Neofunctionalization in vertebrates: the example of retinoic acid receptors.

Understanding the role of gene duplications in establishing vertebrate innovations is one of the main challenges of Evo-Devo (evolution of development) studies. Data on evolutionary changes in gene expression (i.e., evolution of transcription factor-cis-regulatory elements relationships) tell only part of the story; protein function, best studied by biochemical and functional assays, can also change. In this study, we have investigated how gene duplication has affected both the expression and the ligand-binding specificity of retinoic acid receptors (RARs), which play a major role in chordate embryonic development. Mammals have three paralogous RAR genes--RAR alpha, beta, and gamma--which resulted from genome duplications at the origin of vertebrates. By using pharmacological ligands selective for specific paralogues, we have studied the ligand-binding capacities of RARs from diverse chordates species. We have found that RAR beta-like binding selectivity is a synapomorphy of all chordate RARs, including a reconstructed synthetic RAR representing the receptor present in the ancestor of chordates. Moreover, comparison of expression patterns of the cephalochordate amphioxus and the vertebrates suggests that, of all the RARs, RAR beta expression has remained most similar to that of the ancestral RAR. On the basis of these results together, we suggest that while RAR beta kept the ancestral RAR role, RAR alpha and RAR gamma diverged both in ligand-binding capacity and in expression patterns. We thus suggest that neofunctionalization occurred at both the expression and the functional levels to shape RAR roles during development in vertebrates.

A joint back calculation model for the imputation of the date of HIV infection in a prevalent cohort.

In studies of the natural history of HIV-1 infection, the time scale of primary interest is the time since infection. Unfortunately, this time is very often unknown for HIV infection and using the follow-up time instead of the time since infection is likely to provide biased results because of onset confounding. Laboratory markers such as the CD4 T-cell count carry important information concerning disease progression and can be used to predict the unknown date of infection. Previous work on this topic has made use of only one CD4 measurement or based the imputation on incident patients only. However, because of considerable intrinsic variability in CD4 levels and because incident cases are different from prevalent cases, back calculation based on only one CD4 determination per person or on characteristics of the incident sub-cohort may provide unreliable results. Therefore, we propose a methodology based on the repeated individual CD4 T-cells marker measurements that use both incident and prevalent cases to impute the unknown date of infection. Our approach uses joint modelling of the time since infection, the CD4 time path and the drop-out process. This methodology has been applied to estimate the CD4 slope and impute the unknown date of infection in HIV patients from the Swiss HIV Cohort Study. A procedure based on the comparison of different slope estimates is proposed to assess the goodness of fit of the imputation. Results of simulation studies indicated that the imputation procedure worked well, despite the intrinsic high volatility of the CD4 marker.

Evaluation of risk perception related to drug use during pregnancy: a Swiss survey

Introduction Health care professionals' perception of risk mayimpact on therapeutic management of women during pregnancy.Since the thalidomide tragedy, the use of drugs during pregnancygenerates fear. This concern might affect the estimation of the riskassociated with drug intake during pregnancy, leading to prematurediscontinuation of a required treatment, superfluous anxiety orpointless termination of a desired pregnancy. Although data regardingthe security of drugs during pregnancy are still scarce, a few specializedinformation sources exist providing reliable recommendationsfor daily practice. This study aimed at characterizing therisk perception associated with drugs during pregnancy in a sample ofSwiss health care professionals.Materials & Methods An online French and German survey was sentby email to the Swiss professional societies of Pharmacists, Gynecologists,Mid-wives and Pediatricians. The questionnaire wasconstructed to assess (a) the characteristics of the population and theopinion of the professionals regarding the medication use pattern intheir pregnant patients, (b) to evaluate the sources of information usedduring their practice and finally (c) to assess their risk perceptionassociated with drugs during pregnancy. Results were analyzed bydescriptive statistics.Results A total of 1,310 questionnaires were collected (18% responserate). Most health care professionals believe that 30-60% of theirpregnant patients are taking at least one treatment during their pregnancyand that 80% are adherent to it. A large majority think,however, that women are anxious when they must take their medication.More than 80% of health professionals commonly use theSwiss Drug Reference Book (Compendium) to assess the risk associatedwith drugs during pregnancy, despite the uniformly low levelof credibility and utility they express about this reference. Except forsome gynecologists, the majority of professionals are not aware of ordo not use specialized books. The majority of participants thinkwrongly that more than 30% of drugs are teratogenic. About 20% ofthem are not aware of the risk associated with paracetamol intakeduring pregnancy. More than 70% agree that phytotherapeutic mixturesare not safer than conventional drugs, with the exception of midwiveswho tend to overestimate the safety of such drugs. With thenotable exception of gynecologists, the risk related to drug intake wasoverall overestimated.Discussion & Conclusion Swiss professionals differ in their perceptionof the risk associated with drugs during pregnancy and tend tooverestimate it. The differences might be attributed to the level oftraining and awareness of specialized sources offering a realisticestimation of the risk. Further efforts are needed to expand thetraining and the tools for health care professionals to optimize druguse during pregnancy.

From the Apennines to the Alps: colonization genetics of the naturally expanding Italian wolf (Canis lupus) population

Wolves in Italy strongly declined in the past and were confined south of the Alps since the turn of the last century, reduced in the 1970s to approximately 100 individuals surviving in two fragmented subpopulations in the central-southern Apennines. The Italian wolves are presently expanding in the Apennines, and started to recolonize the western Alps in Italy, France and Switzerland about 16 years ago. In this study, we used a population genetic approach to elucidate some aspects of the wolf recolonization process. DNA extracted from 3068 tissue and scat samples collected in the Apennines (the source populations) and in the Alps (the colony), were genotyped at 12 microsatellite loci aiming to assess (i) the strength of the bottleneck and founder effects during the onset of colonization; (ii) the rates of gene flow between source and colony; and (iii) the minimum number of colonizers that are needed to explain the genetic variability observed in the colony. We identified a total of 435 distinct wolf genotypes, which showed that wolves in the Alps: (i) have significantly lower genetic diversity (heterozygosity, allelic richness, number of private alleles) than wolves in the Apennines; (ii) are genetically distinct using pairwise F(ST) values, population assignment test and Bayesian clustering; (iii) are not in genetic equilibrium (significant bottleneck test). Spatial autocorrelations are significant among samples separated up to c. 230 km, roughly correspondent to the apparent gap in permanent wolf presence between the Alps and north Apennines. The estimated number of first-generation migrants indicates that migration has been unidirectional and male-biased, from the Apennines to the Alps, and that wolves in southern Italy did not contribute to the Alpine population. These results suggest that: (i) the Alps were colonized by a few long-range migrating wolves originating in the north Apennine subpopulation; (ii) during the colonization process there has been a moderate bottleneck; and (iii) gene flow between sources and colonies was moderate (corresponding to 1.25-2.50 wolves per generation), despite high potential for dispersal. Bottleneck simulations showed that a total of c. 8-16 effective founders are needed to explain the genetic diversity observed in the Alps. Levels of genetic diversity in the expanding Alpine wolf population, and the permanence of genetic structuring, will depend on the future rates of gene flow among distinct wolf subpopulation fragments.

Mechanisms and evolutionary patterns of mammalian and avian dosage compensation.

As a result of sex chromosome differentiation from ancestral autosomes, male mammalian cells only contain one X chromosome. It has long been hypothesized that X-linked gene expression levels have become doubled in males to restore the original transcriptional output, and that the resulting X overexpression in females then drove the evolution of X inactivation (XCI). However, this model has never been directly tested and patterns and mechanisms of dosage compensation across different mammals and birds generally remain little understood. Here we trace the evolution of dosage compensation using extensive transcriptome data from males and females representing all major mammalian lineages and birds. Our analyses suggest that the X has become globally upregulated in marsupials, whereas we do not detect a global upregulation of this chromosome in placental mammals. However, we find that a subset of autosomal genes interacting with X-linked genes have become downregulated in placentals upon the emergence of sex chromosomes. Thus, different driving forces may underlie the evolution of XCI and the highly efficient equilibration of X expression levels between the sexes observed for both of these lineages. In the egg-laying monotremes and birds, which have partially homologous sex chromosome systems, partial upregulation of the X (Z in birds) evolved but is largely restricted to the heterogametic sex, which provides an explanation for the partially sex-biased X (Z) expression and lack of global inactivation mechanisms in these lineages. Our findings suggest that dosage reductions imposed by sex chromosome differentiation events in amniotes were resolved in strikingly different ways.

Task-shifting in the delivery of hormonal contraceptive methods: Validation of a questionnaire and preliminary results.

Guilbert ER, Morin D, Guilbert AC, Gagnon H, Robitaille J, Richardson M. International Journal of Nursing Practice 2011; 17: 315-321 Task-shifting in the delivery of hormonal contraceptive methods: Validation of a questionnaire and preliminary results In order to palliate the access problem to effective contraceptive methods in Quebec, Canada, as well as to legitimate nurses' practices in family planning, a collaborative agreement was developed that allow nurses, in conjunction with pharmacists, to give hormonal contraceptives to healthy women of reproductive age for a 6 month period. Training in hormonal contraception was offered to targeted nurses before they could begin this practice. A questionnaire, based on Rogers's theory of diffusion of innovations, was elaborated and validated to specifically evaluate this phenomenon. Preliminary results show that the translation of training into practice might be suboptimal. The validated questionnaire can now be used to fully understand the set of factors influencing this new practice.

Prevalence of patients' difficulties in swallowing solid oral dosage forms

Introduction Swallowing difficulties, or dysphagia, can occur in anyage group, although it is most common among elderly people. It canaffect patients' ability to take solid oral dosage forms, thus compromisingmedication adherence. Although literature is poor, availabledata show that prevalence in the general population ranges from 25 to60%. Prevalence in community pharmacies needs to be explored.Materials & Methods Community pharmacies were recruited from arandom selection in three Swiss states: Basel-Stadt (BS), Basel-Landschaft (BL) and Lausanne (LA). Patients' ability to swallowsolid oral medications was enquired with a semi-structured interview;the interviewer spent 4 h in each included pharmacy. Each consecutivepatient (18 years and older) entering the pharmacy with aprescription for at least 3 different solid oral forms was enrolled.Study was approved by the Lausanne ethics committee.Results Sixty pharmacies took part in the study (20 in BS, 10 in BL,30 in LA) between March and May 2010. Patient inclusion rate was77.8% (410/527). Prevalence of swallowing disorders was 22.4% (92/410). Patients with swallowing disorders were older (mean age: 67.5± 16 years vs. 63.0 ± 14 years, range 19-96; p = 0.03) and moreoften women (69.6% vs. 59.1%; Chi2 = 3.3, p = 0.04) than patientswithout swallowing disorders. They had on average 4.6 ± 2.7 drugswith a mean number of 5.5 ± 3.3 tablets or capsules to take daily,which didn't differ from the number of drugs taken by patientswithout swallowing difficulties (4.9 ± 2.5 drugs and 5.9 ± 3.5 tablets;n.s.). The difficulty was mainly related to the big size (63%) orthe quality of pill coating (rough, sticky, 14%). Twenty-one patients(37.5%) stated that their swallowing disorders resulted in nonadherence, rated as rarely (12 patients), sometimes (6 patients), veryoften (1 patient) or always (2 patients). According to patients, nopharmacist and only 2 physicians enquired about patients' swallowingissue.Discussion & Conclusion Swallowing difficulties are frequent amongpatients in community pharmacies in Switzerland with an estimatedprevalence of 22%. The problem resulted in non adherence or partialadherence in at least 35% of these patients. However, pharmacists andphysicians did not routinely inquire about the disorder. Guidelinesshould be developed for promoting systematic approaches of patientsin community pharmacies.

Essays on the treatment of cash flows under stochastic interest rates

Abstract This paper shows how to calculate recursively the moments of the accumulated and discounted value of cash flows when the instantaneous rates of return follow a conditional ARMA process with normally distributed innovations. We investigate various moment based approaches to approximate the distribution of the accumulated value of cash flows and we assess their performance through stochastic Monte-Carlo simulations. We discuss the potential use in insurance and especially in the context of Asset-Liability Management of pension funds.

Evolution under monogamy feminizes gene expression in Drosophila melanogaster.

Many genes have evolved sexually dimorphic expression as a consequence of divergent selection on males and females. However, because the sexes share a genome, the extent to which evolution can shape gene expression independently in each sex is controversial. Here, we use experimental evolution to reveal suboptimal sex-specific expression for much of the genome. By enforcing a monogamous mating system in populations of Drosophila melanogaster for over 100 generations, we eliminated major components of selection on males: female choice and male-male competition. If gene expression is subject to sexually antagonistic selection, relaxed selection on males should cause evolution towards female optima. Monogamous males and females show this pattern of feminization in both the whole-body and head transcriptomes. Genes with male-biased expression patterns evolved decreased expression under monogamy, while genes with female-biased expression evolved increased expression, relative to polygamous populations. Our results demonstrate persistent and widespread evolutionary tension between male and female adaptation.

Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing.

Determination of the precise composition and variation of microbiota in cystic fibrosis lungs is crucial since chronic inflammation due to microorganisms leads to lung damage and ultimately, death. However, this constitutes a major technical challenge. Culturing of microorganisms does not provide a complete representation of a microbiota, even when using culturomics (high-throughput culture). So far, only PCR-based metagenomics have been investigated. However, these methods are biased towards certain microbial groups, and suffer from uncertain quantification of the different microbial domains. We have explored whole genome sequencing (WGS) using the Illumina high-throughput technology applied directly to DNA extracted from sputa obtained from two cystic fibrosis patients. To detect all microorganism groups, we used four procedures for DNA extraction, each with a different lysis protocol. We avoided biases due to whole DNA amplification thanks to the high efficiency of current Illumina technology. Phylogenomic classification of the reads by three different methods produced similar results. Our results suggest that WGS provides, in a single analysis, a better qualitative and quantitative assessment of microbiota compositions than cultures and PCRs. WGS identified a high quantity of Haemophilus spp. (patient 1) or Staphylococcus spp. plus Streptococcus spp. (patient 2) together with low amounts of anaerobic (Veillonella, Prevotella, Fusobacterium) and aerobic bacteria (Gemella, Moraxella, Granulicatella). WGS suggested that fungal members represented very low proportions of the microbiota, which were detected by cultures and PCRs because of their selectivity. The future increase of reads' sizes and decrease in cost should ensure the usefulness of WGS for the characterisation of microbiota.

Obesity in Switzerland: a critical assessment of prevalence in children and adults.

The objective was to analyze the situation in Switzerland regarding the prevalence of overweight or obesity in children, adolescents and adults. The data were compared with France, an adjacent much larger country. The results showed that there is a definitive lack of objective information in Switzerland on the prevalence of obesity at different ages. As in other European studies, the fact that many national surveys are classically based on subject interviews (self-reported weights and heights rather than measured values) implies that the overweight/obesity prevalence is largely underestimated in adulthood. For example, in a recent Swiss epidemiological study, the prevalence of obesity (BMI greater than 30 kg/m(2)) averaged 6-7% in young men and women (25-34 y), the prevalence being underestimated by a factor of two to three when body weight was self-reported rather than measured. This phenomenon has already been observed in previous European studies. It is concluded that National Surveys based on telephone interviews generally produce biased obesity prevalence results, although the direction of the changes in prevalence of obesity and its evolution with repeated surveys using strict standardized methodology may be evaluated correctly. Therefore, these surveys should be complemented by large-scale epidemiological studies (based on measured anthropomeric variables rather than declared) covering the different linguistic areas of Switzerland. An epidemiological body weight (BMI) monitoring surveillance system, using a harmonized methodology among European countries, would help to accurately assess differences in obesity prevalence across Europe without methodological bias. It will permit monitoring of the dynamic evolution of obesity prevalence as well as the development of appropriate strategies (taking into account the specificity of each country) for obesity prevention and treatment.

Extraction and concentration of vapors from fire debris for forensic purposes: evaluation of the use of Radiello Passive Air Sampler

The Radiello Passive Air Sampler is one of the latest innovations developed for the sampling of pollutants in the air by passive headspace. It has been reported that its properties allow an enhanced sensitivity, reproducibility and adsorption capacity. It therefore appears to be of interest in the extraction of potential residues of ignitable liquids present in fire debris when arson is suspected. A theoretical approach and several laboratory tests have made it possible to precisely characterize in a forensic perspective the potential of the device in extracting and concentrating the vapors of ignitable liquids found in fire debris. Despite some advantages, the Radiello device appears to be less efficient than traditional axial symmetry samplers.

Non-random autosome segregation: a stepping stone for the evolution of sex chromosome complexes?

A new study in Caenorhabditis elegans shows that homologous autosomes segregate non-randomly with the sex chromosome in the heterogametic sex. Segregation occurs according to size, small autosomes segregating with, and large autosomes segregating away from the X-chromosome. Such sex-biased transmission of autosomes could facilitate the spread of sexually antagonistic alleles whose effects favor the fitness of one sex at the expense of the other. This may provide a first step toward the evolution of new sex determination systems.

Antagonistes de l'angiotensine II et cancer: un bilan rassurant [Angiotensin II receptor blockers (ARBs) and cancer: a reassuring balance].

The effects of drugs on new cancer and cancer-related death are a major concern. Recently, a meta-analysis raised the possibility that ARBs might have an adverse impact in this respect. This point of view was highly debated until the publication of two other meta-analyses which did not demonstrate any increased risk of new cancer occurrence as well as of cancer related-death with the use of ARBs in patients with hypertension, heart failure and/or nephropathy. This illustrates that the results of meta-analyses should be interpreted cautiously and critically in order to avoid biased conclusions. Overall the bulk of evidence today indicates that ARBs are not associated with an increased cancer risk.

Procedure for human saphenous veins ex vivo perfusion and external reinforcement.

The mainstay of contemporary therapies for extensive occlusive arterial disease is venous bypass graft. However, its durability is threatened by intimal hyperplasia (IH) that eventually leads to vessel occlusion and graft failure. Mechanical forces, particularly low shear stress and high wall tension, are thought to initiate and to sustain these cellular and molecular changes, but their exact contribution remains to be unraveled. To selectively evaluate the role of pressure and shear stress on the biology of IH, an ex vivo perfusion system (EVPS) was created to perfuse segments of human saphenous veins under arterial regimen (high shear stress and high pressure). Further technical innovations allowed the simultaneous perfusion of two segments from the same vein, one reinforced with an external mesh. Veins were harvested using a no-touch technique and immediately transferred to the laboratory for assembly in the EVPS. One segment of the freshly isolated vein was not perfused (control, day 0). The two others segments were perfused for up to 7 days, one being completely sheltered with a 4 mm (diameter) external mesh. The pressure, flow velocity, and pulse rate were continuously monitored and adjusted to mimic the hemodynamic conditions prevailing in the femoral artery. Upon completion of the perfusion, veins were dismounted and used for histological and molecular analysis. Under ex vivo conditions, high pressure perfusion (arterial, mean = 100 mm Hg) is sufficient to generate IH and remodeling of human veins. These alterations are reduced in the presence of an external polyester mesh.