Methylation-Sensitive Expression of a DNA Demethylase Gene Serves As an Epigenetic Rheostat

Genomes must balance active suppression of transposable elements (TEs) with the need to maintain gene expression. In Arabidopsis, euchromatic TEs are targeted by RNA-directed DNA methylation (RdDM). Conversely, active DNA demethylation prevents accumulation of methylation at genes proximal to these TEs. It is unknown how a cellular balance between methylation and demethylation activities is achieved. Here we show that both RdDM and DNA demethylation are highly active at a TE proximal to the major DNA demethylase gene ROS1. Unexpectedly, and in contrast to most other genomic targets, expression of ROS1 is promoted by DNA methylation and antagonized by DNA demethylation. We demonstrate that inducing methylation in the ROS1 proximal region is sufficient to restore ROS1 expression in an RdDM mutant. Additionally, methylation-sensitive expression of ROS1 is conserved in other species, suggesting it is adaptive. We propose that the ROS1 locus functions as an epigenetic rheostat, tuning the level of demethylase activity in response to methylation alterations, thus ensuring epigenomic stability.     

Chemical Composition and Allelopathic Potential of Essential Oils Obtained from Acacia cyanophylla Lindl. Cultivated in Tunisia

Acacia cyanophylla Lindl . (Fabaceae), synonym Acacia saligna (Labill .) H. L.Wendl ., native to West Australia and naturalized in North Africa and South Europe, was introduced in Tunisia for rangeland rehabilitation, particularly in the semiarid zones. In addition, this evergreen tree represents a potential forage resource, particularly during periods of drought. A. cyanophylla is abundant in Tunisia and some other Mediterranean countries. The chemical composition of the essential oils obtained by hydrodistillation from different plant parts, viz., roots, stems, phyllodes, flowers, and pods (fully mature fruits without seeds), was characterized for the first time here. According to GC‐FID and GC/MS analyses, the principal compound in the phyllode and flower oils was dodecanoic acid ( 4 ), representing 22.8 and 66.5% of the total oil, respectively. Phenylethyl salicylate ( 8 ; 34.9%), heptyl valerate ( 3 ; 17.3%), and nonadecane (36%) were the main compounds in the root, stem, and pod oils, respectively. The phyllode and flower oils were very similar, containing almost the same compounds. Nevertheless, the phyllode oil differed from the flower oil for its higher contents of hexahydrofarnesyl acetone ( 6 ), linalool ( 1 ), pentadecanal, α‐terpineol, and benzyl benzoate ( 5 ) and its lower content of 4 . Principal component and hierarchical cluster analyses separated the five essential oils into four groups, each characterized by its main constituents. Furthermore, the allelopathic activity of each oil was evaluated using lettuce (Lactuca sativa L.) as a plant model. The phyllode, flower, and pod oils exhibited a strong allelopathic activity against lettuce.     

Serotype Distribution,Antibiotic Resistance and Clonality of Streptococcus pneumoniae Isolated from Immunocompromised Patients in Tunisia

BackgroundPneumococcal disease, a major cause of morbidity and mortality globally, has higher incidence among young children, the elderly and the immunocompromised of all ages. In Tunisia, pneumococcal conjugate vaccines (PCVs) are not included in the national immunization program. Also, few studies have described the epidemiology of S. pneumoniae in this country and, in particular, no molecular typing studies have been performed. The aim of this study was to evaluate serotype distribution, antimicrobial resistance and clonality of Streptococcus pneumoniae isolated from neutropenic patients in Tunisia.MethodsFifty-nine S. pneumoniae were isolated from infection (n = 31) and colonization (n = 28) sites of patients (children and adults) attending the National Centre of Bone Marrow Transplantation in Tunis between 2005–2011. All isolates were characterized by serotype, antimicrobial resistance pattern and multilocus sequence typing (MLST).ResultsThe majority (66.1%) of the isolates belonged to five serotypes all included in PCVs: 6B, 9V, 14, 19F and 23F. The potential coverage of the 10-valent and 13-valent PCV was of 71.2% and 76.3% respectively. Resistance rates were very high and 69.5% of the isolates were multidrug resistant: non-susceptibility rates to penicillin, amoxicillin and cefotaxime were 66.1%, 40.7% and 27.1%, respectively; resistance rates to erythromycin, clindamycin, tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole, were 69.5%, 61.0%, 37.3%, 22.0% and 67.8%, respectively. The most frequent serotypes had STs characteristic of multidrug resistant international clones known to be highly successful and important causes of pneumococcal infection: Spain 23F-ST81, France 9V/14-ST156, Spain 6B-ST90, 19F-ST320, and Portugal 19F-ST177.ConclusionsThe majority of S. pneumoniae strains recovered from immunocompromised patients in Tunisia are representatives of multidrug resistant pandemic clones that express serotypes targeted by PCVs. To contain the burden of pneumococcal disease and improve treatment choices among Tunisian immunocompromised patients PCVs should be offered to all of them.     

Partitioning Detectability Components in Populations Subject to Within-Season Temporary Emigration Using Binomial Mixture Models

Detectability of individual animals is highly variable and nearly always < 1; imperfect detection must be accounted for to reliably estimate population sizes and trends. Hierarchical models can simultaneously estimate abundance and effective detection probability, but there are several different mechanisms that cause variation in detectability. Neglecting temporary emigration can lead to biased population estimates because availability and conditional detection probability are confounded. In this study, we extend previous hierarchical binomial mixture models to account for multiple sources of variation in detectability. The state process of the hierarchical model describes ecological mechanisms that generate spatial and temporal patterns in abundance, while the observation model accounts for the imperfect nature of counting individuals due to temporary emigration and false absences. We illustrate our model’s potential advantages, including the allowance of temporary emigration between sampling periods, with a case study of southern red-backed salamanders Plethodon serratus. We fit our model and a standard binomial mixture model to counts of terrestrial salamanders surveyed at 40 sites during 3–5 surveys each spring and fall 2010–2012. Our models generated similar parameter estimates to standard binomial mixture models. Aspect was the best predictor of salamander abundance in our case study; abundance increased as aspect became more northeasterly. Increased time-since-rainfall strongly decreased salamander surface activity (i.e. availability for sampling), while higher amounts of woody cover objects and rocks increased conditional detection probability (i.e. probability of capture, given an animal is exposed to sampling). By explicitly accounting for both components of detectability, we increased congruence between our statistical modeling and our ecological understanding of the system. We stress the importance of choosing survey locations and protocols that maximize species availability and conditional detection probability to increase population parameter estimate reliability.     

Effect of Energy Under-Reporting on Secular Trends of Dietary Patterns in a Mediterranean Population

BackgroundDiet is an important factor in the prevention of chronic diseases. Analysis of secular trends of dietary patterns can be biased by energy under-reporting. Therefore, the objective of the present study was to analyse the impact of energy under-reporting on dietary patterns and secular trends in dietary patterns defined by cluster analysis.ResultsThree clusters, “healthy”, “mixed” and “western”, were identified for both surveys. The “mixed” cluster was the predominant cluster in both surveys. Excluding EUR reduced the proportion of the “mixed” cluster up to 6.40% in the 2000 survey; this caused secular trend increase in the prevalence of the “mixed” pattern. Cross-classification analysis of all participants and PER’ data showed substantial agreement in cluster assignments: 68.7% in 2000 and 84.4% in 2005. Excluding EUR did not cause meaningful (≥15%) changes in the “healthy” pattern. It provoked changes in consumption of some food groups in the “mixed” and “western” patterns: mainly decreases of unhealthy foods within the 2000 and increases of unhealthy foods within the 2005 surveys. Secular trend effects of EUR were similar to those within the 2005 survey. Excluding EUR reversed the direction of secular trends in consumption of several food groups in PER in the “mixed” and “western” patterns.ConclusionsEUR affected distribution of participants between dietary patterns within and between surveys, secular trends in food group consumption and amount of food consumed in all, but not in the “healthy” pattern. Our findings emphasize threats from energy under-reporting in dietary data analysis.     

Efficient Differentiation of Steroidogenic and Germ-Like Cells from Epigenetically-Related iPSCs Derived from Ovarian Granulosa Cells

To explore restoration of ovarian function using epigenetically-related, induced pluripotent stem cells (iPSCs), we functionally evaluated the epigenetic memory of novel iPSC lines, derived from mouse and human ovarian granulosa cells (GCs) using c-Myc, Klf4, Sox2 and Oct4 retroviral vectors. The stem cell identity of the mouse and human GC-derived iPSCs (mGriPSCs, hGriPSCs) was verified by demonstrating embryonic stem cell (ESC) antigen expression using immunocytochemistry and RT-PCR analysis, as well as formation of embryoid bodies (EBs) and teratomas that are capable of differentiating into cells from all three germ layers. GriPSCs’ gene expression profiles associate more closely with those of ESCs than of the originating GCs as demonstrated by genome-wide analysis of mRNA and microRNA. A comparative analysis of EBs generated from three different mouse cell lines (mGriPSCs; fibroblast-derived iPSC, mFiPSCs; G4 embryonic stem cells, G4 mESCs) revealed that differentiated mGriPSC-EBs synthesize 10-fold more estradiol (E2) than either differentiated FiPSC- or mESC-EBs under identical culture conditions. By contrast, mESC-EBs primarily synthesize progesterone (P4) and FiPSC-EBs produce neither E2 nor P4. Differentiated mGriPSC-EBs also express ovarian markers (AMHR, FSHR, Cyp19a1, ER and Inha) as well as markers of early gametogenesis (Mvh, Dazl, Gdf9, Boule and Zp1) more frequently than EBs of the other cell lines. These results provide evidence of preferential homotypic differentiation of mGriPSCs into ovarian cell types. Collectively, our data support the hypothesis that generating iPSCs from the desired tissue type may prove advantageous due to the iPSCs’ epigenetic memory.     

Exploring the Prevalence of Disrespect and Abuse during Childbirth in Kenya

Background

Poor quality of care including fear of disrespect and abuse (D&A) perpetuated by health workers influences women’s decisions to seek maternity care. Key manifestations of D&A include: physical abuse, non-consented care, non-confidential care, non-dignified care, discrimination, abandonment, and detention in facilities. This paper describes manifestations of D&A experienced in Kenya and measures their prevalence.

Methods

This paper is based on baseline data collected during a before-and-after study designed to measure the effect of a package of interventions to reduce the prevalence of D&A experienced by women during labor and delivery in thirteen Kenyan health facilities. Data were collected through an exit survey of 641 women discharged from postnatal wards. We present percentages of D&A manifestations and odds ratios of its relationship with demographic characteristics using a multivariate fixed effects logistic regression model.

Results

Twenty percent of women reported any form of D&A. Manifestations of D&A includes: non-confidential care (8.5%), non-dignified care (18%), neglect or abandonment (14.3%), Non-consensual care (4.3%) physical abuse (4.2%) and, detainment for non-payment of fees (8.1). Women aged 20-29 years were less likely to experience non-confidential care compared to those under 19; OR: [0.6 95% CI (0.36, 0.90); p=0.017]. Clients with no companion during delivery were less likely to experience inappropriate demands for payment; OR: [0.49 (0.26, 0.95); p=0.037]; while women with higher parities were three times more likely to be detained for lack of payment and five times more likely to be bribed compared to those experiencing there first birth.

Conclusion

One out of five women experienced feeling humiliated during labor and delivery. Six categories of D&A during childbirth in Kenya were reported. Understanding the prevalence of D&A is critical in developing interventions at national, health facility and community levels to address the factors and drivers that influence D&A in facilities and to encourage clients’ future facility utilization.     

Knowledge and Uses of African Pangolins as a Source of Traditional Medicine in Ghana

Traditional medicine has been practised in Ghana for centuries with the majority of Ghanaians still patronising the services of traditional healers. Throughout Africa a large number of people use pangolins as a source of traditional medicine, however, there is a dearth of information on the use of animals in folk medicine in Ghana, in particular the use of pangolins. The aim of this study was to determine the prevalent use of pangolins and the level of knowledge of pangolin use among traditional healers in Ghana for the treatment of human ailments. Data was gathered from 48 traditional healers using semi-structured interviews on the traditional medicinal use of pangolin body parts in the Kumasi metropolis of Ghana. The cultural importance index, relative frequency of citation, informant agreement ratio and use agreement values were calculated to ascertain the most culturally important pangolin body part as well as the level of knowledge dissemination among traditional healers with regards pangolin body parts. Our study revealed that 13 body parts of pangolins are used to treat various medicinal ailments. Pangolin scales and bones were the most prevalent prescribed body parts and indicated the highest cultural significance among traditional healing practices primarily for the treatment of spiritual protection, rheumatism, financial rituals and convulsions. Despite being classified under Schedule 1 of Ghana’s Wildlife Conservation Act of 1971 (LI 685), that prohibits anyone from hunting or being in possession of a pangolin, our results indicated that the use of pangolins for traditional medicinal purposes is widespread among traditional healers in Ghana. A study on the population status and ecology of the three species of African pangolins occurring in Ghana is urgently required in order to determine the impact this harvest for traditional medical purposes has on their respective populations as current levels appear to be unmonitored and unsustainable.