detected using a competitive Luminex immunoassay that measures antibodies to type-specific, neutralizing epitopes on the virus-like particles.

Results
A total of 4,731 women (median age 35, age range 14-54) were included, of which 4,211 were sexually active women (median age 37) and 520 virgins (median age 18). Low risk HPV 6 was the most common serotype detected (7.3%), followed by HPV 16 (5.6%), HPV 11 (2.9%), and HPV 18 (1.9%). Overall HPV seroprevalence to any type was significantly higher among sexually active women (15.8%) than virgins (2.5%) (P = 0.005). Overall seroprevalence among sexually active women gradually increased with age. Women from rural regions had significantly lower overall seroprevalence (Odds Ratio (OR) = 0.7; 95% CI: 0.6-0.9, versus metropolitan regions, P < 0.001). With increasing number of sexual partners, women were at higher risk of seropositivity of any type (OR = 2.6; 95% CI: 1.7-3.9 for > = 4 partners versus 1 partner, P < 0.001). Wives were at higher risk of seropositivity for HPV 16/18/6/11 when reporting having a husband who had an extramarital sexual relationship (OR = 2.0; 95% CI: 1.6-2.5, versus those whose husbands having no such relationship, P < 0.001). There was a strong association between HPV 16 seropositivity and presence of high-grade cervical lesions (OR = 6.5; 95% CI: 3.7-11.4, versus normal cervix, P < 0.001).

Conclusions
HPV seroprevalence differed significantly by age, geography, and sexual behavior within China, which all should be considered when implementing an optimal prophylactic HPV vaccination program in China.
Quality of guidelines on the management of diabetes in pregnancy: a systematic review
Authors: Greuter Marjolein JE , van Emmerik Nathalie MA , Wouters Maurice GAJ , van Tulder Maurits W 
Published: June 2012

AbstractBackgroundDiabetes during pregnancy can lead to severe risks for both mother and fetus when it is not managed properly. The use of rigorously developed guidelines with a robust implementation process can have a positive influence on the management of diabetes during pregnancy. This study aims to compare recommendations and assess the quality of clinical guidelines on gestational diabetes mellitus (GDM) and pre-existing diabetes mellitus during pregnancy.MethodsGuidelines were selected by searching PubMed, the Guideline Clearing House and Google. All guidelines developed since 2000 on diabetes during pregnancy in English or Dutch were considered. Recommendations of the guidelines were compared. Furthermore, the quality was assessed by two authors independently, using the AGREE instrument.ResultsEight guidelines were included. According to the AGREE instrument, the quality of most guidelines was low. The domains editorial independence, stakeholder involvement and rigour of development had the lowest scores. Recommendations were mainly comparable on glycemic control, preconceptional counseling and prenatal care and labour. Differences between recommendations were found for screening on GDM and induction of labour.ConclusionsThe quality of most guidelines concerning the management of diabetes during pregnancy needs to be improved. A more systematic approach in the development of these guidelines, more attention for updating procedures and piloting of the guidelines and involvement of target users and patients is recommended.
On residents’ satisfaction with community health services after health care system reform in Shanghai, China, 2011
Authors: Li Zhijian , Hou Jiale , Lu Lin , Tang Shenglan , Ma Jin 
Published: June 2012

Abstract

Background
Health care system reform is a major issue in many countries and therefore how to evaluate the effects of changes is incredibly important. This study measured residents’ satisfaction with community health care service in Shanghai, China, and aimed to evaluate the effect of recent health care system reform.

Methods
Face-to-face interviews were performed with a stratified random sample of 2212 residents of the Shanghai residents using structured questionnaires. In addition, 972 valid responses were retrieved from internet contact. Controlling for sex, age, income and education, the study used logistic regression modeling to analyze factors associated with satisfaction and to explain the factors that affect the residents’ satisfaction.

Results
Comparing current attitudes with those held at the initial implementation of the reform in this investigation, four dimensions of health care were analyzed: 1) the health insurance system; 2) essential drugs; 3) basic clinical services; and 4) public health services. Satisfaction across all dimensions improved since the reform was initiated, but differences of satisfaction level were found among most dimensions and groups. Residents currently expressed greater satisfaction with clinical service (average score=3.79, with 5 being most satisfied) and the public health/preventive services (average score=3.62); but less satisfied with the provision of essential drugs (average score=3.20) and health insurance schemes (average score=3.23). The disadvantaged groups (the elderly, the retired, those with only an elementary education, those with lower incomes) had overall poorer satisfaction levels on these four aspects of health care (P<0.01). 25.39% of the respondents thought that their financial burden had increased and 38.49% thought that drugs had become more expensive.

Conclusion
The respondents showed more satisfaction with the clinical services (average score=3.79) and public health services/interventions (average score=3.79); and less satisfaction with the health insurance system (average score=3.23) and the essential drug system (average score=3.20). Disadvantaged groups showed lower satisfaction levels overall relative to non-disadvantaged groups.
The plant coumarins auraptene and lacinartin as potential multifunctional therapeutic agents for treating periodontal disease
Authors: Marquis Annie , Genovese Salvatore , Epifano Francesco , Grenier Daniel 
Published: June 2012

Abstract

Background
Periodontal diseases are bacterial infections leading to chronic inflammation disorders that are frequently observed in adults. In the present study, we evaluated the effect of auraptene and lacinartin, two natural oxyprenylated coumarins, on the growth, adherence properties, and collagenase activity of Porphyromonas gingivalis. We also investigated the capacity of these compounds to reduce cytokine and matrix metalloproteinase (MMP) secretion by lipopolysaccharide (LPS)-stimulated macrophages and to inhibit MMP-9 activity.

Methods
Microplate dilution assays were performed to determine the effect of auraptene and lacinartin on P. gingivalis growth as well as biofilm formation stained with crystal violet. Adhesion of FITC-labeled P. gingivalis to oral epithelial cells was monitored by fluorometry. The effects of auraptene and lacinartin on LPS-induced cytokine and MMP secretion by macrophages were determined by immunological assays. Fluorogenic assays were used to evaluate the capacity of the two coumarins to inhibit the activity of P. gingivalis collagenase and MMP-9.

Results
Only lacinartin completely inhibited P. gingivalis growth in a complex culture medium. However, under iron-limiting conditions, auraptene and lacinartin both inhibited the growth of P. gingivalis. Lacinartin also inhibited biofilm formation by P. gingivalis and promoted biofilm desorption. Both compounds prevented the adherence of P. gingivalis to oral epithelial cells, dose-dependently reduced the secretion of cytokines (IL-8 and TNF-α) and MMP-8 and MMP-9 by LPS-stimulated macrophages, and inhibited MMP-9 activity. Lacinartin also inhibited P. gingivalis collagenase activity.

Conclusions
By acting on multiple targets, including pathogenic bacteria, tissue-destructive enzymes, and the host inflammatory response, auraptene and lacinartin may be promising natural compounds for preventing and treating periodontal diseases.
Impairment of the cell-to-matrix adhesion and cytotoxicity induced by the Mediterranean jellyfish Pelagia noctiluca venom and its fractions in cultured glioblastoma cells
Authors: Ayed Yosra , Bousabbeh Manel , Mabrouk Hazem Ben , Morjen Maram , Marrakchi Naziha , Bacha Hassen 
Published: June 2012

Abstract

Background
The biodiversity of the marine environment and the associated chemical diversity constitute a practically unlimited source of new active substances in the field of the development of bioactive products. In our study, we have investigated the efficiency of the venom from the Mediterranean jellyfish, Pelagia noctiluca and its fractions for anti-proliferative and anti-cell adhesion to cell–extracellular matrix activities.

Results
Our experiments have indicated that the separation of the Mediterranean jellyfish Pelagia noctiluca crude venom extract by sephadex G-75 chromatography led to four fractions (F1, F2, F3, and F4). Among the four fractions F1 and F3 were cytotoxic against U87 cells with IC50 values of 125 and 179 μg/ml respectively. The venom, F1, F2 and F 3 showed significant anti-proliferative activity in time-dependent manner. Our results also suggest that these fractions and the venom are able to inhibit cell adhesion to fibrinogen in dose-dependent manner. This inhibition is reliant on its ability to interact with integrins.

Conclusions
To conclude, we have demonstrated for the first time that Pelagia noctiluca venom and its fractions especially (F1 and F2) display potent anti-tumoral properties. Separation by sephadex G-75 chromatography give rise to more active fractions than the crude venom extract. The purification and the determination of chemical structures of compounds of these active fractions are under investigation. Overall, Pelagia noctiluca venom may has the potential to serve as a template for future anticancer-drug development.
Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots
Authors: Wu Min , Kwoh Chee-Keong , Przytycka Teresa M , Li Jing , Zheng Jie 
Published: June 2012

Abstract
The regulatory mechanism of recombination is a fundamental problem in genomics, with wide applications in genome-wide association studies, birth-defect diseases, molecular evolution, cancer research, etc. In mammalian genomes, recombination events cluster into short genomic regions called "recombination hotspots". Recently, a 13-mer motif enriched in hotspots is identified as a candidate cis-regulatory element of human recombination hotspots; moreover, a zinc finger protein, PRDM9, binds to this motif and is associated with variation of recombination phenotype in human and mouse genomes, thus is a trans-acting regulator of recombination hotspots. However, this pair of cis and trans-regulators covers only a fraction of hotspots, thus other regulators of recombination hotspots remain to be discovered. In this paper, we propose an approach to predicting additional trans-regulators from DNA-binding proteins by comparing their enrichment of binding sites in hotspots. Applying this approach on newly mapped mouse hotspots genome-wide, we confirmed that PRDM9 is a major trans-regulator of hotspots. In addition, a list of top candidate trans-regulators of mouse hotspots is reported. Using GO analysis we observed that the top genes are enriched with function of histone modification, highlighting the epigenetic regulatory mechanisms of recombination hotspots.